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User:Robert Dutnall/Chem331 Tutorial2b

2011-09-01T18:26:24Z

Robert Dutnall:

== Biochemistry Tutorial #2 - Secondary Structure (Part 2) ==

==β-strands and β-sheets==

The second major secondary structure element is the β-sheet. β-sheets are composed of two or more segments of polypeptide mainchain in β-strand conformation. In a β-strand, the polypeptide mainchain is in a mostly extended conformation. As their name implies, β-sheets are relatively flat, planar-like structures made up of β-strands arranged side-by-side. They come in three flavors: parallel, anti-parallel and mixed, which differ in terms of the orientation of each component strand (with respect to the direction of the mainchain from N-terminus to C-terminus).

Note that the mainchain of a β-strand is not perfectly fully extended (Φ ≠ φ ≠ 180o) and that the mainchain actually slowly twists (this is more obvious if you look at a long segment of β-strand). Thus β-sheets are not completely flat and also exhibit some twisting (this is also more obvious if you look at sheets made of many β-strands).

==Parallel β-sheet==

Parallel β-sheets are composed of β-strands that all point in the same direction. Each β-strand has mainchain dihedral angles as follows: Φ ~ -120o, φ ~ +105o.

<Structure load='Tut_parallel_bsheet.pdb' size='500' frame='true' align='left' caption='' scene='User:Robert_Dutnall/Sandbox_1_sheets/Parallel_load/2'/>

The sheet shown here is composed of three strands in parallel orientation. All the atoms are shown (C = green; N = blue; O = red; S = yellow; H = white).

<scene name='User:Robert_Dutnall/Sandbox_1_sheets/Parallel_mainchain/2'>Click here</scene> to show only the polypeptide mainchain (NH, Cα, and C=O).

Identify the N- and C-termini of each strand. <scene name='User:Robert_Dutnall/Sandbox_1_sheets/Parallel_mainchain_labels/6'>Click here to see if you were correct.</scene>

As the structure rotates you should be able to see the extended nature of each strand and the parallel orientation of the three strands.

<scene name='User:Robert_Dutnall/Sandbox_1_sheets/Parallel_mainchain_labels_face/2'>Click here</scene> to stop the structure spinning and view the sheet from roughly perpendicular to its flat plane, with each strand running left-to-right (N- to C-terminus).

<scene name='User:Robert_Dutnall/Sandbox_1_sheets/Parallel_mainchain_labels_side/2'>Click here</scene> to stop the structure spinning and view the sheet from roughly edge-on to its flat plane.

<scene name='User:Robert_Dutnall/Sandbox_1_sheets/Parallel_mainchain_labels/6'>Click here to start the structure spinning again.</scene> Look at the structure carefully and identify the mainchain NH and C=O groups. What is the orientation of these groups with respect to the long axis of each strand? What the orientation of these groups with respect to the flat plane of the sheet?

 

===Hydrogen Bonds in Parallel Sheets===
<Structure load='Tut_parallel_bsheet.pdb' size='500' frame='true' align='left' caption='' scene='User:Robert_Dutnall/Sandbox_1_sheets/Parallel_mainchain_labels_hb/5'/>
Hydrogen bonds have now been added to the structure. The hydrogen bonds connect backbone NH groups of one strand with the C=O groups of another. The N-H group is the hydrogen bond donor, the oxygen in the C=O group is the acceptor (N-H--->O=C). Each hydrogen bond is approximately 3.0 Angstroms (0.3 nm) in length (measured between the N and the O).

You should be able to see that the mainchain NH and C=O groups are involved in hydrogen bonds. In each strand the mainchain NH and C=O groups point to opposite sides of the mainchain (because of the almost fully extended conformation). The strands line up in the sheet so that the NH and C=O groups are parallel to plane of the sheet and lie opposite each other in pairs. This means that hydrogen bonds can be made between the strands of the sheet. <scene name='User:Robert_Dutnall/Sandbox_1_sheets/Parallel_mainchain_labels_hb_z/5'>Click here to zoom in to show some of the hydrogen bonds more clearly.</scene>

<scene name='User:Robert_Dutnall/Sandbox_1_sheets/Parallel_mainchain_labels_hb/5'>Click here to zoom out again.</scene> You should also notice that all of the NH and C=O groups that lie between strands are involved in hydrogen bonds. Only the groups on the edges of the sheet do not have hydrogen bond partners. However, as with helix capping, if this sheet were part of a larger protein, other residues would supply groups to hydrogen bond to most if not all of these.

<scene name='User:Robert_Dutnall/Sandbox_1_sheets/Parallel_sidechains/2'>Click here to show the side chains again.</scene> You are looking roughly edge-on to the flat plane of the sheet and the atoms of each amino side chain have been colored light blue to show them more clearly.

What is the general orientation of the side chains with respect to each strand and the sheet? You should observe that the side chains are approximately perpendicular to the flat plane of the sheet. Along each strand, the side chains alternate direction. You can see this more clearly if we color the side chains in one strand alternately. <scene name='User:Robert_Dutnall/Sandbox_1_sheets/Parallel_strand_alt/3'>Click here</scene> to freeze the view and color the side chains along one strand blue-purple-blue-purple...etc.

If we apply this to all the strands (<scene name='User:Robert_Dutnall/Sandbox_1_sheets/Parallel_sidechains_alt/2'>click here</scene>) you can see that all the sidechains above the plane of the sheet are purple, and all those below are blue.

 

==Anti-Parallel β-sheet==

Anti-parallel β-sheets are composed of β-strands that alternate in direction. Each β-strand has mainchain dihedral angles as follows: Φ ~ -150o, φ ~ +135o.

<Structure load='Tut_antiparallel_bsheet.pdb' size='500' frame='true' align='left' caption='' scene='User:Robert_Dutnall/Sandbox_1_sheets/Antiparallel_load/3'/>
The sheet shown here is composed of three strands in anti-parallel orientation. All the atoms are shown (C = green; N = blue; O = red; S = yellow; H = white).

<scene name='User:Robert_Dutnall/Sandbox_1_sheets/Antiparallel_mainchain/3'>Click here</scene> to show only the polypeptide mainchain of each strand (NH, Cα, and C=O).

Identify the N- and C-termini of each strand. <scene name='User:Robert_Dutnall/Sandbox_1_sheets/Antiparallel_mainchain_labels/1'>Click here to see if you were correct.</scene>

As the structure rotates you should be able to see the extended nature of each strand and the parallel orientation of the three strands.

<scene name='User:Robert_Dutnall/Sandbox_1_sheets/Antipara_mainchain_labels_face/1'>Click here</scene> to stop the structure spinning and view the sheet from roughly perpendicular to its flat plane.

<scene name='User:Robert_Dutnall/Sandbox_1_sheets/Antipara_mainchain_labels_side/1'>Click here</scene> to stop the structure spinning and view the sheet from roughly edge-on to its flat plane.

<scene name='User:Robert_Dutnall/Sandbox_1_sheets/Antiparallel_mainchain_labels/1'>Click here to start the structure spinning again.</scene> Look at the structure carefully and identify the mainchain NH and C=O groups. In each strand the mainchain NH and C=O groups point to opposite sides of the mainchain. The strands line up in the sheet so that these NH and C=O groups are parallel to plane of the sheet and lie opposite each other so that they can make hydrogen bonds.

 

===Hydrogen Bonds in Antiparallel Sheets===
<Structure load='Tut_antiparallel_bsheet.pdb' size='500' frame='true' align='left' caption='' scene='User:Robert_Dutnall/Sandbox_1_sheets/Antipara_mainchain_hbonds/1'/>

I'll reset the structure and add hydrogen bonds. The hydrogen bonds connect backbone NH groups and C=O groups. The N-H group is the hydrogen bond donor, the oxygen in the C=O group is the acceptor (N-H--->O=C). Each hydrogen bond is approximately 3.0 Angstroms (0.3 nm) in length (measured between the N and the O).

You should be able to see that the mainchain NH and C=O groups are involved in hydrogen bonds between the strands of the sheet. <scene name='User:Robert_Dutnall/Sandbox_1_sheets/Antipara_mainchain_hbonds_z/1'>Click here to zoom in to show some of the hydrogen bonds more clearly.</scene>

<scene name='User:Robert_Dutnall/Sandbox_1_sheets/Antipara_mainchain_hbonds/1'>Click here to zoom out again.</scene> You should notice that all of the NH and C=O groups that lie between strands are involved in hydrogen bonds. Only the groups on the edges of the sheet do not have hydrogen bond partners, but if this sheet were part of a larger protein, other residues would supply groups to hydrogen bond to most if not all of these.

Two of the strands in this sheet are connected by a β-turn. <scene name='User:Robert_Dutnall/Sandbox_1_sheets/Antipara_mainchain_turn/2'>Click here</scene> to show the β-turn. The carbon atoms of the amino acids that define the turn have been colored orange. The turn allows a segment of polypeptide to reverse direction in a short distance. In this case it also allows two strands to interact in an antiparallel fashion. <scene name='User:Robert_Dutnall/Sandbox_1_sheets/Antipara_mainchain_turn_zoom/3'>Click here to zoom in on the turn and reorient it to show more clearly.</scene> '''Is this a Type I or Type II β-turn? (Write down your answer so you can submit it to your instructor)'''

<scene name='User:Robert_Dutnall/Sandbox_1_sheets/Antipara_mainchain_sidechains/1'>Click here to zoom out again.</scene> In this view, some of the residues at the turn have been omitted and you are looking roughly edge-on to the flat plane of the sheet. Sidechains have been added and the atoms of each amino side chain have been colored blue or purple in an alternating fashion.

The side chains are approximately perpendicular to the flat plane of the sheet. Along each strand, the side chains alternate direction (above the plane, below the plane, above the plane...) so you should be able to see that all the sidechains above the plane of the sheet are purple, and all those below are blue.

 

==A mixed β-sheet==

The sheet shown below is composed of four strands. All the atoms are shown (C = green; N = blue; O = red; S = yellow; H = white). This is a mixed β-sheet. Some of the strands are parallel, some are antiparallel.
<Structure load='Mixed_sheet.pdb' size='500' frame='true' align='left' caption='' scene='User:Robert_Dutnall/Sandbox_1_sheets/Mixed_sheet_load/1'/>

<scene name='User:Robert_Dutnall/Sandbox_1_sheets/Mixed_sheet_mainchain/2'>Click here</scene> to show only the polypeptide mainchain of each strand (NH, Cα, and C=O).

'''What is the orientation of each pair of strands (parallel or antiparallel)?'''

Click below to highlight the strands in pairs (pair 1, pair 2 and pair 3). The carbon atoms will be highlighted in orange.

<scene name='User:Robert_Dutnall/Sandbox_1_sheets/Mixed_sheet_mainchain_pair1/1'>Pair 1.</scene>

<scene name='User:Robert_Dutnall/Sandbox_1_sheets/Mixed_sheet_mainchain_pair2/1'>Pair 2.</scene>

<scene name='User:Robert_Dutnall/Sandbox_1_sheets/Mixed_sheet_mainchain_pair3/1'>Pair 3.</scene>

'''Write down your answers for pair 1, pair 2 and pair 3 to submit to your instructor.'''

'''That's it. You are finished with Tutorial 2. Remember to submit your answers to the questions from this tutorial to your instructor.'''
= =
[[User:Robert Dutnall/Chem331_Tutorial2a|Click here if you want to go back to the first part of this tutorial.]]

User:Robert Dutnall/Chem331 Tutorial2a

2011-09-01T18:14:27Z

Robert Dutnall:

== Biochemistry Tutorial #2 - Secondary Structure (Part 1) ==

The secondary structure of a protein is defined by the local conformation of its backbone (polypeptide mainchain). There are two major types of regular secondary structures in proteins: helices and sheets. There are also regular turn structures. Turns often connect one element of secondary structure to another in the overall fold of the protein. Other parts of the protein mainchain may adopt more irregularly defined loops. This tutorial will focus mainly on helices and sheets.

''Note: in these tutorials, the images are 3D interactive images. You can manipulate them as you wish to get a better view of the molecules.''

You can rotate the structures by holding down the right mouse button and dragging. At any time you can click the 'toggle spin' button in box to stop/start the structure spinning.

Other things you can do:
::To rotate: left drag
::To Zoom: scroll button or shift + left drag
::To Translate: ctrl + right drag
::Right click to bring up an options menu

==Helices==

In helices, the polypeptide mainchain twists into a path that resembles a spiral staircase. Just like spiral staircases, helices come in different forms, depending on how tightly twisted the mainchain is. The form of a helix can be described by parameters such as the number of steps (amino acids) it takes to complete a turn (a 360o rotation around the long axis of the helix), and how far you travel along the helix axis in one complete turn. Helices can also be left-handed or right-handed. For proteins composed of L-amino acids, helices are almost always right-handed (a notable exception is the type I poly-proline helix). Although several types of helix form are possible, two regular helices are very common in proteins: the α-helix and the 310-helix.

==The α-helix==

α-helices are the most common type of regular helix found in proteins. They are characterized by the following helix parameters:
::Dihedral angles: Φ ~ -60o, φ ~ -45o
::Repeat (number of residues per turn) = 3.6
::Rise (translation along axis per amino acid residue) = 1.5 Angstroms (0.15 nm)
::Twist (rotation around axis per amino acid residue) = 100o (= 360o/repeat)
::Pitch (translation along axis per turn) = 5.4 Angstroms (= 0.54 nm = Repeat x Rise)

The helix shown below is a 19 amino acid chain in α-helical conformation.
<Structure load='Tut_alpha_helix.pdb' size='500' frame='true' align='left' caption='' scene='User:Robert_Dutnall/Sandbox_1_alpha_helix/A_helix_load/1'/>

All the atoms are shown in this initial orientation (C = green; N = blue; O = red; S = yellow; H = white). The helix axis runs vertically, approximately parallel to the plane of the screen.

<scene name='User:Robert_Dutnall/Sandbox_1_alpha_helix/A_helix_mainchain/3'>Click here</scene> to show only the polypeptide mainchain (NH, Cα, and C=O).

Identify the N- and C-termini. <scene name='User:Robert_Dutnall/Sandbox_1_alpha_helix/A_helix_mainchain_label/4'>Click here to see if you were correct.</scene>

<scene name='User:Robert_Dutnall/Sandbox_1_alpha_helix/A_helix_mainchain_label_ribbon/3'>Click here to add a ribbon that will help show the path of the mainchain. </scene> You should be able to see that it is helical with a right-handed twist (you rotate to the right as you move along the helix axis).

Click the "toggle spin" button in the box to stop the structure from rotating. Now use your mouse to rotate the structure to look down the helix axis. If you have any problems with finding this view, <scene name='User:Robert_Dutnall/Sandbox_1_alpha_helix/A_helix_mainchain_label_axis/3'>click here </scene>to zoom in and look down the helix axis from the N-terminal end.

 

===Hydrogen Bonding in α-helices===
<Structure load='Tut_alpha_helix.pdb' size='500' frame='true' align='left' caption='' scene='User:Robert_Dutnall/Sandbox_1_alpha_helix/A_helix_mainchain_label/4'/>
I'll reset the structure for you. Now, look at the structure carefully and identify the mainchain NH and C=O groups. What is the orientation of these groups with respect to the helix axis?

<scene name='User:Robert_Dutnall/Sandbox_1_alpha_helix/A_helix_mainchain_label_hbonds/10'>Click here to zoom in a little and add hydrogen bonds for the mainchain (dashed lines).</scene> The hydrogen bonds connect backbone NH groups and C=O groups. The N-H group is the hydrogen bond donor, the oxygen in the C=O group is the acceptor (N-H--->O=C). Each hydrogen bond is approximately 3.0 Angstroms (0.3 nm) in length (measured between the N and the O). These hydrogen bonds connect amino acids that are spaced 4 residues apart in the primary sequence. The NH group is from amino acid X and the O is from amino acid X-4 (where X is the number of the amino acid in the sequence).

<scene name='User:Robert_Dutnall/Sandbox_1_alpha_helix/A_helix_mainchain_label_hbonds/9'>Click here to zoom out again.</scene> You should be able to see that all of the mainchain NH and C=O groups are involved in hydrogen bonds. This is possible because 1) all the mainchain NH groups and C=O groups are parallel to the helix axis, 2) all the NH groups point toward the N-terminus of the helix, and 3) all the C=O groups point toward the C-terminus. Only the NH groups in the first (N-terminal) turn, and the C=O groups in the last (C-terminal) turn of the helix do not have hydrogen bonding partners. However, if this helix were part of a larger protein, these groups would participate in hydrogen bonds with other parts of the protein. This is called 'helix capping' and the other groups involved are typically from amino acid side chains (that are called 'helix capping residues').

<scene name='User:Robert_Dutnall/Sandbox_1_alpha_helix/A_helix_sidechains/3'>Click here to show the side chains again.</scene> The atoms of each amino side chain have been colored light blue to show them more clearly. <scene name='User:Robert_Dutnall/Sandbox_1_alpha_helix/A_helix_sidechains_axis/1'>Click here to change the view to look down the helix axis.</scene>

What is the general orientation of the side chains with respect to the helix axis? You should observe that each side chain points away from the helix axis, but points down toward the N-terminus of the helix (this is clearer if you only show the first bond of each side chain: <scene name='User:Robert_Dutnall/Sandbox_1_alpha_helix/A_helix_sidechains_cropped/1'>click here</scene> or <scene name='User:Robert_Dutnall/Sandbox_1_alpha_helix/A_helix_sidechains_cropped/2'>click here</scene>).

 
==The 310-helix==

310-helices are also found in proteins but are less common than α-helices. They are characterized by the following helix parameters:
::Dihedral angles: Φ ~ -49o, φ ~ -26o
::Repeat (number of residues per turn) = 3.0
::Rise (translation along axis per amino acid residue) = 2.0 Angstroms (0.2 nm)
::Twist (rotation around axis per amino acid residue) = 120o (= 360o/repeat)
::Pitch (translation along axis per turn) = 6.0 Angstroms (= 0.6 nm = Repeat x Rise)

The helix shown below is a 19 amino acid chain in 310-helical conformation.
<Structure load='Tut_3-10_helix.pdb' size='500' frame='true' align='left' caption='' scene='User:Robert_Dutnall/Sandbox_1_alpha_helix/310_helix_load/4'/>

All the atoms are shown in this initial orientation (C = green; N = blue; O = red; S = yellow; H = white). The helix axis runs vertically, approximately parallel to the plane of the screen.

<scene name='User:Robert_Dutnall/Sandbox_1_alpha_helix/310_helix_mainchain/2'>Click here</scene> to show only the polypeptide mainchain (NH, Cα, and C=O). The N- and C-termini are labeled.

<scene name='User:Robert_Dutnall/Sandbox_1_alpha_helix/310_helix_mainchain_ribbon/2'>Click here to add a ribbon that will help show the path of the mainchain. </scene> You should be able to see that just like the α-helix, it is helical with a right-handed twist, and again, all the mainchain NH groups point toward the N-terminus, and all the mainchain C=O groups point toward the C-terminus.

The difference between an α-helix and a 310-helix lies in the helix parameters. A 310-helix is more tightly twisted so that the mainchain completes one turn every 3 amino acids (instead of 3.6 for the α-helix). This also results in a larger rise and pitch so that the 310-helix is longer than an α-helix (of the same number of residues).

<scene name='User:Robert_Dutnall/Sandbox_1_alpha_helix/310_helix_mainchain_axis/1'>Click here </scene>to zoom in and look down the helix axis from the N-terminal end. You'll be able to see the triangular shape of the mainchain.

 

===Hydrogen Bonding in 3-10 Helices===
<Structure load='Tut_3-10_helix.pdb' size='500' frame='true' align='left' caption='' scene='User:Robert_Dutnall/Sandbox_1_alpha_helix/310_helix_mainchain_hbonds/1'/>
I've zoomed back out and turned on the hydrogen bonds for the mainchain. Once again, all of the mainchain NH and C=O groups are involved in hydrogen bonds. However, now the hydrogen bonds connect amino acids that are spaced 3 residues apart in the primary sequence. The NH group is from amino acid X and the O is from amino acid X-3 (where X is the number of the amino acid in the sequence). <scene name='User:Robert_Dutnall/Sandbox_1_alpha_helix/310_helix_mainchain_hbonds/2'>Click here</scene> to zoom in and you should be able to see this more clearly.

<scene name='User:Robert_Dutnall/Sandbox_1_alpha_helix/310_helix_sidechains/1'>Click here to zoom out and show the side chains again.</scene> The atoms of each amino side chain have been colored light blue to show them more clearly. <scene name='User:Robert_Dutnall/Sandbox_1_alpha_helix/310_helix_sidechains_axis/2'>Click here to change the view to look down the helix axis.</scene>

As for the α-helix, each side chain points away from the helix axis, and points down toward the N-terminus of the helix. However, because the 310-helix repeat parameter is an integer (= 3.0), the side chains are spaced 120o apart and form 3 distinct sides to the helix. You'll see this more clearly if the side chains are colored in groups to show this (residues 1,4,7,10 etc are blue; residues 2,5,8,11 etc are purple; residues 3,6,9,12 etc are yellow): <scene name='User:Robert_Dutnall/Sandbox_1_alpha_helix/310_helix_sidechains_tricolor/1'>click here to look from the side</scene> or <scene name='User:Robert_Dutnall/Sandbox_1_alpha_helix/310_helix_sidechains_tricol_ax/1'>click here to view down the helix axis</scene>.

<scene name='User:Robert_Dutnall/Sandbox_1_alpha_helix/310_helix_load/4'>Click here to reset the view of the helix.</scene>

'''What is the identity of the N-terminal amino acid?'''

'''What is the identity of the C-terminal amino acid?'''

'''Write down these answers so that you can submit them to your instructor at the end of this tutorial.'''

= =
[[User:Robert Dutnall/Chem331_Tutorial2b|Click here to go on to part 2 of this tutorial.]]

User:Robert Dutnall/Chem331 Tutorial1b

2011-08-29T19:52:43Z

Robert Dutnall:

== Biochemistry Tutorial #1 - Peptides (Part 2)==

===Let's look at another dipeptide.===

Identify each amino acid in this dipeptide.
<Structure load='CysAsp3.pdb' size='400' frame='true' align='left' caption='Second Dipeptide' scene='User:Stephen_Mills/Sandbox_2_Peptide_tutorial_2/Cysaspstart/1' />

What is the short-hand notation for this dipeptide?

<scene name='User:Stephen_Mills/Sandbox_2_Peptide_tutorial_2/Cysasplabels/2'>Click here to show the labels on each amino acid.</scene>

Identify which amino acid is at the N-terminus and which is at the C-terminus.

<scene name='User:Stephen_Mills/Sandbox_2_Peptide_tutorial_2/Cysasptermini/1'>Click here to label each terminus.</scene>

Identify the α carbons of each amino acid.

<scene name='User:Stephen_Mills/Sandbox_2_Peptide_tutorial_2/Cysaspalphas/1'>Click here to have them highlighted.</scene>

Identify the atoms involved in the peptide bond in this dipeptide.

<scene name='User:Stephen_Mills/Sandbox_2_Peptide_tutorial_2/Cysaspamide/1'>Click here to have those atoms change color.</scene>

Now, measure the distance between the α carbons.
<scene name='User:Stephen_Mills/Sandbox_2_Peptide_tutorial_2/Cysaspmeasure/1'>Click here to get a good starting configuration.</scene>

To measure a distance, Double click on the first atom, then double click on the second atom. You may need to rotate the molecule a bit to see the distance well. Try it now.

'''Write down this distance and submit it to your instructor.'''
 

==Oligopeptides==

Now you are ready to work with oligopeptides, or polymers composed of 3-20 amino acid residues. These polymers are linear; that is, each amino acid is linked to it's neighbor in a head-to-tail fashion rather than forming branched chains. You will be observing a 5mer in this tutorial.

<Structure load='GDCRY.pdb' size='500' frame='true' align='left' caption='' scene='User:Stephen_Mills/Sandbox_2_Peptide_tutorial_2/Pentapeptide_start/1' />

For this part, you may need to resize and move the molecule around. To remind you: 
To Rotate: left drag 
To Zoom: scroll button or shift + left drag 
To Translate: ctrl + right drag (On a Mac, this doesn't work in FireFox, but does work in Safari). 

'''Identify where Y and R are located in this oligopeptide.'''

<scene name='User:Stephen_Mills/Sandbox_2_Peptide_tutorial_2/Pentapeptide_yr/2'>Click here to have Y and R colored purple.</scene>

Notice that the NH of Y is bonded to the carbonyl of R.

Also notice how the bulky side-chains point away from the backbone of the peptide.

'''Identify where C and D are located in this peptide.'''
<scene name='User:Stephen_Mills/Sandbox_2_Peptide_tutorial_2/Pentapeptide_cd/2'>
Click here to have C and D colored purple.</scene>

Notice how Cysteine's thiol (SH) group points outward from the 5mer backbone at an angle that would allow for the stable formation of the disulfide bond. 

'''Identify the remaining amino acid in this peptide.''' 

'''Write down the short-hand notation for this pentapeptide, in the correct order from the N-terminus to the C-terminus and submit this to your instructor.'''

 

==Last Part!!==

Now a test peptide.
<Structure load='WHENISPIEDAY3.pdb' size='600' frame='true' align='left' caption='' scene='User:Stephen_Mills/Sandbox_2_Peptide_tutorial_2/Test_peptide/1' />

'''Identify the sequence of this peptide and submit the answer to your instructor.''' 
You will probably need to move the molecule around and rotate it to see the whole structure.

When you write it down (using one letter codes), it will spell out a question.

'''Submit the sequence of the peptide '''''and''''' the answer to the question'''
 

'''Congratulations! You have just finished the first Biochemistry Tutorial'''

User:Robert Dutnall/Chem331 Tutorial2b

2011-08-29T19:51:24Z

Robert Dutnall: New page: == Biochemistry Tutorial #2 - Secondary Structure (Part 2) == ==β-strands and β-sheets== The second major secondary structure element is the β-sheet. β-sheets are composed of two or ...

== Biochemistry Tutorial #2 - Secondary Structure (Part 2) ==

==β-strands and β-sheets==

The second major secondary structure element is the β-sheet. β-sheets are composed of two or more segments of polypeptide mainchain in β-strand conformation. In a β-strand, the polypeptide mainchain is in a mostly extended conformation. As their name implies, β-sheets are relatively flat, planar-like structures made up of β-strands arranged side-by-side. They come in three flavors: parallel, anti-parallel and mixed, which differ in terms of the orientation of each component strand (with respect to the direction of the mainchain from N-terminus to C-terminus).

Note that the mainchain of a β-strand is not perfectly fully extended (Φ ≠ φ ≠ 180o) and that the mainchain actually slowly twists (this is more obvious if you look at a long segment of β-strand). Thus β-sheets are not completely flat and also exhibit some twisting (this is also more obvious if you look at sheets made of many β-strands).

==Parallel β-sheet==

Parallel β-sheets are composed of β-strands that all point in the same direction. Each β-strand has mainchain dihedral angles as follows: Φ ~ -120o, φ ~ +105o.

The sheet shown below is composed of three strands in parallel orientation. All the atoms are shown (C = green; N = blue; O = red; S = yellow; H = white).
<Structure load='Tut_parallel_bsheet.pdb' size='500' frame='true' align='left' caption='' scene='User:Robert_Dutnall/Sandbox_1_sheets/Parallel_load/2'/>

<scene name='User:Robert_Dutnall/Sandbox_1_sheets/Parallel_mainchain/2'>Click here</scene> to show only the polypeptide mainchain (NH, Cα, and C=O).

Identify the N- and C-termini of each strand. <scene name='User:Robert_Dutnall/Sandbox_1_sheets/Parallel_mainchain_labels/6'>Click here to see if you were correct.</scene>

As the structure rotates you should be able to see the extended nature of each strand and the parallel orientation of the three strands.

<scene name='User:Robert_Dutnall/Sandbox_1_sheets/Parallel_mainchain_labels_face/2'>Click here</scene> to stop the structure spinning and view the sheet from roughly perpendicular to its flat plane, with each strand running left-to-right (N- to C-terminus).

<scene name='User:Robert_Dutnall/Sandbox_1_sheets/Parallel_mainchain_labels_side/2'>Click here</scene> to stop the structure spinning and view the sheet from roughly edge-on to its flat plane.

<scene name='User:Robert_Dutnall/Sandbox_1_sheets/Parallel_mainchain_labels/6'>Click here to start the structure spinning again.</scene> Look at the structure carefully and identify the mainchain NH and C=O groups. What is the orientation of these groups with respect to the long axis of each strand? What the orientation of these groups with respect to the flat plane of the sheet?

<scene name='User:Robert_Dutnall/Sandbox_1_sheets/Parallel_mainchain_labels_hb/5'>Click here to add hydrogen bonds for the mainchain (dashed lines).</scene> The hydrogen bonds connect backbone NH groups and C=O groups. The N-H group is the hydrogen bond donor, the oxygen in the C=O group is the acceptor (N-H--->O=C). Each hydrogen bond is approximately 3.0 Angstroms (0.3 nm) in length (measured between the N and the O).

You should be able to see that the mainchain NH and C=O groups are involved in hydrogen bonds. In each strand the mainchain NH and C=O groups point to opposite sides of the mainchain (because of the almost fully extended conformation). The strands line up in the sheet so that the NH and C=O groups are parallel to plane of the sheet and lie opposite each other in pairs. This means that hydrogen bonds can be made between the strands of the sheet. <scene name='User:Robert_Dutnall/Sandbox_1_sheets/Parallel_mainchain_labels_hb_z/5'>Click here to zoom in to show some of the hydrogen bonds more clearly.</scene>

<scene name='User:Robert_Dutnall/Sandbox_1_sheets/Parallel_mainchain_labels_hb/5'>Click here to zoom out again.</scene> You should also notice that all of the NH and C=O groups that lie between strands are involved in hydrogen bonds. Only the groups on the edges of the sheet do not have hydrogen bond partners. However, as with helix capping, if this sheet were part of a larger protein, other residues would supply groups to hydrogen bond to most if not all of these.

<scene name='User:Robert_Dutnall/Sandbox_1_sheets/Parallel_sidechains/2'>Click here to show the side chains again.</scene> You are looking roughly edge-on to the flat plane of the sheet and the atoms of each amino side chain have been colored light blue to show them more clearly.

What is the general orientation of the side chains with respect to each strand and the sheet? You should observe that the side chains are approximately perpendicular to the flat plane of the sheet. Along each strand, the side chains alternate direction. You can see this more clearly if we color the side chains in one strand alternately. <scene name='User:Robert_Dutnall/Sandbox_1_sheets/Parallel_strand_alt/3'>Click here</scene> to freeze the view and color the side chains along one strand blue-purple-blue-purple...etc.

If we apply this to all the strands (<scene name='User:Robert_Dutnall/Sandbox_1_sheets/Parallel_sidechains_alt/2'>click here</scene>) you can see that all the sidechains above the plane of the sheet are purple, and all those below are blue.

==Anti-Parallel β-sheet==

Anti-parallel β-sheets are composed of β-strands that alternate in direction. Each β-strand has mainchain dihedral angles as follows: Φ ~ -150o, φ ~ +135o.

The sheet shown below is composed of three strands in anti-parallel orientation. All the atoms are shown (C = green; N = blue; O = red; S = yellow; H = white).
<Structure load='Tut_antiparallel_bsheet.pdb' size='500' frame='true' align='left' caption='' scene='User:Robert_Dutnall/Sandbox_1_sheets/Antiparallel_load/3'/>

<scene name='User:Robert_Dutnall/Sandbox_1_sheets/Antiparallel_mainchain/3'>Click here</scene> to show only the polypeptide mainchain of each strand (NH, Cα, and C=O).

Identify the N- and C-termini of each strand. <scene name='User:Robert_Dutnall/Sandbox_1_sheets/Antiparallel_mainchain_labels/1'>Click here to see if you were correct.</scene>

As the structure rotates you should be able to see the extended nature of each strand and the parallel orientation of the three strands.

<scene name='User:Robert_Dutnall/Sandbox_1_sheets/Antipara_mainchain_labels_face/1'>Click here</scene> to stop the structure spinning and view the sheet from roughly perpendicular to its flat plane.

<scene name='User:Robert_Dutnall/Sandbox_1_sheets/Antipara_mainchain_labels_side/1'>Click here</scene> to stop the structure spinning and view the sheet from roughly edge-on to its flat plane.

<scene name='User:Robert_Dutnall/Sandbox_1_sheets/Antiparallel_mainchain_labels/1'>Click here to start the structure spinning again.</scene> Look at the structure carefully and identify the mainchain NH and C=O groups. In each strand the mainchain NH and C=O groups point to opposite sides of the mainchain. The strands line up in the sheet so that these NH and C=O groups are parallel to plane of the sheet and lie opposite each other so that they can make hydrogen bonds.

<scene name='User:Robert_Dutnall/Sandbox_1_sheets/Antipara_mainchain_hbonds/1'>Click here to add hydrogen bonds for the mainchain (dashed lines).</scene> The hydrogen bonds connect backbone NH groups and C=O groups. The N-H group is the hydrogen bond donor, the oxygen in the C=O group is the acceptor (N-H--->O=C). Each hydrogen bond is approximately 3.0 Angstroms (0.3 nm) in length (measured between the N and the O).

You should be able to see that the mainchain NH and C=O groups are involved in hydrogen bonds between the strands of the sheet. <scene name='User:Robert_Dutnall/Sandbox_1_sheets/Antipara_mainchain_hbonds_z/1'>Click here to zoom in to show some of the hydrogen bonds more clearly.</scene>

<scene name='User:Robert_Dutnall/Sandbox_1_sheets/Antipara_mainchain_hbonds/1'>Click here to zoom out again.</scene> You should notice that all of the NH and C=O groups that lie between strands are involved in hydrogen bonds. Only the groups on the edges of the sheet do not have hydrogen bond partners, but if this sheet were part of a larger protein, other residues would supply groups to hydrogen bond to most if not all of these.

Two of the strands in this sheet are connected by a β-turn. <scene name='User:Robert_Dutnall/Sandbox_1_sheets/Antipara_mainchain_turn/2'>Click here</scene> to show the β-turn. The carbon atoms of the amino acids that define the turn have been colored orange. The turn allows a segment of polypeptide to reverse direction in a short distance. In this case it also allows two strands to interact in an antiparallel fashion. <scene name='User:Robert_Dutnall/Sandbox_1_sheets/Antipara_mainchain_turn_zoom/3'>Click here to zoom in on the turn and reorient it to show more clearly.</scene> '''Is this a Type I or Type II β-turn? (Write down your answer so you can submit it to your instructor)'''

<scene name='User:Robert_Dutnall/Sandbox_1_sheets/Antipara_mainchain_sidechains/1'>Click here to zoom out again.</scene> In this view, some of the residues at the turn have been omitted and you are looking roughly edge-on to the flat plane of the sheet. Sidechains have been added and the atoms of each amino side chain have been colored blue or purple in an alternating fashion.

The side chains are approximately perpendicular to the flat plane of the sheet. Along each strand, the side chains alternate direction (above the plane, below the plane, above the plane...) so you should be able to see that all the sidechains above the plane of the sheet are purple, and all those below are blue.

==A mixed β-sheet==

The sheet shown below is composed of four strands. All the atoms are shown (C = green; N = blue; O = red; S = yellow; H = white). This is a mixed β-sheet. Some of the strands are parallel, some are antiparallel.
<Structure load='Mixed_sheet.pdb' size='500' frame='true' align='left' caption='' scene='User:Robert_Dutnall/Sandbox_1_sheets/Mixed_sheet_load/1'/>

<scene name='User:Robert_Dutnall/Sandbox_1_sheets/Mixed_sheet_mainchain/2'>Click here</scene> to show only the polypeptide mainchain of each strand (NH, Cα, and C=O).

'''What is the orientation of each pair of strands (parallel or antiparallel)?'''

Click below to highlight the strands in pairs (pair 1, pair 2 and pair 3). The carbon atoms will be highlighted in orange.

<scene name='User:Robert_Dutnall/Sandbox_1_sheets/Mixed_sheet_mainchain_pair1/1'>Pair 1.</scene>

<scene name='User:Robert_Dutnall/Sandbox_1_sheets/Mixed_sheet_mainchain_pair2/1'>Pair 2.</scene>

<scene name='User:Robert_Dutnall/Sandbox_1_sheets/Mixed_sheet_mainchain_pair3/1'>Pair 3.</scene>

'''Write down your answers for pair 1, pair 2 and pair 3 to submit to your instructor.'''

'''That's it. You are finished with Tutorial 2. Remember to submit your answers to the questions from this tutorial to your instructor.'''
= =
[[User:Robert Dutnall/Chem331_Tutorial2a|Click here if you want to go back to the first part of this tutorial.]]

User:Robert Dutnall/Chem331 Tutorial2a

2011-08-29T19:50:20Z

Robert Dutnall: New page: == Biochemistry Tutorial #2 - Secondary Structure (Part 1) == The secondary structure of a protein is defined by the local conformation of its backbone (polypeptide mainchain). There are ...

== Biochemistry Tutorial #2 - Secondary Structure (Part 1) ==

The secondary structure of a protein is defined by the local conformation of its backbone (polypeptide mainchain). There are two major types of regular secondary structures in proteins: helices and sheets. There are also regular turn structures. Turns often connect one element of secondary structure to another in the overall fold of the protein. Other parts of the protein mainchain may adopt more irregularly defined loops. This tutorial will focus mainly on helices and sheets.

''Note: in these tutorials, the images are 3D interactive images. You can manipulate them as you wish to get a better view of the molecules.''

You can rotate the structures by holding down the right mouse button and dragging. At any time you can click the 'toggle spin' button in box to stop/start the structure spinning.

Other things you can do:
::To rotate: left drag
::To Zoom: scroll button or shift + left drag
::To Translate: ctrl + right drag
::Right click to bring up an options menu

==Helices==

In helices, the polypeptide mainchain twists into a path that resembles a spiral staircase. Just like spiral staircases, helices come in different forms, depending on how tightly twisted the mainchain is. The form of a helix can be described by parameters such as the number of steps (amino acids) it takes to complete a turn (a 360o rotation around the long axis of the helix), and how far you travel along the helix axis in one complete turn. Helices can also be left-handed or right-handed. For proteins composed of L-amino acids, helices are almost always right-handed (a notable exception is the type I poly-proline helix). Although several types of helix form are possible, two regular helices are very common in proteins: the α-helix and the 310-helix.

==The α-helix==

α-helices are the most common type of regular helix found in proteins. They are characterized by the following helix parameters:
::Dihedral angles: Φ ~ -60o, φ ~ -45o
::Repeat (number of residues per turn) = 3.6
::Rise (translation along axis per amino acid residue) = 1.5 Angstroms (0.15 nm)
::Twist (rotation around axis per amino acid residue) = 100o (= 360o/repeat)
::Pitch (translation along axis per turn) = 5.4 Angstroms (= 0.54 nm = Repeat x Rise)

The helix shown below is a 19 amino acid chain in α-helical conformation.
<Structure load='Tut_alpha_helix.pdb' size='500' frame='true' align='left' caption='' scene='User:Robert_Dutnall/Sandbox_1_alpha_helix/A_helix_load/1'/>

All the atoms are shown in this initial orientation (C = green; N = blue; O = red; S = yellow; H = white). The helix axis runs vertically, approximately parallel to the plane of the screen.

<scene name='User:Robert_Dutnall/Sandbox_1_alpha_helix/A_helix_mainchain/3'>Click here</scene> to show only the polypeptide mainchain (NH, Cα, and C=O).

Identify the N- and C-termini. <scene name='User:Robert_Dutnall/Sandbox_1_alpha_helix/A_helix_mainchain_label/4'>Click here to see if you were correct.</scene>

<scene name='User:Robert_Dutnall/Sandbox_1_alpha_helix/A_helix_mainchain_label_ribbon/3'>Click here to add a ribbon that will help show the path of the mainchain. </scene> You should be able to see that it is helical with a right-handed twist (you rotate to the right as you move along the helix axis).

Click the "toggle spin" button in the box to stop the structure from rotating. Now use your mouse to rotate the structure to look down the helix axis. If you have any problems with finding this view, <scene name='User:Robert_Dutnall/Sandbox_1_alpha_helix/A_helix_mainchain_label_axis/3'>click here </scene>to zoom in and look down the helix axis from the N-terminal end.

<scene name='User:Robert_Dutnall/Sandbox_1_alpha_helix/A_helix_mainchain_label/4'>Click here to zoom out again.</scene> Look at the structure carefully and identify the mainchain NH and C=O groups. What is the orientation of these groups with respect to the helix axis?

<scene name='User:Robert_Dutnall/Sandbox_1_alpha_helix/A_helix_mainchain_label_hbonds/10'>Click here to zoom in a little and add hydrogen bonds for the mainchain (dashed lines).</scene> The hydrogen bonds connect backbone NH groups and C=O groups. The N-H group is the hydrogen bond donor, the oxygen in the C=O group is the acceptor (N-H--->O=C). Each hydrogen bond is approximately 3.0 Angstroms (0.3 nm) in length (measured between the N and the O). These hydrogen bonds connect amino acids that are spaced 4 residues apart in the primary sequence. The NH group is from amino acid X and the O is from amino acid X-4 (where X is the number of the amino acid in the sequence).

<scene name='User:Robert_Dutnall/Sandbox_1_alpha_helix/A_helix_mainchain_label_hbonds/9'>Click here to zoom out again.</scene> You should be able to see that all of the mainchain NH and C=O groups are involved in hydrogen bonds. This is possible because 1) all the mainchain NH groups and C=O groups are parallel to the helix axis, 2) all the NH groups point toward the N-terminus of the helix, and 3) all the C=O groups point toward the C-terminus. Only the NH groups in the first (N-terminal) turn, and the C=O groups in the last (C-terminal) turn of the helix do not have hydrogen bonding partners. However, if this helix were part of a larger protein, these groups would participate in hydrogen bonds with other parts of the protein. This is called 'helix capping' and the other groups involved are typically from amino acid side chains (that are called 'helix capping residues').

<scene name='User:Robert_Dutnall/Sandbox_1_alpha_helix/A_helix_sidechains/3'>Click here to show the side chains again.</scene> The atoms of each amino side chain have been colored light blue to show them more clearly. <scene name='User:Robert_Dutnall/Sandbox_1_alpha_helix/A_helix_sidechains_axis/1'>Click here to change the view to look down the helix axis.</scene>

What is the general orientation of the side chains with respect to the helix axis? You should observe that each side chain points away from the helix axis, but points down toward the N-terminus of the helix (this is clearer if you only show the first bond of each side chain: <scene name='User:Robert_Dutnall/Sandbox_1_alpha_helix/A_helix_sidechains_cropped/1'>click here</scene> or <scene name='User:Robert_Dutnall/Sandbox_1_alpha_helix/A_helix_sidechains_cropped/2'>click here</scene>).

==The 310-helix==

310-helices are also found in proteins but are less common than α-helices. They are characterized by the following helix parameters:
::Dihedral angles: Φ ~ -49o, φ ~ -26o
::Repeat (number of residues per turn) = 3.0
::Rise (translation along axis per amino acid residue) = 2.0 Angstroms (0.2 nm)
::Twist (rotation around axis per amino acid residue) = 120o (= 360o/repeat)
::Pitch (translation along axis per turn) = 6.0 Angstroms (= 0.6 nm = Repeat x Rise)

The helix shown below is a 19 amino acid chain in 310-helical conformation.
<Structure load='Tut_3-10_helix.pdb' size='500' frame='true' align='left' caption='' scene='User:Robert_Dutnall/Sandbox_1_alpha_helix/310_helix_load/4'/>

All the atoms are shown in this initial orientation (C = green; N = blue; O = red; S = yellow; H = white). The helix axis runs vertically, approximately parallel to the plane of the screen.

<scene name='User:Robert_Dutnall/Sandbox_1_alpha_helix/310_helix_mainchain/2'>Click here</scene> to show only the polypeptide mainchain (NH, Cα, and C=O). The N- and C-termini are labeled.

<scene name='User:Robert_Dutnall/Sandbox_1_alpha_helix/310_helix_mainchain_ribbon/2'>Click here to add a ribbon that will help show the path of the mainchain. </scene> You should be able to see that just like the α-helix, it is helical with a right-handed twist, and again, all the mainchain NH groups point toward the N-terminus, and all the mainchain C=O groups point toward the C-terminus.

The difference between an α-helix and a 310-helix lies in the helix parameters. A 310-helix is more tightly twisted so that the mainchain completes one turn every 3 amino acids (instead of 3.6 for the α-helix). This also results in a larger rise and pitch so that the 310-helix is longer than an α-helix (of the same number of residues).

<scene name='User:Robert_Dutnall/Sandbox_1_alpha_helix/310_helix_mainchain_axis/1'>Click here </scene>to zoom in and look down the helix axis from the N-terminal end. You'll be able to see the triangular shape of the mainchain.

<scene name='User:Robert_Dutnall/Sandbox_1_alpha_helix/310_helix_mainchain_hbonds/1'>Click here to zoom out again and display hydrogen bonds for the mainchain.</scene> Once again, all of the mainchain NH and C=O groups are involved in hydrogen bonds. However, now the hydrogen bonds connect amino acids that are spaced 3 residues apart in the primary sequence. The NH group is from amino acid X and the O is from amino acid X-3 (where X is the number of the amino acid in the sequence). <scene name='User:Robert_Dutnall/Sandbox_1_alpha_helix/310_helix_mainchain_hbonds/2'>Click here</scene> to zoom in and you should be able to see this more clearly.

<scene name='User:Robert_Dutnall/Sandbox_1_alpha_helix/310_helix_sidechains/1'>Click here to zoom out and show the side chains again.</scene> The atoms of each amino side chain have been colored light blue to show them more clearly. <scene name='User:Robert_Dutnall/Sandbox_1_alpha_helix/310_helix_sidechains_axis/2'>Click here to change the view to look down the helix axis.</scene>

As for the α-helix, each side chain points away from the helix axis, and points down toward the N-terminus of the helix. However, because the 310-helix repeat parameter is an integer (= 3.0), the side chains are spaced 120o apart and form 3 distinct sides to the helix. You'll see this more clearly if the side chains are colored in groups to show this (residues 1,4,7,10 etc are blue; residues 2,5,8,11 etc are purple; residues 3,6,9,12 etc are yellow): <scene name='User:Robert_Dutnall/Sandbox_1_alpha_helix/310_helix_sidechains_tricolor/1'>click here to look from the side</scene> or <scene name='User:Robert_Dutnall/Sandbox_1_alpha_helix/310_helix_sidechains_tricol_ax/1'>click here to view down the helix axis</scene>.

<scene name='User:Robert_Dutnall/Sandbox_1_alpha_helix/310_helix_load/4'>Click here to reset the view of the helix.</scene>

'''What is the identity of the N-terminal amino acid?'''

'''What is the identity of the C-terminal amino acid?'''

'''Write down these answers so that you can submit them to your instructor at the end of this tutorial.'''

= =
[[User:Robert Dutnall/Chem331_Tutorial2b|Click here to go on to part 2 of this tutorial.]]

User:Robert Dutnall/Chem331 Tutorial1b

2011-08-29T19:48:36Z

Robert Dutnall:

== Biochemistry Tutorial #1 - Peptides (Part 2)==

===Let's look at another dipeptide.===

Identify each amino acid in this dipeptide.
<Structure load='CysAsp3.pdb' size='400' frame='true' align='left' caption='Second Dipeptide' scene='User:Stephen_Mills/Sandbox_2_Peptide_tutorial_2/Cysaspstart/1' />

What is the short-hand notation for this dipeptide?

<scene name='User:Stephen_Mills/Sandbox_2_Peptide_tutorial_2/Cysasplabels/2'>Click here to show the labels on each amino acid.</scene>

Identify which amino acid is at the N-terminus and which is at the C-terminus.

<scene name='User:Stephen_Mills/Sandbox_2_Peptide_tutorial_2/Cysasptermini/1'>Click here to label each terminus.</scene>

Identify the α carbons of each amino acid.

<scene name='User:Stephen_Mills/Sandbox_2_Peptide_tutorial_2/Cysaspalphas/1'>Click here to have them highlighted.</scene>

Identify the atoms involved in the peptide bond in this dipeptide.

<scene name='User:Stephen_Mills/Sandbox_2_Peptide_tutorial_2/Cysaspamide/1'>Click here to have those atoms change color.</scene>

Now, measure the distance between the α carbons.
<scene name='User:Stephen_Mills/Sandbox_2_Peptide_tutorial_2/Cysaspmeasure/1'>Click here to get a good starting configuration.</scene>

To measure a distance, Double click on the first atom, then double click on the second atom. You may need to rotate the molecule a bit to see the distance well. Try it now.

'''Write down this distance and submit it to your instructor.'''
 

==Oligopeptides==

Now you are ready to work with oligopeptides, or polymers composed of 3-20 amino acid residues. These polymers are linear; that is, each amino acid is linked to it's neighbor in a head-to-tail fashion rather than forming branched chains. You will be observing a 5mer in this tutorial.

<Structure load='GDCRY.pdb' size='500' frame='true' align='left' caption='' scene='User:Stephen_Mills/Sandbox_2_Peptide_tutorial_2/Pentapeptide_start/1' />

For this part, you may need to resize and move the molecule around. To remind you: 
To Rotate: left drag 
To Zoom: scroll button or shift + left drag 
To Translate: ctrl + right drag (On a Mac, this doesn't work in FireFox, but does work in Safari). 

'''Identify where Y and R are located in this oligopeptide.'''

<scene name='User:Stephen_Mills/Sandbox_2_Peptide_tutorial_2/Pentapeptide_yr/2'>Click here to have Y and R colored purple.</scene>

Notice that the NH of Y is bonded to the carbonyl of R.

Also notice how the bulky side-chains point away from the backbone of the peptide.

'''Identify where C and D are located in this peptide.'''
<scene name='User:Stephen_Mills/Sandbox_2_Peptide_tutorial_2/Pentapeptide_cd/2'>
Click here to have C and D colored purple.</scene>

Notice how Cysteine's thiol (SH) group points outward from the 5mer backbone at an angle that would allow for the stable formation of the disulfide bond. 

'''Identify the remaining amino acid in this peptide.''' 

'''Write down the short-hand notation for this pentapeptide, in the correct order from the N-terminus to the C-terminus and submit this to your instructor.'''

 

==Last Part!!==

Now a test peptide.
<Structure load='WHENISPIEDAY3.pdb' size='600' frame='true' align='left' caption='' scene='User:Stephen_Mills/Sandbox_2_Peptide_tutorial_2/Test_peptide/1' />

'''Identify the sequence of this peptide and submit the answer to your instructor.''' 
You will probably need to move the molecule around and rotate it to see the whole structure.

When you write it down, it will spell out a question.

'''Submit the sequence of the peptide '''''and''''' the answer to the question'''
 

'''Congratulations! You have just finished the first Biochemistry Tutorial'''

User:Robert Dutnall/Chem331 Tutorial1a

2011-08-29T19:46:45Z

Robert Dutnall:

== Biochemistry Tutorial #1 - Peptides (Part 1)==

The alpha amino acids polymerize, or bond, through the elimination of a water molecule. Polymers composed of two amino acid residues are known as dipeptides. Longer polymers are called oligopeptides (up to around 20 amino acids) or polypeptides (> 20 amino acids). Proteins can contain any number of amino acids linked together but each has a unique length (number of amino acids) and sequence (the identity and order of amino acids in the polymer).

In this excercise, you will identify amino acids, the amino and carboxy groups involved in the peptide bond, look at peptide bonds and oligopeptide structure and finally also examine disulfide bonds.

==Which amino acid is this?==

<Structure load='Arginine.pdb' size='300' frame='true' align='left' caption='' scene='User:Stephen_Mills/Sandbox_2_Peptide_tutorial/Arginine/3' />

Scroll down when you know what it is.

''Note: in these tutorials, the images are 3D interactive images. You can manipulate them as you wish to get a better view of the molecules.''

You can rotate the amino acid by holding down the right mouse button and dragging.

Other things you can do:
::To rotate: left drag
::To Zoom: scroll button or shift + left drag
::To Translate: ctrl + right drag
::Right click to bring up an options menu

 

= =
<Structure load='Arginine.pdb' size='300' frame='true' align='left' caption='' scene='User:Stephen_Mills/Sandbox_2_Peptide_tutorial/Arginine/3' />

This is Arginine (Arg, R) and amino acid with a positively charged side chain.

Identify the α-amino and α-carboxy groups involved in peptide bond formation.

<scene name='User:Stephen_Mills/Sandbox_2_Peptide_tutorial/Argininelabels/1'>Click here to see the N and C groups labelled.</scene>

== ==
<Structure load='Arginine.pdb' size='300' frame='true' align='left' caption=' ' scene='User:Stephen_Mills/Sandbox_2_Peptide_tutorial/Tyrosine/1' />

<big>'''Name the new amino acid.'''</big>

Scroll down to get the answer
 
 
 

= =

<Structure load='Arginine.pdb' size='300' frame='true' align='left' caption=' ' scene='User:Stephen_Mills/Sandbox_2_Peptide_tutorial/Tyrosine/1' />

This is Tyrosine (Tyr, Y), an aromatic amino acid

Again, identify the amino and carboxy groups involved in peptide bond formation.

<scene name='User:Stephen_Mills/Sandbox_2_Peptide_tutorial/Tyrosinelabels/1'>Click here to have the N and C groups labeled.</scene>

 

==Alpha Carbons==
Now here are both structures.
Identify the α-carbons on each amino acid.

<Structure load='Arginine.pdb' size='300' frame='true' align='left' caption='Arginine' scene='User:Stephen_Mills/Sandbox_2_Peptide_tutorial/Arginine/3' />

<scene name='User:Stephen_Mills/Sandbox_2_Peptide_tutorial/Argininealpha/2'>Click here</scene> to label the α-carbon on Arginine.

<Structure load='Tyrosine.pdb' size='300' frame='true' align='right' caption='Tyrosine' scene='User:Stephen_Mills/Sandbox_2_Peptide_tutorial/Tyrosine/1' />

<scene name='User:Stephen_Mills/Sandbox_2_Peptide_tutorial/Tyrosinealpha/2'>Click here</scene> to label the α-carbon on Tyrosine.

 

==Dipeptides==

Identify the main chain groups and side chains of this dipeptide.

Distinguish which end is the amino terminus and which amino acid is at the carboxyl terminus?

Which amino acid is at the N terminus? Which is at the C terminus?

<Structure load='ArgTyr.pdb' size='500' frame='true' align='left' caption='' scene='User:Stephen_Mills/Sandbox_2_Peptide_tutorial/Argtyr/1' />

<scene name='User:Stephen_Mills/Sandbox_2_Peptide_tutorial/Argtyrtermini/1'>Click here to label the N and C termini.</scene>

<scene name='User:Stephen_Mills/Peptide_tutorial_1/Argtyraalabels/2'>Click here to label the two amino acids.</scene>

Scroll down for more.

<Structure load='ArgTyr.pdb' size='500' frame='true' align='left' caption='' scene='User:Stephen_Mills/Peptide_tutorial_1/Argtyraalabels/2' />

Notice that the Arginine is on the amino terminal end and the Tyrosine is on the carboxy terminal end.

The short way to name this dipeptide is: <big>'''Arg-Tyr'''</big> or <big>'''RY'''</big>

 
Identify the atoms involved in the peptide bond between Tyrosine and Arginine

<scene name='User:Stephen_Mills/Peptide_tutorial_1/Argtyramide/3'>Click here to change the color of those atoms to purple.</scene>

Peptide bonds almost always assume the trans conformation: that in which successive alpha carbon atoms are on opposite sides of the peptide (C-N) bond joining them. <scene name='User:Stephen_Mills/Peptide_tutorial_1/Argtyrtransamide/3'>Click here to show this trans bond.</scene> The exception are peptide bonds involving proline (when P is on the C-terminal side of the bond) - these can be trans or cis.
 

==Backbone Atoms==

<Structure load='ArgTyr.pdb' size='500' frame='true' align='left' caption='' scene='User:Stephen_Mills/Sandbox_2_Peptide_tutorial/Argtyr/1' />

If the R groups (side chains) of the amino acids are no longer displayed, then you will be looking at the backbone of the dipeptide. <scene name='User:Stephen_Mills/Sandbox_2_Peptide_tutorial/Argtyrbackbone/1'>Click here to turn off the side chains.</scene>

This dipeptide has a completely extended conformation.

Rotate the molecule and you should notice how planar the peptide bond is.

[[User:Robert Dutnall/Chem331_Tutorial1b|Click here to go on to the next part of this tutorial.]]

User:Robert Dutnall/Chem331 Tutorial1b

2011-08-29T19:42:34Z

Robert Dutnall: New page: ==Peptide 2:== ===Let's look at another dipeptide.=== Identify each amino acid in this dipeptide. <Structure load='CysAsp3.pdb' size='400' frame='true' align='left' caption='Second Dipep...

==Peptide 2:==

===Let's look at another dipeptide.===

Identify each amino acid in this dipeptide.
<Structure load='CysAsp3.pdb' size='400' frame='true' align='left' caption='Second Dipeptide' scene='User:Stephen_Mills/Sandbox_2_Peptide_tutorial_2/Cysaspstart/1' />

What is the short-hand notation for this dipeptide?

<scene name='User:Stephen_Mills/Sandbox_2_Peptide_tutorial_2/Cysasplabels/2'>Click here to show the labels on each amino acid.</scene>

Identify which amino acid is at the N-terminus and which is at the C-terminus.

<scene name='User:Stephen_Mills/Sandbox_2_Peptide_tutorial_2/Cysasptermini/1'>Click here to label each terminus.</scene>

Identify the α carbons of each amino acid.

<scene name='User:Stephen_Mills/Sandbox_2_Peptide_tutorial_2/Cysaspalphas/1'>Click here to have them highlighted.</scene>

Identify the atoms involved in the peptide bond in this dipeptide.

<scene name='User:Stephen_Mills/Sandbox_2_Peptide_tutorial_2/Cysaspamide/1'>Click here to have those atoms change color.</scene>

Now, measure the distance between the α carbons.
<scene name='User:Stephen_Mills/Sandbox_2_Peptide_tutorial_2/Cysaspmeasure/1'>Click here to get a good starting configuration.</scene>

To measure a distance, Double click on the first atom, then double click on the second atom. You may need to rotate the molecule a bit to see the distance well. Try it now.

'''Write down this distance and submit it to your instructor.'''
 

==Oligopeptides==

Now you are ready to work with oligopeptides, or polymers composed of 3-20 amino acid residues. These polymers are linear; that is, each amino acid is linked to it's neighbor in a head-to-tail fashion rather than forming branched chains. You will be observing a 5mer in this tutorial.

<Structure load='GDCRY.pdb' size='500' frame='true' align='left' caption='' scene='User:Stephen_Mills/Sandbox_2_Peptide_tutorial_2/Pentapeptide_start/1' />

For this part, you may need to resize and move the molecule around. To remind you: 
To Rotate: left drag 
To Zoom: scroll button or shift + left drag 
To Translate: ctrl + right drag (On a Mac, this doesn't work in FireFox, but does work in Safari). 

'''Identify where Y and R are located in this oligopeptide.'''

<scene name='User:Stephen_Mills/Sandbox_2_Peptide_tutorial_2/Pentapeptide_yr/2'>Click here to have Y and R colored purple.</scene>

Notice that the NH of Y is bonded to the carbonyl of R.

Also notice how the bulky side-chains point away from the backbone of the peptide.

'''Identify where C and D are located in this peptide.'''
<scene name='User:Stephen_Mills/Sandbox_2_Peptide_tutorial_2/Pentapeptide_cd/2'>
Click here to have C and D colored purple.</scene>

Notice how Cysteine's thiol (SH) group points outward from the 5mer backbone at an angle that would allow for the stable formation of the disulfide bond. 

'''Identify the remaining amino acid in this peptide.''' 

'''Write down the short-hand notation for this pentapeptide, in the correct order from the N-terminus to the C-terminus and submit this to your instructor.'''

 

==Last Part!!==

Now a test peptide.
<Structure load='WHENISPIEDAY3.pdb' size='600' frame='true' align='left' caption='' scene='User:Stephen_Mills/Sandbox_2_Peptide_tutorial_2/Test_peptide/1' />

'''Identify the sequence of this peptide and submit the answer to your instructor.''' 
You will probably need to move the molecule around and rotate it to see the whole structure.

When you write it down, it will spell out a question.

'''Submit the sequence of the peptide '''''and''''' the answer to the question'''
 

'''Congratulations! You have just finished the first Biochemistry Tutorial'''

User:Robert Dutnall/Chem331 Tutorial1a

2011-08-29T19:39:31Z

Robert Dutnall: New page: == Biochemistry Tutorial #1 - Peptides Pt. 1== The alpha amino acids polymerize, or bond, through the elimination of a water molecule. Polymers composed of two amino acid residues are kno...

== Biochemistry Tutorial #1 - Peptides Pt. 1==

The alpha amino acids polymerize, or bond, through the elimination of a water molecule. Polymers composed of two amino acid residues are known as dipeptides. Longer polymers are called oligopeptides (up to around 20 amino acids) or polypeptides (> 20 amino acids). Proteins can contain any number of amino acids linked together but each has a unique length (number of amino acids) and sequence (the identity and order of amino acids in the polymer).

In this excercise, you will identify amino acids, the amino and carboxy groups involved in the peptide bond, look at peptide bonds and oligopeptide structure and finally also examine disulfide bonds.

==Which amino acid is this?==

<Structure load='Arginine.pdb' size='300' frame='true' align='left' caption='' scene='User:Stephen_Mills/Sandbox_2_Peptide_tutorial/Arginine/3' />

Scroll down when you know what it is.

''Note: in these tutorials, the images are 3D interactive images. You can manipulate them as you wish to get a better view of the molecules.''

You can rotate the amino acid by holding down the right mouse button and dragging.

Other things you can do:
::To rotate: left drag
::To Zoom: scroll button or shift + left drag
::To Translate: ctrl + right drag
::Right click to bring up an options menu

 

= =
<Structure load='Arginine.pdb' size='300' frame='true' align='left' caption='' scene='User:Stephen_Mills/Sandbox_2_Peptide_tutorial/Arginine/3' />

This is Arginine (Arg, R) and amino acid with a positively charged side chain.

Identify the α-amino and α-carboxy groups involved in peptide bond formation.

<scene name='User:Stephen_Mills/Sandbox_2_Peptide_tutorial/Argininelabels/1'>Click here to see the N and C groups labelled.</scene>

== ==
<Structure load='Arginine.pdb' size='300' frame='true' align='left' caption=' ' scene='User:Stephen_Mills/Sandbox_2_Peptide_tutorial/Tyrosine/1' />

<big>'''Name the new amino acid.'''</big>

Scroll down to get the answer
 
 
 

= =

<Structure load='Arginine.pdb' size='300' frame='true' align='left' caption=' ' scene='User:Stephen_Mills/Sandbox_2_Peptide_tutorial/Tyrosine/1' />

This is Tyrosine (Tyr, Y), an aromatic amino acid

Again, identify the amino and carboxy groups involved in peptide bond formation.

<scene name='User:Stephen_Mills/Sandbox_2_Peptide_tutorial/Tyrosinelabels/1'>Click here to have the N and C groups labeled.</scene>

 

==Alpha Carbons==
Now here are both structures.
Identify the α-carbons on each amino acid.

<Structure load='Arginine.pdb' size='300' frame='true' align='left' caption='Arginine' scene='User:Stephen_Mills/Sandbox_2_Peptide_tutorial/Arginine/3' />

<scene name='User:Stephen_Mills/Sandbox_2_Peptide_tutorial/Argininealpha/2'>Click here</scene> to label the α-carbon on Arginine.

<Structure load='Tyrosine.pdb' size='300' frame='true' align='right' caption='Tyrosine' scene='User:Stephen_Mills/Sandbox_2_Peptide_tutorial/Tyrosine/1' />

<scene name='User:Stephen_Mills/Sandbox_2_Peptide_tutorial/Tyrosinealpha/2'>Click here</scene> to label the α-carbon on Tyrosine.

 

==Dipeptides==

Identify the main chain groups and side chains of this dipeptide.

Distinguish which end is the amino terminus and which amino acid is at the carboxyl terminus?

Which amino acid is at the N terminus? Which is at the C terminus?

<Structure load='ArgTyr.pdb' size='500' frame='true' align='left' caption='' scene='User:Stephen_Mills/Sandbox_2_Peptide_tutorial/Argtyr/1' />

<scene name='User:Stephen_Mills/Sandbox_2_Peptide_tutorial/Argtyrtermini/1'>Click here to label the N and C termini.</scene>

<scene name='User:Stephen_Mills/Peptide_tutorial_1/Argtyraalabels/2'>Click here to label the two amino acids.</scene>

Scroll down for more.

<Structure load='ArgTyr.pdb' size='500' frame='true' align='left' caption='' scene='User:Stephen_Mills/Peptide_tutorial_1/Argtyraalabels/2' />

Notice that the Arginine is on the amino terminal end and the Tyrosine is on the carboxy terminal end.

The short way to name this dipeptide is: <big>'''Arg-Tyr'''</big> or <big>'''RY'''</big>

 
Identify the atoms involved in the peptide bond between Tyrosine and Arginine

<scene name='User:Stephen_Mills/Peptide_tutorial_1/Argtyramide/3'>Click here to change the color of those atoms to purple.</scene>

Peptide bonds almost always assume the trans conformation: that in which successive alpha carbon atoms are on opposite sides of the peptide (C-N) bond joining them. <scene name='User:Stephen_Mills/Peptide_tutorial_1/Argtyrtransamide/3'>Click here to show this trans bond.</scene> The exception are peptide bonds involving proline (when P is on the C-terminal side of the bond) - these can be trans or cis.
 

==Backbone Atoms==

<Structure load='ArgTyr.pdb' size='500' frame='true' align='left' caption='' scene='User:Stephen_Mills/Sandbox_2_Peptide_tutorial/Argtyr/1' />

If the R groups (side chains) of the amino acids are no longer displayed, then you will be looking at the backbone of the dipeptide. <scene name='User:Stephen_Mills/Sandbox_2_Peptide_tutorial/Argtyrbackbone/1'>Click here to turn off the side chains.</scene>

This dipeptide has a completely extended conformation.

Rotate the molecule and you should notice how planar the peptide bond is.

[[User:Stephen Mills/Peptide tutorial_2|Click here to go on to the next part of this tutorial.]]

User:Robert Dutnall/Sandbox 1 sheets

2011-08-29T19:02:55Z

Robert Dutnall:

== Biochemistry Tutorial #2 - Secondary Structure (Part 2) ==

==β-strands and β-sheets==

The second major secondary structure element is the β-sheet. β-sheets are composed of two or more segments of polypeptide mainchain in β-strand conformation. In a β-strand, the polypeptide mainchain is in a mostly extended conformation. As their name implies, β-sheets are relatively flat, planar-like structures made up of β-strands arranged side-by-side. They come in three flavors: parallel, anti-parallel and mixed, which differ in terms of the orientation of each component strand (with respect to the direction of the mainchain from N-terminus to C-terminus).

Note that the mainchain of a β-strand is not perfectly fully extended (Φ ≠ φ ≠ 180o) and that the mainchain actually slowly twists (this is more obvious if you look at a long segment of β-strand). Thus β-sheets are not completely flat and also exhibit some twisting (this is also more obvious if you look at sheets made of many β-strands).

==Parallel β-sheet==

Parallel β-sheets are composed of β-strands that all point in the same direction. Each β-strand has mainchain dihedral angles as follows: Φ ~ -120o, φ ~ +105o.

The sheet shown below is composed of three strands in parallel orientation. All the atoms are shown (C = green; N = blue; O = red; S = yellow; H = white).
<Structure load='Tut_parallel_bsheet.pdb' size='500' frame='true' align='left' caption='' scene='User:Robert_Dutnall/Sandbox_1_sheets/Parallel_load/2'/>

<scene name='User:Robert_Dutnall/Sandbox_1_sheets/Parallel_mainchain/2'>Click here</scene> to show only the polypeptide mainchain (NH, Cα, and C=O).

Identify the N- and C-termini of each strand. <scene name='User:Robert_Dutnall/Sandbox_1_sheets/Parallel_mainchain_labels/6'>Click here to see if you were correct.</scene>

As the structure rotates you should be able to see the extended nature of each strand and the parallel orientation of the three strands.

<scene name='User:Robert_Dutnall/Sandbox_1_sheets/Parallel_mainchain_labels_face/2'>Click here</scene> to stop the structure spinning and view the sheet from roughly perpendicular to its flat plane, with each strand running left-to-right (N- to C-terminus).

<scene name='User:Robert_Dutnall/Sandbox_1_sheets/Parallel_mainchain_labels_side/2'>Click here</scene> to stop the structure spinning and view the sheet from roughly edge-on to its flat plane.

<scene name='User:Robert_Dutnall/Sandbox_1_sheets/Parallel_mainchain_labels/6'>Click here to start the structure spinning again.</scene> Look at the structure carefully and identify the mainchain NH and C=O groups. What is the orientation of these groups with respect to the long axis of each strand? What the orientation of these groups with respect to the flat plane of the sheet?

<scene name='User:Robert_Dutnall/Sandbox_1_sheets/Parallel_mainchain_labels_hb/5'>Click here to add hydrogen bonds for the mainchain (dashed lines).</scene> The hydrogen bonds connect backbone NH groups and C=O groups. The N-H group is the hydrogen bond donor, the oxygen in the C=O group is the acceptor (N-H--->O=C). Each hydrogen bond is approximately 3.0 Angstroms (0.3 nm) in length (measured between the N and the O).

You should be able to see that the mainchain NH and C=O groups are involved in hydrogen bonds. In each strand the mainchain NH and C=O groups point to opposite sides of the mainchain (because of the almost fully extended conformation). The strands line up in the sheet so that the NH and C=O groups are parallel to plane of the sheet and lie opposite each other in pairs. This means that hydrogen bonds can be made between the strands of the sheet. <scene name='User:Robert_Dutnall/Sandbox_1_sheets/Parallel_mainchain_labels_hb_z/5'>Click here to zoom in to show some of the hydrogen bonds more clearly.</scene>

<scene name='User:Robert_Dutnall/Sandbox_1_sheets/Parallel_mainchain_labels_hb/5'>Click here to zoom out again.</scene> You should also notice that all of the NH and C=O groups that lie between strands are involved in hydrogen bonds. Only the groups on the edges of the sheet do not have hydrogen bond partners. However, as with helix capping, if this sheet were part of a larger protein, other residues would supply groups to hydrogen bond to most if not all of these.

<scene name='User:Robert_Dutnall/Sandbox_1_sheets/Parallel_sidechains/2'>Click here to show the side chains again.</scene> You are looking roughly edge-on to the flat plane of the sheet and the atoms of each amino side chain have been colored light blue to show them more clearly.

What is the general orientation of the side chains with respect to each strand and the sheet? You should observe that the side chains are approximately perpendicular to the flat plane of the sheet. Along each strand, the side chains alternate direction. You can see this more clearly if we color the side chains in one strand alternately. <scene name='User:Robert_Dutnall/Sandbox_1_sheets/Parallel_strand_alt/3'>Click here</scene> to freeze the view and color the side chains along one strand blue-purple-blue-purple...etc.

If we apply this to all the strands (<scene name='User:Robert_Dutnall/Sandbox_1_sheets/Parallel_sidechains_alt/2'>click here</scene>) you can see that all the sidechains above the plane of the sheet are purple, and all those below are blue.

==Anti-Parallel β-sheet==

Anti-parallel β-sheets are composed of β-strands that alternate in direction. Each β-strand has mainchain dihedral angles as follows: Φ ~ -150o, φ ~ +135o.

The sheet shown below is composed of three strands in anti-parallel orientation. All the atoms are shown (C = green; N = blue; O = red; S = yellow; H = white).
<Structure load='Tut_antiparallel_bsheet.pdb' size='500' frame='true' align='left' caption='' scene='User:Robert_Dutnall/Sandbox_1_sheets/Antiparallel_load/3'/>

<scene name='User:Robert_Dutnall/Sandbox_1_sheets/Antiparallel_mainchain/3'>Click here</scene> to show only the polypeptide mainchain of each strand (NH, Cα, and C=O).

Identify the N- and C-termini of each strand. <scene name='User:Robert_Dutnall/Sandbox_1_sheets/Antiparallel_mainchain_labels/1'>Click here to see if you were correct.</scene>

As the structure rotates you should be able to see the extended nature of each strand and the parallel orientation of the three strands.

<scene name='User:Robert_Dutnall/Sandbox_1_sheets/Antipara_mainchain_labels_face/1'>Click here</scene> to stop the structure spinning and view the sheet from roughly perpendicular to its flat plane.

<scene name='User:Robert_Dutnall/Sandbox_1_sheets/Antipara_mainchain_labels_side/1'>Click here</scene> to stop the structure spinning and view the sheet from roughly edge-on to its flat plane.

<scene name='User:Robert_Dutnall/Sandbox_1_sheets/Antiparallel_mainchain_labels/1'>Click here to start the structure spinning again.</scene> Look at the structure carefully and identify the mainchain NH and C=O groups. In each strand the mainchain NH and C=O groups point to opposite sides of the mainchain. The strands line up in the sheet so that these NH and C=O groups are parallel to plane of the sheet and lie opposite each other so that they can make hydrogen bonds.

<scene name='User:Robert_Dutnall/Sandbox_1_sheets/Antipara_mainchain_hbonds/1'>Click here to add hydrogen bonds for the mainchain (dashed lines).</scene> The hydrogen bonds connect backbone NH groups and C=O groups. The N-H group is the hydrogen bond donor, the oxygen in the C=O group is the acceptor (N-H--->O=C). Each hydrogen bond is approximately 3.0 Angstroms (0.3 nm) in length (measured between the N and the O).

You should be able to see that the mainchain NH and C=O groups are involved in hydrogen bonds between the strands of the sheet. <scene name='User:Robert_Dutnall/Sandbox_1_sheets/Antipara_mainchain_hbonds_z/1'>Click here to zoom in to show some of the hydrogen bonds more clearly.</scene>

<scene name='User:Robert_Dutnall/Sandbox_1_sheets/Antipara_mainchain_hbonds/1'>Click here to zoom out again.</scene> You should notice that all of the NH and C=O groups that lie between strands are involved in hydrogen bonds. Only the groups on the edges of the sheet do not have hydrogen bond partners, but if this sheet were part of a larger protein, other residues would supply groups to hydrogen bond to most if not all of these.

Two of the strands in this sheet are connected by a β-turn. <scene name='User:Robert_Dutnall/Sandbox_1_sheets/Antipara_mainchain_turn/2'>Click here</scene> to show the β-turn. The carbon atoms of the amino acids that define the turn have been colored orange. The turn allows a segment of polypeptide to reverse direction in a short distance. In this case it also allows two strands to interact in an antiparallel fashion. <scene name='User:Robert_Dutnall/Sandbox_1_sheets/Antipara_mainchain_turn_zoom/3'>Click here to zoom in on the turn and reorient it to show more clearly.</scene> '''Is this a Type I or Type II β-turn? (Write down your answer so you can submit it to your instructor)'''

<scene name='User:Robert_Dutnall/Sandbox_1_sheets/Antipara_mainchain_sidechains/1'>Click here to zoom out again.</scene> In this view, some of the residues at the turn have been omitted and you are looking roughly edge-on to the flat plane of the sheet. Sidechains have been added and the atoms of each amino side chain have been colored blue or purple in an alternating fashion.

The side chains are approximately perpendicular to the flat plane of the sheet. Along each strand, the side chains alternate direction (above the plane, below the plane, above the plane...) so you should be able to see that all the sidechains above the plane of the sheet are purple, and all those below are blue.

==A mixed β-sheet==

The sheet shown below is composed of four strands. All the atoms are shown (C = green; N = blue; O = red; S = yellow; H = white). This is a mixed β-sheet. Some of the strands are parallel, some are antiparallel.
<Structure load='Mixed_sheet.pdb' size='500' frame='true' align='left' caption='' scene='User:Robert_Dutnall/Sandbox_1_sheets/Mixed_sheet_load/1'/>

<scene name='User:Robert_Dutnall/Sandbox_1_sheets/Mixed_sheet_mainchain/2'>Click here</scene> to show only the polypeptide mainchain of each strand (NH, Cα, and C=O).

'''What is the orientation of each pair of strands (parallel or antiparallel)?'''

Click below to highlight the strands in pairs (pair 1, pair 2 and pair 3). The carbon atoms will be highlighted in orange.

<scene name='User:Robert_Dutnall/Sandbox_1_sheets/Mixed_sheet_mainchain_pair1/1'>Pair 1.</scene>

<scene name='User:Robert_Dutnall/Sandbox_1_sheets/Mixed_sheet_mainchain_pair2/1'>Pair 2.</scene>

<scene name='User:Robert_Dutnall/Sandbox_1_sheets/Mixed_sheet_mainchain_pair3/1'>Pair 3.</scene>

'''Write down your answers for pair 1, pair 2 and pair 3 to submit to your instructor.'''

'''That's it. You are finished with Tutorial 2. Remember to submit your answers to the questions from this tutorial to your instructor.'''
= =
[[User:Robert Dutnall/Sandbox_1_alpha_helix|Click here if you want to go back to the first part of this tutorial.]]

User:Robert Dutnall/Sandbox 1 sheets

2011-08-29T19:01:01Z

Robert Dutnall:

== Biochemistry Tutorial #2 - Secondary Structure (Part 2) ==

==β-strands and β-sheets==

The second major secondary structure element is the β-sheet. β-sheets are composed of two or more segments of polypeptide mainchain in β-strand conformation. In a β-strand, the polypeptide mainchain is in a mostly extended conformation. As their name implies, β-sheets are relatively flat, planar-like structures made up of β-strands arranged side-by-side. They come in three flavors: parallel, anti-parallel and mixed, which differ in terms of the orientation of each component strand (with respect to the direction of the mainchain from N-terminus to C-terminus).

Note that the mainchain of a β-strand is not perfectly fully extended (Φ ≠ φ ≠ 180o) and that the mainchain actually slowly twists (this is more obvious if you look at a long segment of β-strand). Thus β-sheets are not completely flat and also exhibit some twisting (this is also more obvious if you look at sheets made of many β-strands).

==Parallel β-sheet==

Parallel β-sheets are composed of β-strands that all point in the same direction. Each β-strand has mainchain dihedral angles as follows: Φ ~ -120o, φ ~ +105o.

The sheet shown below is composed of three strands in parallel orientation. All the atoms are shown (C = green; N = blue; O = red; S = yellow; H = white).
<Structure load='Tut_parallel_bsheet.pdb' size='500' frame='true' align='left' caption='' scene='User:Robert_Dutnall/Sandbox_1_sheets/Parallel_load/2'/>

<scene name='User:Robert_Dutnall/Sandbox_1_sheets/Parallel_mainchain/2'>Click here</scene> to show only the polypeptide mainchain (NH, Cα, and C=O).

Identify the N- and C-termini of each strand. <scene name='User:Robert_Dutnall/Sandbox_1_sheets/Parallel_mainchain_labels/6'>Click here to see if you were correct.</scene>

As the structure rotates you should be able to see the extended nature of each strand and the parallel orientation of the three strands.

<scene name='User:Robert_Dutnall/Sandbox_1_sheets/Parallel_mainchain_labels_face/2'>Click here</scene> to stop the structure spinning and view the sheet from roughly perpendicular to its flat plane, with each strand running left-to-right (N- to C-terminus).

<scene name='User:Robert_Dutnall/Sandbox_1_sheets/Parallel_mainchain_labels_side/2'>Click here</scene> to stop the structure spinning and view the sheet from roughly edge-on to its flat plane.

<scene name='User:Robert_Dutnall/Sandbox_1_sheets/Parallel_mainchain_labels/6'>Click here to start the structure spinning again.</scene> Look at the structure carefully and identify the mainchain NH and C=O groups. What is the orientation of these groups with respect to the long axis of each strand? What the orientation of these groups with respect to the flat plane of the sheet?

<scene name='User:Robert_Dutnall/Sandbox_1_sheets/Parallel_mainchain_labels_hb/5'>Click here to add hydrogen bonds for the mainchain (dashed lines).</scene> The hydrogen bonds connect backbone NH groups and C=O groups. The N-H group is the hydrogen bond donor, the oxygen in the C=O group is the acceptor (N-H--->O=C). Each hydrogen bond is approximately 3.0 Angstroms (0.3 nm) in length (measured between the N and the O).

You should be able to see that the mainchain NH and C=O groups are involved in hydrogen bonds. In each strand the mainchain NH and C=O groups point to opposite sides of the mainchain (because of the almost fully extended conformation). The strands line up in the sheet so that the NH and C=O groups are parallel to plane of the sheet and lie opposite each other in pairs. This means that hydrogen bonds can be made between the strands of the sheet. <scene name='User:Robert_Dutnall/Sandbox_1_sheets/Parallel_mainchain_labels_hb_z/5'>Click here to zoom in to show some of the hydrogen bonds more clearly.</scene>

<scene name='User:Robert_Dutnall/Sandbox_1_sheets/Parallel_mainchain_labels_hb/5'>Click here to zoom out again.</scene> You should also notice that all of the NH and C=O groups that lie between strands are involved in hydrogen bonds. Only the groups on the edges of the sheet do not have hydrogen bond partners. However, as with helix capping, if this sheet were part of a larger protein, other residues would supply groups to hydrogen bond to most if not all of these.

<scene name='User:Robert_Dutnall/Sandbox_1_sheets/Parallel_sidechains/2'>Click here to show the side chains again.</scene> You are looking roughly edge-on to the flat plane of the sheet and the atoms of each amino side chain have been colored light blue to show them more clearly.

What is the general orientation of the side chains with respect to each strand and the sheet? You should observe that the side chains are approximately perpendicular to the flat plane of the sheet. Along each strand, the side chains alternate direction. You can see this more clearly if we color the side chains in one strand alternately. <scene name='User:Robert_Dutnall/Sandbox_1_sheets/Parallel_strand_alt/3'>Click here</scene> to freeze the view and color the side chains along one strand blue-purple-blue-purple...etc.

If we apply this to all the strands (<scene name='User:Robert_Dutnall/Sandbox_1_sheets/Parallel_sidechains_alt/2'>click here</scene>) you can see that all the sidechains above the plane of the sheet are purple, and all those below are blue.

==Anti-Parallel β-sheet==

Anti-parallel β-sheets are composed of β-strands that alternate in direction. Each β-strand has mainchain dihedral angles as follows: Φ ~ -150o, φ ~ +135o.

The sheet shown below is composed of three strands in anti-parallel orientation. All the atoms are shown (C = green; N = blue; O = red; S = yellow; H = white).
<Structure load='Tut_antiparallel_bsheet.pdb' size='500' frame='true' align='left' caption='' scene='User:Robert_Dutnall/Sandbox_1_sheets/Antiparallel_load/3'/>

<scene name='User:Robert_Dutnall/Sandbox_1_sheets/Antiparallel_mainchain/3'>Click here</scene> to show only the polypeptide mainchain of each strand (NH, Cα, and C=O).

Identify the N- and C-termini of each strand. <scene name='User:Robert_Dutnall/Sandbox_1_sheets/Antiparallel_mainchain_labels/1'>Click here to see if you were correct.</scene>

As the structure rotates you should be able to see the extended nature of each strand and the parallel orientation of the three strands.

<scene name='User:Robert_Dutnall/Sandbox_1_sheets/Antipara_mainchain_labels_face/1'>Click here</scene> to stop the structure spinning and view the sheet from roughly perpendicular to its flat plane.

<scene name='User:Robert_Dutnall/Sandbox_1_sheets/Antipara_mainchain_labels_side/1'>Click here</scene> to stop the structure spinning and view the sheet from roughly edge-on to its flat plane.

<scene name='User:Robert_Dutnall/Sandbox_1_sheets/Antiparallel_mainchain_labels/1'>Click here to start the structure spinning again.</scene> Look at the structure carefully and identify the mainchain NH and C=O groups. In each strand the mainchain NH and C=O groups point to opposite sides of the mainchain. The strands line up in the sheet so that these NH and C=O groups are parallel to plane of the sheet and lie opposite each other so that they can make hydrogen bonds.

<scene name='User:Robert_Dutnall/Sandbox_1_sheets/Antipara_mainchain_hbonds/1'>Click here to add hydrogen bonds for the mainchain (dashed lines).</scene> The hydrogen bonds connect backbone NH groups and C=O groups. The N-H group is the hydrogen bond donor, the oxygen in the C=O group is the acceptor (N-H--->O=C). Each hydrogen bond is approximately 3.0 Angstroms (0.3 nm) in length (measured between the N and the O).

You should be able to see that the mainchain NH and C=O groups are involved in hydrogen bonds between the strands of the sheet. <scene name='User:Robert_Dutnall/Sandbox_1_sheets/Antipara_mainchain_hbonds_z/1'>Click here to zoom in to show some of the hydrogen bonds more clearly.</scene>

<scene name='User:Robert_Dutnall/Sandbox_1_sheets/Antipara_mainchain_hbonds/1'>Click here to zoom out again.</scene> You should notice that all of the NH and C=O groups that lie between strands are involved in hydrogen bonds. Only the groups on the edges of the sheet do not have hydrogen bond partners, but if this sheet were part of a larger protein, other residues would supply groups to hydrogen bond to most if not all of these.

Two of the strands in this sheet are connected by a β-turn. <scene name='User:Robert_Dutnall/Sandbox_1_sheets/Antipara_mainchain_turn/2'>Click here</scene> to show the β-turn. The carbon atoms of the amino acids that define the turn have been colored orange. The turn allows a segment of polypeptide to reverse direction in a short distance. In this case it also allows two strands to interact in an antiparallel fashion. <scene name='User:Robert_Dutnall/Sandbox_1_sheets/Antipara_mainchain_turn_zoom/3'>Click here to zoom in on the turn and reorient it to show more clearly.</scene> '''Is this a Type I or Type II β-turn? (Write down your answer so you can submit it to your instructor)'''

<scene name='User:Robert_Dutnall/Sandbox_1_sheets/Antipara_mainchain_sidechains/1'>Click here to zoom out again.</scene> In this view, some of the residues at the turn have been omitted and you are looking roughly edge-on to the flat plane of the sheet. Sidechains have been added and the atoms of each amino side chain have been colored blue or purple in an alternating fashion.

The side chains are approximately perpendicular to the flat plane of the sheet. Along each strand, the side chains alternate direction (above the plane, below the plane, above the plane...) so you should be able to see that all the sidechains above the plane of the sheet are purple, and all those below are blue.

==A mixed β-sheet==

The sheet shown below is composed of four strands. All the atoms are shown (C = green; N = blue; O = red; S = yellow; H = white). This is a mixed β-sheet. Some of the strands are parallel, some are antiparallel.
<Structure load='Mixed_sheet.pdb' size='500' frame='true' align='left' caption='' scene='User:Robert_Dutnall/Sandbox_1_sheets/Mixed_sheet_load/1'/>

<scene name='User:Robert_Dutnall/Sandbox_1_sheets/Mixed_sheet_mainchain/2'>Click here</scene> to show only the polypeptide mainchain of each strand (NH, Cα, and C=O).

'''What is the orientation of each pair of strands (parallel or antiparallel)?'''

Click below to highlight the strands in pairs (pair 1, pair 2 and pair 3). The carbon atoms will be highlighted in orange.

<scene name='User:Robert_Dutnall/Sandbox_1_sheets/Mixed_sheet_mainchain_pair1/1'>Pair 1.</scene>

<scene name='User:Robert_Dutnall/Sandbox_1_sheets/Mixed_sheet_mainchain_pair2/1'>Pair 2.</scene>

<scene name='User:Robert_Dutnall/Sandbox_1_sheets/Mixed_sheet_mainchain_pair3/1'>Pair 3.</scene>

'''Write down your answers for pair 1, pair 2 and pair 3 to submit to your instructor.'''

'''That's it. You are finished with Tutorial 2. Remember to submit your answers to the questions to your instructor.'''
= =
[[User:Robert Dutnall/Sandbox_1_alpha_helix|Click here if you want to go back to the first part of this tutorial.]]

User:Robert Dutnall/Sandbox 1 sheets

2011-08-29T19:00:13Z

Robert Dutnall:

== Biochemistry Tutorial #2 - Secondary Structure (Part 2) ==

==β-strands and β-sheets==

The second major secondary structure element is the β-sheet. β-sheets are composed of two or more segments of polypeptide mainchain in β-strand conformation. In a β-strand, the polypeptide mainchain is in a mostly extended conformation. As their name implies, β-sheets are relatively flat, planar-like structures made up of β-strands arranged side-by-side. They come in three flavors: parallel, anti-parallel and mixed, which differ in terms of the orientation of each component strand (with respect to the direction of the mainchain from N-terminus to C-terminus).

Note that the mainchain of a β-strand is not perfectly fully extended (Φ ≠ φ ≠ 180o) and that the mainchain actually slowly twists (this is more obvious if you look at a long segment of β-strand). Thus β-sheets are not completely flat and also exhibit some twisting (this is also more obvious if you look at sheets made of many β-strands).

==Parallel β-sheet==

Parallel β-sheets are composed of β-strands that all point in the same direction. Each β-strand has mainchain dihedral angles as follows: Φ ~ -120o, φ ~ +105o.

The sheet shown below is composed of three strands in parallel orientation. All the atoms are shown (C = green; N = blue; O = red; S = yellow; H = white).
<Structure load='Tut_parallel_bsheet.pdb' size='500' frame='true' align='left' caption='' scene='User:Robert_Dutnall/Sandbox_1_sheets/Parallel_load/2'/>

<scene name='User:Robert_Dutnall/Sandbox_1_sheets/Parallel_mainchain/2'>Click here</scene> to show only the polypeptide mainchain (NH, Cα, and C=O).

Identify the N- and C-termini of each strand. <scene name='User:Robert_Dutnall/Sandbox_1_sheets/Parallel_mainchain_labels/6'>Click here to see if you were correct.</scene>

As the structure rotates you should be able to see the extended nature of each strand and the parallel orientation of the three strands.

<scene name='User:Robert_Dutnall/Sandbox_1_sheets/Parallel_mainchain_labels_face/2'>Click here</scene> to stop the structure spinning and view the sheet from roughly perpendicular to its flat plane, with each strand running left-to-right (N- to C-terminus).

<scene name='User:Robert_Dutnall/Sandbox_1_sheets/Parallel_mainchain_labels_side/2'>Click here</scene> to stop the structure spinning and view the sheet from roughly edge-on to its flat plane.

<scene name='User:Robert_Dutnall/Sandbox_1_sheets/Parallel_mainchain_labels/6'>Click here to start the structure spinning again.</scene> Look at the structure carefully and identify the mainchain NH and C=O groups. What is the orientation of these groups with respect to the long axis of each strand? What the orientation of these groups with respect to the flat plane of the sheet?

<scene name='User:Robert_Dutnall/Sandbox_1_sheets/Parallel_mainchain_labels_hb/5'>Click here to add hydrogen bonds for the mainchain (dashed lines).</scene> The hydrogen bonds connect backbone NH groups and C=O groups. The N-H group is the hydrogen bond donor, the oxygen in the C=O group is the acceptor (N-H--->O=C). Each hydrogen bond is approximately 3.0 Angstroms (0.3 nm) in length (measured between the N and the O).

You should be able to see that the mainchain NH and C=O groups are involved in hydrogen bonds. In each strand the mainchain NH and C=O groups point to opposite sides of the mainchain (because of the almost fully extended conformation). The strands line up in the sheet so that the NH and C=O groups are parallel to plane of the sheet and lie opposite each other in pairs. This means that hydrogen bonds can be made between the strands of the sheet. <scene name='User:Robert_Dutnall/Sandbox_1_sheets/Parallel_mainchain_labels_hb_z/5'>Click here to zoom in to show some of the hydrogen bonds more clearly.</scene>

<scene name='User:Robert_Dutnall/Sandbox_1_sheets/Parallel_mainchain_labels_hb/5'>Click here to zoom out again.</scene> You should also notice that all of the NH and C=O groups that lie between strands are involved in hydrogen bonds. Only the groups on the edges of the sheet do not have hydrogen bond partners. However, as with helix capping, if this sheet were part of a larger protein, other residues would supply groups to hydrogen bond to most if not all of these.

<scene name='User:Robert_Dutnall/Sandbox_1_sheets/Parallel_sidechains/2'>Click here to show the side chains again.</scene> You are looking roughly edge-on to the flat plane of the sheet and the atoms of each amino side chain have been colored light blue to show them more clearly.

What is the general orientation of the side chains with respect to each strand and the sheet? You should observe that the side chains are approximately perpendicular to the flat plane of the sheet. Along each strand, the side chains alternate direction. You can see this more clearly if we color the side chains in one strand alternately. <scene name='User:Robert_Dutnall/Sandbox_1_sheets/Parallel_strand_alt/3'>Click here</scene> to freeze the view and color the side chains along one strand blue-purple-blue-purple...etc.

If we apply this to all the strands (<scene name='User:Robert_Dutnall/Sandbox_1_sheets/Parallel_sidechains_alt/2'>click here</scene>) you can see that all the sidechains above the plane of the sheet are purple, and all those below are blue.

==Anti-Parallel β-sheet==

Anti-parallel β-sheets are composed of β-strands that alternate in direction. Each β-strand has mainchain dihedral angles as follows: Φ ~ -150o, φ ~ +135o.

The sheet shown below is composed of three strands in anti-parallel orientation. All the atoms are shown (C = green; N = blue; O = red; S = yellow; H = white).
<Structure load='Tut_antiparallel_bsheet.pdb' size='500' frame='true' align='left' caption='' scene='User:Robert_Dutnall/Sandbox_1_sheets/Antiparallel_load/3'/>

<scene name='User:Robert_Dutnall/Sandbox_1_sheets/Antiparallel_mainchain/3'>Click here</scene> to show only the polypeptide mainchain of each strand (NH, Cα, and C=O).

Identify the N- and C-termini of each strand. <scene name='User:Robert_Dutnall/Sandbox_1_sheets/Antiparallel_mainchain_labels/1'>Click here to see if you were correct.</scene>

As the structure rotates you should be able to see the extended nature of each strand and the parallel orientation of the three strands.

<scene name='User:Robert_Dutnall/Sandbox_1_sheets/Antipara_mainchain_labels_face/1'>Click here</scene> to stop the structure spinning and view the sheet from roughly perpendicular to its flat plane.

<scene name='User:Robert_Dutnall/Sandbox_1_sheets/Antipara_mainchain_labels_side/1'>Click here</scene> to stop the structure spinning and view the sheet from roughly edge-on to its flat plane.

<scene name='User:Robert_Dutnall/Sandbox_1_sheets/Antiparallel_mainchain_labels/1'>Click here to start the structure spinning again.</scene> Look at the structure carefully and identify the mainchain NH and C=O groups. In each strand the mainchain NH and C=O groups point to opposite sides of the mainchain. The strands line up in the sheet so that these NH and C=O groups are parallel to plane of the sheet and lie opposite each other so that they can make hydrogen bonds.

<scene name='User:Robert_Dutnall/Sandbox_1_sheets/Antipara_mainchain_hbonds/1'>Click here to add hydrogen bonds for the mainchain (dashed lines).</scene> The hydrogen bonds connect backbone NH groups and C=O groups. The N-H group is the hydrogen bond donor, the oxygen in the C=O group is the acceptor (N-H--->O=C). Each hydrogen bond is approximately 3.0 Angstroms (0.3 nm) in length (measured between the N and the O).

You should be able to see that the mainchain NH and C=O groups are involved in hydrogen bonds between the strands of the sheet. <scene name='User:Robert_Dutnall/Sandbox_1_sheets/Antipara_mainchain_hbonds_z/1'>Click here to zoom in to show some of the hydrogen bonds more clearly.</scene>

<scene name='User:Robert_Dutnall/Sandbox_1_sheets/Antipara_mainchain_hbonds/1'>Click here to zoom out again.</scene> You should notice that all of the NH and C=O groups that lie between strands are involved in hydrogen bonds. Only the groups on the edges of the sheet do not have hydrogen bond partners, but if this sheet were part of a larger protein, other residues would supply groups to hydrogen bond to most if not all of these.

Two of the strands in this sheet are connected by a β-turn. <scene name='User:Robert_Dutnall/Sandbox_1_sheets/Antipara_mainchain_turn/2'>Click here</scene> to show the β-turn. The carbon atoms of the amino acids that define the turn have been colored orange. The turn allows a segment of polypeptide to reverse direction in a short distance. In this case it also allows two strands to interact in an antiparallel fashion. <scene name='User:Robert_Dutnall/Sandbox_1_sheets/Antipara_mainchain_turn_zoom/3'>Click here to zoom in on the turn and reorient it to show more clearly.</scene> '''Is this a Type I or Type II β-turn? (Write down your answer so you can submit it to your instructor)'''

<scene name='User:Robert_Dutnall/Sandbox_1_sheets/Antipara_mainchain_sidechains/1'>Click here to zoom out again.</scene> In this view, some of the residues at the turn have been omitted and you are looking roughly edge-on to the flat plane of the sheet. Sidechains have been added and the atoms of each amino side chain have been colored blue or purple in an alternating fashion.

The side chains are approximately perpendicular to the flat plane of the sheet. Along each strand, the side chains alternate direction (above the plane, below the plane, above the plane...) so you should be able to see that all the sidechains above the plane of the sheet are purple, and all those below are blue.

==A mixed β-sheet==

The sheet shown below is composed of four strands. All the atoms are shown (C = green; N = blue; O = red; S = yellow; H = white). This is a mixed β-sheet. Some of the strands are parallel, some are antiparallel.
<Structure load='Mixed_sheet.pdb' size='500' frame='true' align='left' caption='' scene='User:Robert_Dutnall/Sandbox_1_sheets/Mixed_sheet_load/1'/>

<scene name='User:Robert_Dutnall/Sandbox_1_sheets/Mixed_sheet_mainchain/2'>Click here</scene> to show only the polypeptide mainchain of each strand (NH, Cα, and C=O).

'''What is the orientation of each pair of strands (parallel or antiparallel)?'''

Click below to highlight the strands in pairs (pair 1, pair 2 and pair 3). The carbon atoms will be highlighted in orange.

<scene name='User:Robert_Dutnall/Sandbox_1_sheets/Mixed_sheet_mainchain_pair1/1'>Pair 1.</scene>

<scene name='User:Robert_Dutnall/Sandbox_1_sheets/Mixed_sheet_mainchain_pair2/1'>Pair 2.</scene>

<scene name='User:Robert_Dutnall/Sandbox_1_sheets/Mixed_sheet_mainchain_pair3/1'>Pair 3.</scene>

'''Write down your answers for pair 1, pair 2 and pair 3 to submit to your instructor.'''

That's it. You are finished with Tutorial 2. Remember to submit your answers to the questions to your instructor.
= =
[[User:Robert Dutnall/Sandbox_1_alpha_helix|Click here to go on to back to the first part of this tutorial.]]

User:Robert Dutnall/Sandbox 1 alpha helix

2011-08-29T18:59:07Z

Robert Dutnall:

== Biochemistry Tutorial #2 - Secondary Structure (Part 1) ==

The secondary structure of a protein is defined by the local conformation of its backbone (polypeptide mainchain). There are two major types of regular secondary structures in proteins: helices and sheets. There are also regular turn structures. Turns often connect one element of secondary structure to another in the overall fold of the protein. Other parts of the protein mainchain may adopt more irregularly defined loops. This tutorial will focus mainly on helices and sheets.

''Note: in these tutorials, the images are 3D interactive images. You can manipulate them as you wish to get a better view of the molecules.''

You can rotate the structures by holding down the right mouse button and dragging. At any time you can click the 'toggle spin' button in box to stop/start the structure spinning.

Other things you can do:
::To rotate: left drag
::To Zoom: scroll button or shift + left drag
::To Translate: ctrl + right drag
::Right click to bring up an options menu

==Helices==

In helices, the polypeptide mainchain twists into a path that resembles a spiral staircase. Just like spiral staircases, helices come in different forms, depending on how tightly twisted the mainchain is. The form of a helix can be described by parameters such as the number of steps (amino acids) it takes to complete a turn (a 360o rotation around the long axis of the helix), and how far you travel along the helix axis in one complete turn. Helices can also be left-handed or right-handed. For proteins composed of L-amino acids, helices are almost always right-handed (a notable exception is the type I poly-proline helix). Although several types of helix form are possible, two regular helices are very common in proteins: the α-helix and the 310-helix.

==The α-helix==

α-helices are the most common type of regular helix found in proteins. They are characterized by the following helix parameters:
::Dihedral angles: Φ ~ -60o, φ ~ -45o
::Repeat (number of residues per turn) = 3.6
::Rise (translation along axis per amino acid residue) = 1.5 Angstroms (0.15 nm)
::Twist (rotation around axis per amino acid residue) = 100o (= 360o/repeat)
::Pitch (translation along axis per turn) = 5.4 Angstroms (= 0.54 nm = Repeat x Rise)

The helix shown below is a 19 amino acid chain in α-helical conformation.
<Structure load='Tut_alpha_helix.pdb' size='500' frame='true' align='left' caption='' scene='User:Robert_Dutnall/Sandbox_1_alpha_helix/A_helix_load/1'/>

All the atoms are shown in this initial orientation (C = green; N = blue; O = red; S = yellow; H = white). The helix axis runs vertically, approximately parallel to the plane of the screen.

<scene name='User:Robert_Dutnall/Sandbox_1_alpha_helix/A_helix_mainchain/3'>Click here</scene> to show only the polypeptide mainchain (NH, Cα, and C=O).

Identify the N- and C-termini. <scene name='User:Robert_Dutnall/Sandbox_1_alpha_helix/A_helix_mainchain_label/4'>Click here to see if you were correct.</scene>

<scene name='User:Robert_Dutnall/Sandbox_1_alpha_helix/A_helix_mainchain_label_ribbon/3'>Click here to add a ribbon that will help show the path of the mainchain. </scene> You should be able to see that it is helical with a right-handed twist (you rotate to the right as you move along the helix axis).

Click the "toggle spin" button in the box to stop the structure from rotating. Now use your mouse to rotate the structure to look down the helix axis. If you have any problems with finding this view, <scene name='User:Robert_Dutnall/Sandbox_1_alpha_helix/A_helix_mainchain_label_axis/3'>click here </scene>to zoom in and look down the helix axis from the N-terminal end.

<scene name='User:Robert_Dutnall/Sandbox_1_alpha_helix/A_helix_mainchain_label/4'>Click here to zoom out again.</scene> Look at the structure carefully and identify the mainchain NH and C=O groups. What is the orientation of these groups with respect to the helix axis?

<scene name='User:Robert_Dutnall/Sandbox_1_alpha_helix/A_helix_mainchain_label_hbonds/10'>Click here to zoom in a little and add hydrogen bonds for the mainchain (dashed lines).</scene> The hydrogen bonds connect backbone NH groups and C=O groups. The N-H group is the hydrogen bond donor, the oxygen in the C=O group is the acceptor (N-H--->O=C). Each hydrogen bond is approximately 3.0 Angstroms (0.3 nm) in length (measured between the N and the O). These hydrogen bonds connect amino acids that are spaced 4 residues apart in the primary sequence. The NH group is from amino acid X and the O is from amino acid X-4 (where X is the number of the amino acid in the sequence).

<scene name='User:Robert_Dutnall/Sandbox_1_alpha_helix/A_helix_mainchain_label_hbonds/9'>Click here to zoom out again.</scene> You should be able to see that all of the mainchain NH and C=O groups are involved in hydrogen bonds. This is possible because 1) all the mainchain NH groups and C=O groups are parallel to the helix axis, 2) all the NH groups point toward the N-terminus of the helix, and 3) all the C=O groups point toward the C-terminus. Only the NH groups in the first (N-terminal) turn, and the C=O groups in the last (C-terminal) turn of the helix do not have hydrogen bonding partners. However, if this helix were part of a larger protein, these groups would participate in hydrogen bonds with other parts of the protein. This is called 'helix capping' and the other groups involved are typically from amino acid side chains (that are called 'helix capping residues').

<scene name='User:Robert_Dutnall/Sandbox_1_alpha_helix/A_helix_sidechains/3'>Click here to show the side chains again.</scene> The atoms of each amino side chain have been colored light blue to show them more clearly. <scene name='User:Robert_Dutnall/Sandbox_1_alpha_helix/A_helix_sidechains_axis/1'>Click here to change the view to look down the helix axis.</scene>

What is the general orientation of the side chains with respect to the helix axis? You should observe that each side chain points away from the helix axis, but points down toward the N-terminus of the helix (this is clearer if you only show the first bond of each side chain: <scene name='User:Robert_Dutnall/Sandbox_1_alpha_helix/A_helix_sidechains_cropped/1'>click here</scene> or <scene name='User:Robert_Dutnall/Sandbox_1_alpha_helix/A_helix_sidechains_cropped/2'>click here</scene>).

==The 310-helix==

310-helices are also found in proteins but are less common than α-helices. They are characterized by the following helix parameters:
::Dihedral angles: Φ ~ -49o, φ ~ -26o
::Repeat (number of residues per turn) = 3.0
::Rise (translation along axis per amino acid residue) = 2.0 Angstroms (0.2 nm)
::Twist (rotation around axis per amino acid residue) = 120o (= 360o/repeat)
::Pitch (translation along axis per turn) = 6.0 Angstroms (= 0.6 nm = Repeat x Rise)

The helix shown below is a 19 amino acid chain in 310-helical conformation.
<Structure load='Tut_3-10_helix.pdb' size='500' frame='true' align='left' caption='' scene='User:Robert_Dutnall/Sandbox_1_alpha_helix/310_helix_load/4'/>

All the atoms are shown in this initial orientation (C = green; N = blue; O = red; S = yellow; H = white). The helix axis runs vertically, approximately parallel to the plane of the screen.

<scene name='User:Robert_Dutnall/Sandbox_1_alpha_helix/310_helix_mainchain/2'>Click here</scene> to show only the polypeptide mainchain (NH, Cα, and C=O). The N- and C-termini are labeled.

<scene name='User:Robert_Dutnall/Sandbox_1_alpha_helix/310_helix_mainchain_ribbon/2'>Click here to add a ribbon that will help show the path of the mainchain. </scene> You should be able to see that just like the α-helix, it is helical with a right-handed twist, and again, all the mainchain NH groups point toward the N-terminus, and all the mainchain C=O groups point toward the C-terminus.

The difference between an α-helix and a 310-helix lies in the helix parameters. A 310-helix is more tightly twisted so that the mainchain completes one turn every 3 amino acids (instead of 3.6 for the α-helix). This also results in a larger rise and pitch so that the 310-helix is longer than an α-helix (of the same number of residues).

<scene name='User:Robert_Dutnall/Sandbox_1_alpha_helix/310_helix_mainchain_axis/1'>Click here </scene>to zoom in and look down the helix axis from the N-terminal end. You'll be able to see the triangular shape of the mainchain.

<scene name='User:Robert_Dutnall/Sandbox_1_alpha_helix/310_helix_mainchain_hbonds/1'>Click here to zoom out again and display hydrogen bonds for the mainchain.</scene> Once again, all of the mainchain NH and C=O groups are involved in hydrogen bonds. However, now the hydrogen bonds connect amino acids that are spaced 3 residues apart in the primary sequence. The NH group is from amino acid X and the O is from amino acid X-3 (where X is the number of the amino acid in the sequence). <scene name='User:Robert_Dutnall/Sandbox_1_alpha_helix/310_helix_mainchain_hbonds/2'>Click here</scene> to zoom in and you should be able to see this more clearly.

<scene name='User:Robert_Dutnall/Sandbox_1_alpha_helix/310_helix_sidechains/1'>Click here to zoom out and show the side chains again.</scene> The atoms of each amino side chain have been colored light blue to show them more clearly. <scene name='User:Robert_Dutnall/Sandbox_1_alpha_helix/310_helix_sidechains_axis/2'>Click here to change the view to look down the helix axis.</scene>

As for the α-helix, each side chain points away from the helix axis, and points down toward the N-terminus of the helix. However, because the 310-helix repeat parameter is an integer (= 3.0), the side chains are spaced 120o apart and form 3 distinct sides to the helix. You'll see this more clearly if the side chains are colored in groups to show this (residues 1,4,7,10 etc are blue; residues 2,5,8,11 etc are purple; residues 3,6,9,12 etc are yellow): <scene name='User:Robert_Dutnall/Sandbox_1_alpha_helix/310_helix_sidechains_tricolor/1'>click here to look from the side</scene> or <scene name='User:Robert_Dutnall/Sandbox_1_alpha_helix/310_helix_sidechains_tricol_ax/1'>click here to view down the helix axis</scene>.

<scene name='User:Robert_Dutnall/Sandbox_1_alpha_helix/310_helix_load/4'>Click here to reset the view of the helix.</scene>

'''What is the identity of the N-terminal amino acid?'''

'''What is the identity of the C-terminal amino acid?'''

'''Write down these answers so that you can submit them to your instructor at the end of this tutorial.'''

= =
[[User:Robert Dutnall/Sandbox_1_sheets|Click here to go on to part 2 of this tutorial.]]

User:Robert Dutnall/Sandbox 1 sheets

2011-08-29T18:58:15Z

Robert Dutnall:

== Biochemistry Tutorial #2 - Secondary Structure (Part 2) ==

==β-strands and β-sheets==

The second major secondary structure element is the β-sheet. β-sheets are composed of two or more segments of polypeptide mainchain in β-strand conformation. In a β-strand, the polypeptide mainchain is in a mostly extended conformation. As their name implies, β-sheets are relatively flat, planar-like structures made up of β-strands arranged side-by-side. They come in three flavors: parallel, anti-parallel and mixed, which differ in terms of the orientation of each component strand (with respect to the direction of the mainchain from N-terminus to C-terminus).

Note that the mainchain of a β-strand is not perfectly fully extended (Φ ≠ φ ≠ 180o) and that the mainchain actually slowly twists (this is more obvious if you look at a long segment of β-strand). Thus β-sheets are not completely flat and also exhibit some twisting (this is also more obvious if you look at sheets made of many β-strands).

==Parallel β-sheet==

Parallel β-sheets are composed of β-strands that all point in the same direction. Each β-strand has mainchain dihedral angles as follows: Φ ~ -120o, φ ~ +105o.

The sheet shown below is composed of three strands in parallel orientation. All the atoms are shown (C = green; N = blue; O = red; S = yellow; H = white).
<Structure load='Tut_parallel_bsheet.pdb' size='500' frame='true' align='left' caption='' scene='User:Robert_Dutnall/Sandbox_1_sheets/Parallel_load/2'/>

<scene name='User:Robert_Dutnall/Sandbox_1_sheets/Parallel_mainchain/2'>Click here</scene> to show only the polypeptide mainchain (NH, Cα, and C=O).

Identify the N- and C-termini of each strand. <scene name='User:Robert_Dutnall/Sandbox_1_sheets/Parallel_mainchain_labels/6'>Click here to see if you were correct.</scene>

As the structure rotates you should be able to see the extended nature of each strand and the parallel orientation of the three strands.

<scene name='User:Robert_Dutnall/Sandbox_1_sheets/Parallel_mainchain_labels_face/2'>Click here</scene> to stop the structure spinning and view the sheet from roughly perpendicular to its flat plane, with each strand running left-to-right (N- to C-terminus).

<scene name='User:Robert_Dutnall/Sandbox_1_sheets/Parallel_mainchain_labels_side/2'>Click here</scene> to stop the structure spinning and view the sheet from roughly edge-on to its flat plane.

<scene name='User:Robert_Dutnall/Sandbox_1_sheets/Parallel_mainchain_labels/6'>Click here to start the structure spinning again.</scene> Look at the structure carefully and identify the mainchain NH and C=O groups. What is the orientation of these groups with respect to the long axis of each strand? What the orientation of these groups with respect to the flat plane of the sheet?

<scene name='User:Robert_Dutnall/Sandbox_1_sheets/Parallel_mainchain_labels_hb/5'>Click here to add hydrogen bonds for the mainchain (dashed lines).</scene> The hydrogen bonds connect backbone NH groups and C=O groups. The N-H group is the hydrogen bond donor, the oxygen in the C=O group is the acceptor (N-H--->O=C). Each hydrogen bond is approximately 3.0 Angstroms (0.3 nm) in length (measured between the N and the O).

You should be able to see that the mainchain NH and C=O groups are involved in hydrogen bonds. In each strand the mainchain NH and C=O groups point to opposite sides of the mainchain (because of the almost fully extended conformation). The strands line up in the sheet so that the NH and C=O groups are parallel to plane of the sheet and lie opposite each other in pairs. This means that hydrogen bonds can be made between the strands of the sheet. <scene name='User:Robert_Dutnall/Sandbox_1_sheets/Parallel_mainchain_labels_hb_z/5'>Click here to zoom in to show some of the hydrogen bonds more clearly.</scene>

<scene name='User:Robert_Dutnall/Sandbox_1_sheets/Parallel_mainchain_labels_hb/5'>Click here to zoom out again.</scene> You should also notice that all of the NH and C=O groups that lie between strands are involved in hydrogen bonds. Only the groups on the edges of the sheet do not have hydrogen bond partners. However, as with helix capping, if this sheet were part of a larger protein, other residues would supply groups to hydrogen bond to most if not all of these.

<scene name='User:Robert_Dutnall/Sandbox_1_sheets/Parallel_sidechains/2'>Click here to show the side chains again.</scene> You are looking roughly edge-on to the flat plane of the sheet and the atoms of each amino side chain have been colored light blue to show them more clearly.

What is the general orientation of the side chains with respect to each strand and the sheet? You should observe that the side chains are approximately perpendicular to the flat plane of the sheet. Along each strand, the side chains alternate direction. You can see this more clearly if we color the side chains in one strand alternately. <scene name='User:Robert_Dutnall/Sandbox_1_sheets/Parallel_strand_alt/3'>Click here</scene> to freeze the view and color the side chains along one strand blue-purple-blue-purple...etc.

If we apply this to all the strands (<scene name='User:Robert_Dutnall/Sandbox_1_sheets/Parallel_sidechains_alt/2'>click here</scene>) you can see that all the sidechains above the plane of the sheet are purple, and all those below are blue.

==Anti-Parallel β-sheet==

Anti-parallel β-sheets are composed of β-strands that alternate in direction. Each β-strand has mainchain dihedral angles as follows: Φ ~ -150o, φ ~ +135o.

The sheet shown below is composed of three strands in anti-parallel orientation. All the atoms are shown (C = green; N = blue; O = red; S = yellow; H = white).
<Structure load='Tut_antiparallel_bsheet.pdb' size='500' frame='true' align='left' caption='' scene='User:Robert_Dutnall/Sandbox_1_sheets/Antiparallel_load/3'/>

<scene name='User:Robert_Dutnall/Sandbox_1_sheets/Antiparallel_mainchain/3'>Click here</scene> to show only the polypeptide mainchain of each strand (NH, Cα, and C=O).

Identify the N- and C-termini of each strand. <scene name='User:Robert_Dutnall/Sandbox_1_sheets/Antiparallel_mainchain_labels/1'>Click here to see if you were correct.</scene>

As the structure rotates you should be able to see the extended nature of each strand and the parallel orientation of the three strands.

<scene name='User:Robert_Dutnall/Sandbox_1_sheets/Antipara_mainchain_labels_face/1'>Click here</scene> to stop the structure spinning and view the sheet from roughly perpendicular to its flat plane.

<scene name='User:Robert_Dutnall/Sandbox_1_sheets/Antipara_mainchain_labels_side/1'>Click here</scene> to stop the structure spinning and view the sheet from roughly edge-on to its flat plane.

<scene name='User:Robert_Dutnall/Sandbox_1_sheets/Antiparallel_mainchain_labels/1'>Click here to start the structure spinning again.</scene> Look at the structure carefully and identify the mainchain NH and C=O groups. In each strand the mainchain NH and C=O groups point to opposite sides of the mainchain. The strands line up in the sheet so that these NH and C=O groups are parallel to plane of the sheet and lie opposite each other so that they can make hydrogen bonds.

<scene name='User:Robert_Dutnall/Sandbox_1_sheets/Antipara_mainchain_hbonds/1'>Click here to add hydrogen bonds for the mainchain (dashed lines).</scene> The hydrogen bonds connect backbone NH groups and C=O groups. The N-H group is the hydrogen bond donor, the oxygen in the C=O group is the acceptor (N-H--->O=C). Each hydrogen bond is approximately 3.0 Angstroms (0.3 nm) in length (measured between the N and the O).

You should be able to see that the mainchain NH and C=O groups are involved in hydrogen bonds between the strands of the sheet. <scene name='User:Robert_Dutnall/Sandbox_1_sheets/Antipara_mainchain_hbonds_z/1'>Click here to zoom in to show some of the hydrogen bonds more clearly.</scene>

<scene name='User:Robert_Dutnall/Sandbox_1_sheets/Antipara_mainchain_hbonds/1'>Click here to zoom out again.</scene> You should notice that all of the NH and C=O groups that lie between strands are involved in hydrogen bonds. Only the groups on the edges of the sheet do not have hydrogen bond partners, but if this sheet were part of a larger protein, other residues would supply groups to hydrogen bond to most if not all of these.

Two of the strands in this sheet are connected by a β-turn. <scene name='User:Robert_Dutnall/Sandbox_1_sheets/Antipara_mainchain_turn/2'>Click here</scene> to show the β-turn. The carbon atoms of the amino acids that define the turn have been colored orange. The turn allows a segment of polypeptide to reverse direction in a short distance. In this case it also allows two strands to interact in an antiparallel fashion. <scene name='User:Robert_Dutnall/Sandbox_1_sheets/Antipara_mainchain_turn_zoom/3'>Click here to zoom in on the turn and reorient it to show more clearly.</scene> '''Is this a Type I or Type II β-turn? (Write down your answer so you can submit it to your instructor)'''

<scene name='User:Robert_Dutnall/Sandbox_1_sheets/Antipara_mainchain_sidechains/1'>Click here to zoom out again.</scene> In this view, some of the residues at the turn have been omitted and you are looking roughly edge-on to the flat plane of the sheet. Sidechains have been added and the atoms of each amino side chain have been colored blue or purple in an alternating fashion.

The side chains are approximately perpendicular to the flat plane of the sheet. Along each strand, the side chains alternate direction (above the plane, below the plane, above the plane...) so you should be able to see that all the sidechains above the plane of the sheet are purple, and all those below are blue.

==A mixed β-sheet==

The sheet shown below is composed of four strands. All the atoms are shown (C = green; N = blue; O = red; S = yellow; H = white). This is a mixed β-sheet. Some of the strands are parallel, some are antiparallel.
<Structure load='Mixed_sheet.pdb' size='500' frame='true' align='left' caption='' scene='User:Robert_Dutnall/Sandbox_1_sheets/Mixed_sheet_load/1'/>

<scene name='User:Robert_Dutnall/Sandbox_1_sheets/Mixed_sheet_mainchain/2'>Click here</scene> to show only the polypeptide mainchain of each strand (NH, Cα, and C=O).

'''What is the orientation of each pair of strands (parallel or antiparallel)?'''

Click below to highlight the strands in pairs (pair 1, pair 2 and pair 3). The carbon atoms will be highlighted in orange.

<scene name='User:Robert_Dutnall/Sandbox_1_sheets/Mixed_sheet_mainchain_pair1/1'>Pair 1.</scene>

<scene name='User:Robert_Dutnall/Sandbox_1_sheets/Mixed_sheet_mainchain_pair2/1'>Pair 2.</scene>

<scene name='User:Robert_Dutnall/Sandbox_1_sheets/Mixed_sheet_mainchain_pair3/1'>Pair 3.</scene>

'''Write down your answers for pair 1, pair 2 and pair 3 to submit to your instructor.'''

That's it. You are finished with Tutorial 2. Remember to submit your answers to the questions to your instructor.
= =
[[User:Robert Dutnall/Sandbox_1_alpha_helix|Click here to go on to back to the first part of this tutorial.]]

User:Robert Dutnall/Sandbox 1 sheets

2011-08-29T18:55:00Z

Robert Dutnall:

== Biochemistry Tutorial #2 - Secondary Structure (Part 2) ==

==β-strands and β-sheets==

The second major secondary structure element is the β-sheet. β-sheets are composed of two or more segments of polypeptide mainchain in β-strand conformation. In a β-strand, the polypeptide mainchain is in a mostly extended conformation. As their name implies, β-sheets are relatively flat, planar-like structures made up of β-strands arranged side-by-side. They come in three flavors: parallel, anti-parallel and mixed, which differ in terms of the orientation of each component strand (with respect to the direction of the mainchain from N-terminus to C-terminus).

Note that the mainchain of a β-strand is not perfectly fully extended (Φ ≠ φ ≠ 180o) and that the mainchain actually slowly twists (this is more obvious if you look at a long segment of β-strand). Thus β-sheets are not completely flat and also exhibit some twisting (this is also more obvious if you look at sheets made of many β-strands).

==Parallel β-sheet==

Parallel β-sheets are composed of β-strands that all point in the same direction. Each β-strand has mainchain dihedral angles as follows: Φ ~ -120o, φ ~ +105o.

The sheet shown below is composed of three strands in parallel orientation. All the atoms are shown (C = green; N = blue; O = red; S = yellow; H = white).
<Structure load='Tut_parallel_bsheet.pdb' size='500' frame='true' align='left' caption='' scene='User:Robert_Dutnall/Sandbox_1_sheets/Parallel_load/2'/>

<scene name='User:Robert_Dutnall/Sandbox_1_sheets/Parallel_mainchain/2'>Click here</scene> to show only the polypeptide mainchain (NH, Cα, and C=O).

Identify the N- and C-termini of each strand. <scene name='User:Robert_Dutnall/Sandbox_1_sheets/Parallel_mainchain_labels/6'>Click here to see if you were correct.</scene>

As the structure rotates you should be able to see the extended nature of each strand and the parallel orientation of the three strands.

<scene name='User:Robert_Dutnall/Sandbox_1_sheets/Parallel_mainchain_labels_face/2'>Click here</scene> to stop the structure spinning and view the sheet from roughly perpendicular to its flat plane, with each strand running left-to-right (N- to C-terminus).

<scene name='User:Robert_Dutnall/Sandbox_1_sheets/Parallel_mainchain_labels_side/2'>Click here</scene> to stop the structure spinning and view the sheet from roughly edge-on to its flat plane.

<scene name='User:Robert_Dutnall/Sandbox_1_sheets/Parallel_mainchain_labels/6'>Click here to start the structure spinning again.</scene> Look at the structure carefully and identify the mainchain NH and C=O groups. What is the orientation of these groups with respect to the long axis of each strand? What the orientation of these groups with respect to the flat plane of the sheet?

<scene name='User:Robert_Dutnall/Sandbox_1_sheets/Parallel_mainchain_labels_hb/5'>Click here to add hydrogen bonds for the mainchain (dashed lines).</scene> The hydrogen bonds connect backbone NH groups and C=O groups. The N-H group is the hydrogen bond donor, the oxygen in the C=O group is the acceptor (N-H--->O=C). Each hydrogen bond is approximately 3.0 Angstroms (0.3 nm) in length (measured between the N and the O).

You should be able to see that the mainchain NH and C=O groups are involved in hydrogen bonds. In each strand the mainchain NH and C=O groups point to opposite sides of the mainchain (because of the almost fully extended conformation). The strands line up in the sheet so that the NH and C=O groups are parallel to plane of the sheet and lie opposite each other in pairs. This means that hydrogen bonds can be made between the strands of the sheet. <scene name='User:Robert_Dutnall/Sandbox_1_sheets/Parallel_mainchain_labels_hb_z/5'>Click here to zoom in to show some of the hydrogen bonds more clearly.</scene>

<scene name='User:Robert_Dutnall/Sandbox_1_sheets/Parallel_mainchain_labels_hb/5'>Click here to zoom out again.</scene> You should also notice that all of the NH and C=O groups that lie between strands are involved in hydrogen bonds. Only the groups on the edges of the sheet do not have hydrogen bond partners. However, as with helix capping, if this sheet were part of a larger protein, other residues would supply groups to hydrogen bond to most if not all of these.

<scene name='User:Robert_Dutnall/Sandbox_1_sheets/Parallel_sidechains/2'>Click here to show the side chains again.</scene> You are looking roughly edge-on to the flat plane of the sheet and the atoms of each amino side chain have been colored light blue to show them more clearly.

What is the general orientation of the side chains with respect to each strand and the sheet? You should observe that the side chains are approximately perpendicular to the flat plane of the sheet. Along each strand, the side chains alternate direction. You can see this more clearly if we color the side chains in one strand alternately. <scene name='User:Robert_Dutnall/Sandbox_1_sheets/Parallel_strand_alt/3'>Click here</scene> to freeze the view and color the side chains along one strand blue-purple-blue-purple...etc.

If we apply this to all the strands (<scene name='User:Robert_Dutnall/Sandbox_1_sheets/Parallel_sidechains_alt/2'>click here</scene>) you can see that all the sidechains above the plane of the sheet are purple, and all those below are blue.

==Anti-Parallel β-sheet==

Anti-parallel β-sheets are composed of β-strands that alternate in direction. Each β-strand has mainchain dihedral angles as follows: Φ ~ -150o, φ ~ +135o.

The sheet shown below is composed of three strands in anti-parallel orientation. All the atoms are shown (C = green; N = blue; O = red; S = yellow; H = white).
<Structure load='Tut_antiparallel_bsheet.pdb' size='500' frame='true' align='left' caption='' scene='User:Robert_Dutnall/Sandbox_1_sheets/Antiparallel_load/3'/>

<scene name='User:Robert_Dutnall/Sandbox_1_sheets/Antiparallel_mainchain/3'>Click here</scene> to show only the polypeptide mainchain of each strand (NH, Cα, and C=O).

Identify the N- and C-termini of each strand. <scene name='User:Robert_Dutnall/Sandbox_1_sheets/Antiparallel_mainchain_labels/1'>Click here to see if you were correct.</scene>

As the structure rotates you should be able to see the extended nature of each strand and the parallel orientation of the three strands.

<scene name='User:Robert_Dutnall/Sandbox_1_sheets/Antipara_mainchain_labels_face/1'>Click here</scene> to stop the structure spinning and view the sheet from roughly perpendicular to its flat plane.

<scene name='User:Robert_Dutnall/Sandbox_1_sheets/Antipara_mainchain_labels_side/1'>Click here</scene> to stop the structure spinning and view the sheet from roughly edge-on to its flat plane.

<scene name='User:Robert_Dutnall/Sandbox_1_sheets/Antiparallel_mainchain_labels/1'>Click here to start the structure spinning again.</scene> Look at the structure carefully and identify the mainchain NH and C=O groups. In each strand the mainchain NH and C=O groups point to opposite sides of the mainchain. The strands line up in the sheet so that these NH and C=O groups are parallel to plane of the sheet and lie opposite each other so that they can make hydrogen bonds.

<scene name='User:Robert_Dutnall/Sandbox_1_sheets/Antipara_mainchain_hbonds/1'>Click here to add hydrogen bonds for the mainchain (dashed lines).</scene> The hydrogen bonds connect backbone NH groups and C=O groups. The N-H group is the hydrogen bond donor, the oxygen in the C=O group is the acceptor (N-H--->O=C). Each hydrogen bond is approximately 3.0 Angstroms (0.3 nm) in length (measured between the N and the O).

You should be able to see that the mainchain NH and C=O groups are involved in hydrogen bonds between the strands of the sheet. <scene name='User:Robert_Dutnall/Sandbox_1_sheets/Antipara_mainchain_hbonds_z/1'>Click here to zoom in to show some of the hydrogen bonds more clearly.</scene>

<scene name='User:Robert_Dutnall/Sandbox_1_sheets/Antipara_mainchain_hbonds/1'>Click here to zoom out again.</scene> You should notice that all of the NH and C=O groups that lie between strands are involved in hydrogen bonds. Only the groups on the edges of the sheet do not have hydrogen bond partners, but if this sheet were part of a larger protein, other residues would supply groups to hydrogen bond to most if not all of these.

Two of the strands in this sheet are connected by a β-turn. <scene name='User:Robert_Dutnall/Sandbox_1_sheets/Antipara_mainchain_turn/2'>Click here</scene> to show the β-turn. The carbon atoms of the amino acids that define the turn have been colored orange. The turn allows a segment of polypeptide to reverse direction in a short distance. In this case it also allows two strands to interact in an antiparallel fashion. <scene name='User:Robert_Dutnall/Sandbox_1_sheets/Antipara_mainchain_turn_zoom/3'>Click here to zoom in on the turn and reorient it to show more clearly.</scene> '''Is this a Type I or Type II β-turn? (Write down your answer so you can submit it to your instructor)'''

<scene name='User:Robert_Dutnall/Sandbox_1_sheets/Antipara_mainchain_sidechains/1'>Click here to zoom out again.</scene> In this view, some of the residues at the turn have been omitted and you are looking roughly edge-on to the flat plane of the sheet. Sidechains have been added and the atoms of each amino side chain have been colored blue or purple in an alternating fashion.

The side chains are approximately perpendicular to the flat plane of the sheet. Along each strand, the side chains alternate direction (above the plane, below the plane, above the plane...) so you should be able to see that all the sidechains above the plane of the sheet are purple, and all those below are blue.

==A mixed β-sheet==

The sheet shown below is composed of four strands. All the atoms are shown (C = green; N = blue; O = red; S = yellow; H = white). This is a mixed β-sheet. Some of the strands are parallel, some are antiparallel.
<Structure load='Mixed_sheet.pdb' size='500' frame='true' align='left' caption='' scene='User:Robert_Dutnall/Sandbox_1_sheets/Mixed_sheet_load/1'/>

<scene name='User:Robert_Dutnall/Sandbox_1_sheets/Mixed_sheet_mainchain/2'>Click here</scene> to show only the polypeptide mainchain of each strand (NH, Cα, and C=O).

'''Write down the orientation of each pair of strands (parallel or antiparallel).''' Click below to highlight the strands in pairs (pair 1, pair 2 and pair 3). The carbon atoms will be highlighted in orange.

<scene name='User:Robert_Dutnall/Sandbox_1_sheets/Mixed_sheet_mainchain_pair1/1'>Pair 1.</scene>

<scene name='User:Robert_Dutnall/Sandbox_1_sheets/Mixed_sheet_mainchain_pair2/1'>Pair 2.</scene>

<scene name='User:Robert_Dutnall/Sandbox_1_sheets/Mixed_sheet_mainchain_pair3/1'>Pair 3.</scene>

That's it. You are finished with Tutorial 2. Remember to submit your answers to the questions to your instructor.
= =
[[User:Robert Dutnall/Sandbox_1_alpha_helix|Click here to go on to back to the first part of this tutorial.]]

File:Mixed sheet.pdb

2011-08-29T18:29:42Z

Robert Dutnall:

== Licensing ==
{{self|cc-by-sa-3.0}}

User:Robert Dutnall/Sandbox 1 sheets

2011-08-29T18:29:24Z

Robert Dutnall:

== Biochemistry Tutorial #2 - Secondary Structure (Part 2) ==

==β-strands and β-sheets==

The second major secondary structure element is the β-sheet. β-sheets are composed of two or more segments of polypeptide mainchain in β-strand conformation. In a β-strand, the polypeptide mainchain is in a mostly extended conformation. As their name implies, β-sheets are relatively flat, planar-like structures made up of β-strands arranged side-by-side. They come in three flavors: parallel, anti-parallel and mixed, which differ in terms of the orientation of each component strand (with respect to the direction of the mainchain from N-terminus to C-terminus).

Note that the mainchain of a β-strand is not perfectly fully extended (Φ ≠ φ ≠ 180o) and that the mainchain actually slowly twists (this is more obvious if you look at a long segment of β-strand). Thus β-sheets are not completely flat and also exhibit some twisting (this is also more obvious if you look at sheets made of many β-strands).

==Parallel β-sheet==

Parallel β-sheets are composed of β-strands that all point in the same direction. Each β-strand has mainchain dihedral angles as follows: Φ ~ -120o, φ ~ +105o.

The sheet shown below is composed of three strands in parallel orientation. All the atoms are shown (C = green; N = blue; O = red; S = yellow; H = white).
<Structure load='Tut_parallel_bsheet.pdb' size='500' frame='true' align='left' caption='' scene='User:Robert_Dutnall/Sandbox_1_sheets/Parallel_load/2'/>

<scene name='User:Robert_Dutnall/Sandbox_1_sheets/Parallel_mainchain/2'>Click here</scene> to show only the polypeptide mainchain (NH, Cα, and C=O).

Identify the N- and C-termini of each strand. <scene name='User:Robert_Dutnall/Sandbox_1_sheets/Parallel_mainchain_labels/6'>Click here to see if you were correct.</scene>

As the structure rotates you should be able to see the extended nature of each strand and the parallel orientation of the three strands.

<scene name='User:Robert_Dutnall/Sandbox_1_sheets/Parallel_mainchain_labels_face/2'>Click here</scene> to stop the structure spinning and view the sheet from roughly perpendicular to its flat plane, with each strand running left-to-right (N- to C-terminus).

<scene name='User:Robert_Dutnall/Sandbox_1_sheets/Parallel_mainchain_labels_side/2'>Click here</scene> to stop the structure spinning and view the sheet from roughly edge-on to its flat plane.

<scene name='User:Robert_Dutnall/Sandbox_1_sheets/Parallel_mainchain_labels/6'>Click here to start the structure spinning again.</scene> Look at the structure carefully and identify the mainchain NH and C=O groups. What is the orientation of these groups with respect to the long axis of each strand? What the orientation of these groups with respect to the flat plane of the sheet?

<scene name='User:Robert_Dutnall/Sandbox_1_sheets/Parallel_mainchain_labels_hb/5'>Click here to add hydrogen bonds for the mainchain (dashed lines).</scene> The hydrogen bonds connect backbone NH groups and C=O groups. The N-H group is the hydrogen bond donor, the oxygen in the C=O group is the acceptor (N-H--->O=C). Each hydrogen bond is approximately 3.0 Angstroms (0.3 nm) in length (measured between the N and the O).

You should be able to see that the mainchain NH and C=O groups are involved in hydrogen bonds. In each strand the mainchain NH and C=O groups point to opposite sides of the mainchain (because of the almost fully extended conformation). The strands line up in the sheet so that the NH and C=O groups are parallel to plane of the sheet and lie opposite each other in pairs. This means that hydrogen bonds can be made between the strands of the sheet. <scene name='User:Robert_Dutnall/Sandbox_1_sheets/Parallel_mainchain_labels_hb_z/5'>Click here to zoom in to show some of the hydrogen bonds more clearly.</scene>

<scene name='User:Robert_Dutnall/Sandbox_1_sheets/Parallel_mainchain_labels_hb/5'>Click here to zoom out again.</scene> You should also notice that all of the NH and C=O groups that lie between strands are involved in hydrogen bonds. Only the groups on the edges of the sheet do not have hydrogen bond partners. However, as with helix capping, if this sheet were part of a larger protein, other residues would supply groups to hydrogen bond to most if not all of these.

<scene name='User:Robert_Dutnall/Sandbox_1_sheets/Parallel_sidechains/2'>Click here to show the side chains again.</scene> You are looking roughly edge-on to the flat plane of the sheet and the atoms of each amino side chain have been colored light blue to show them more clearly.

What is the general orientation of the side chains with respect to each strand and the sheet? You should observe that the side chains are approximately perpendicular to the flat plane of the sheet. Along each strand, the side chains alternate direction. You can see this more clearly if we color the side chains in one strand alternately. <scene name='User:Robert_Dutnall/Sandbox_1_sheets/Parallel_strand_alt/3'>Click here</scene> to freeze the view and color the side chains along one strand blue-purple-blue-purple...etc.

If we apply this to all the strands (<scene name='User:Robert_Dutnall/Sandbox_1_sheets/Parallel_sidechains_alt/2'>click here</scene>) you can see that all the sidechains above the plane of the sheet are purple, and all those below are blue.

==Anti-Parallel β-sheet==

Anti-parallel β-sheets are composed of β-strands that alternate in direction. Each β-strand has mainchain dihedral angles as follows: Φ ~ -150o, φ ~ +135o.

The sheet shown below is composed of three strands in anti-parallel orientation. All the atoms are shown (C = green; N = blue; O = red; S = yellow; H = white).
<Structure load='Tut_antiparallel_bsheet.pdb' size='500' frame='true' align='left' caption='' scene='User:Robert_Dutnall/Sandbox_1_sheets/Antiparallel_load/3'/>

<scene name='User:Robert_Dutnall/Sandbox_1_sheets/Antiparallel_mainchain/3'>Click here</scene> to show only the polypeptide mainchain of each strand (NH, Cα, and C=O).

Identify the N- and C-termini of each strand. <scene name='User:Robert_Dutnall/Sandbox_1_sheets/Antiparallel_mainchain_labels/1'>Click here to see if you were correct.</scene>

As the structure rotates you should be able to see the extended nature of each strand and the parallel orientation of the three strands.

<scene name='User:Robert_Dutnall/Sandbox_1_sheets/Antipara_mainchain_labels_face/1'>Click here</scene> to stop the structure spinning and view the sheet from roughly perpendicular to its flat plane.

<scene name='User:Robert_Dutnall/Sandbox_1_sheets/Antipara_mainchain_labels_side/1'>Click here</scene> to stop the structure spinning and view the sheet from roughly edge-on to its flat plane.

<scene name='User:Robert_Dutnall/Sandbox_1_sheets/Antiparallel_mainchain_labels/1'>Click here to start the structure spinning again.</scene> Look at the structure carefully and identify the mainchain NH and C=O groups. In each strand the mainchain NH and C=O groups point to opposite sides of the mainchain. The strands line up in the sheet so that these NH and C=O groups are parallel to plane of the sheet and lie opposite each other so that they can make hydrogen bonds.

<scene name='User:Robert_Dutnall/Sandbox_1_sheets/Antipara_mainchain_hbonds/1'>Click here to add hydrogen bonds for the mainchain (dashed lines).</scene> The hydrogen bonds connect backbone NH groups and C=O groups. The N-H group is the hydrogen bond donor, the oxygen in the C=O group is the acceptor (N-H--->O=C). Each hydrogen bond is approximately 3.0 Angstroms (0.3 nm) in length (measured between the N and the O).

You should be able to see that the mainchain NH and C=O groups are involved in hydrogen bonds between the strands of the sheet. <scene name='User:Robert_Dutnall/Sandbox_1_sheets/Antipara_mainchain_hbonds_z/1'>Click here to zoom in to show some of the hydrogen bonds more clearly.</scene>

<scene name='User:Robert_Dutnall/Sandbox_1_sheets/Antipara_mainchain_hbonds/1'>Click here to zoom out again.</scene> You should notice that all of the NH and C=O groups that lie between strands are involved in hydrogen bonds. Only the groups on the edges of the sheet do not have hydrogen bond partners, but if this sheet were part of a larger protein, other residues would supply groups to hydrogen bond to most if not all of these.

Two of the strands in this sheet are connected by a β-turn. <scene name='User:Robert_Dutnall/Sandbox_1_sheets/Antipara_mainchain_turn/2'>Click here</scene> to show the β-turn. The carbon atoms of the amino acids that define the turn have been colored dark orange. The turn allows a segment of polypeptide to reverse direction in a short distance. In this case it also allows two strands to interact in an antiparallel fashion. <scene name='User:Robert_Dutnall/Sandbox_1_sheets/Antipara_mainchain_turn_zoom/3'>Click here to zoom in on the turn and reorient it to show more clearly.</scene> '''Is this a Type I or Type II β-turn? (Write down your answer so you can submit it to your instructor)'''

<scene name='User:Robert_Dutnall/Sandbox_1_sheets/Antipara_mainchain_sidechains/1'>Click here to zoom out again.</scene> In this view, some of the residues at the turn have been omitted and you are looking roughly edge-on to the flat plane of the sheet. Sidechains have been added and the atoms of each amino side chain have been colored blue or purple in an alternating fashion.

The side chains are approximately perpendicular to the flat plane of the sheet. Along each strand, the side chains alternate direction (above the plane, below the plane, above the plane...) so you should be able to see that all the sidechains above the plane of the sheet are purple, and all those below are blue.

==A mixed β-sheet==

The sheet shown below is composed of four strands. All the atoms are shown (C = green; N = blue; O = red; S = yellow; H = white). This is a mixed β-sheet. Some of the strands are parallel, some are antiparallel
<Structure load='Tut_antiparallel_bsheet.pdb' size='500' frame='true' align='left' caption='' scene='User:Robert_Dutnall/Sandbox_1_sheets/Antiparallel_load/3'/>

<scene name='User:Robert_Dutnall/Sandbox_1_sheets/Antiparallel_mainchain/3'>Click here</scene> to show only the polypeptide mainchain of each strand (NH, Cα, and C=O).

Identify the N- and C-termini of each strand. <scene name='User:Robert_Dutnall/Sandbox_1_sheets/Antiparallel_mainchain_labels/1'>Click here to see if you were correct.</scene>

As the structure rotates you should be able to see the extended nature of each strand and the parallel orientation of the three strands.

<scene name='User:Robert_Dutnall/Sandbox_1_sheets/Antipara_mainchain_labels_face/1'>Click here</scene> to stop the structure spinning and view the sheet from roughly perpendicular to its flat plane.

<scene name='User:Robert_Dutnall/Sandbox_1_sheets/Antipara_mainchain_labels_side/1'>Click here</scene> to stop the structure spinning and view the sheet from roughly edge-on to its flat plane.

<scene name='User:Robert_Dutnall/Sandbox_1_sheets/Antiparallel_mainchain_labels/1'>Click here to start the structure spinning again.</scene> Look at the structure carefully and identify the mainchain NH and C=O groups. In each strand the mainchain NH and C=O groups point to opposite sides of the mainchain. The strands line up in the sheet so that these NH and C=O groups are parallel to plane of the sheet and lie opposite each other so that they can make hydrogen bonds.

<scene name='User:Robert_Dutnall/Sandbox_1_sheets/Antipara_mainchain_hbonds/1'>Click here to add hydrogen bonds for the mainchain (dashed lines).</scene> The hydrogen bonds connect backbone NH groups and C=O groups. The N-H group is the hydrogen bond donor, the oxygen in the C=O group is the acceptor (N-H--->O=C). Each hydrogen bond is approximately 3.0 Angstroms (0.3 nm) in length (measured between the N and the O).

You should be able to see that the mainchain NH and C=O groups are involved in hydrogen bonds between the strands of the sheet. <scene name='User:Robert_Dutnall/Sandbox_1_sheets/Antipara_mainchain_hbonds_z/1'>Click here to zoom in to show some of the hydrogen bonds more clearly.</scene>

<scene name='User:Robert_Dutnall/Sandbox_1_sheets/Antipara_mainchain_hbonds/1'>Click here to zoom out again.</scene> You should notice that all of the NH and C=O groups that lie between strands are involved in hydrogen bonds. Only the groups on the edges of the sheet do not have hydrogen bond partners, but if this sheet were part of a larger protein, other residues would supply groups to hydrogen bond to most if not all of these.

Two of the strands in this sheet are connected by a β-turn. <scene name='User:Robert_Dutnall/Sandbox_1_sheets/Antipara_mainchain_turn/2'>Click here</scene> to show the β-turn. The carbon atoms of the amino acids that define the turn have been colored dark orange. The turn allows a segment of polypeptide to reverse direction in a short distance. In this case it also allows two strands to interact in an antiparallel fashion. <scene name='User:Robert_Dutnall/Sandbox_1_sheets/Antipara_mainchain_turn_zoom/3'>Click here to zoom in on the turn and reorient it to show more clearly.</scene> '''Is this a Type I or Type II β-turn? (Write down your answer so you can submit it to your instructor)'''

<scene name='User:Robert_Dutnall/Sandbox_1_sheets/Antipara_mainchain_sidechains/1'>Click here to zoom out again.</scene> In this view, some of the residues at the turn have been omitted and you are looking roughly edge-on to the flat plane of the sheet. Sidechains have been added and the atoms of each amino side chain have been colored blue or purple in an alternating fashion.

The side chains are approximately perpendicular to the flat plane of the sheet. Along each strand, the side chains alternate direction (above the plane, below the plane, above the plane...) so you should be able to see that all the sidechains above the plane of the sheet are purple, and all those below are blue.

= =
[[User:Robert Dutnall/Sandbox_1_alpha_helix|Click here to go on to back to the first part of this tutorial.]]

User:Robert Dutnall/Sandbox 1 sheets

2011-08-29T18:16:53Z

Robert Dutnall:

User:Robert Dutnall/Sandbox 1 alpha helix

2011-08-29T18:12:20Z

Robert Dutnall:

== Biochemistry Tutorial #2 - Secondary Structure (Part 1) ==

The secondary structure of a protein is defined by the local conformation of its backbone (polypeptide mainchain). There are two major types of regular secondary structures in proteins: helices and sheets. There are also regular turn structures. Turns often connect one element of secondary structure to another in the overall fold of the protein. Other parts of the protein mainchain may adopt more irregularly defined loops. This tutorial will focus mainly on helices and sheets.

''Note: in these tutorials, the images are 3D interactive images. You can manipulate them as you wish to get a better view of the molecules.''

You can rotate the structures by holding down the right mouse button and dragging. At any time you can click the 'toggle spin' button in box to stop/start the structure spinning.

Other things you can do:
::To rotate: left drag
::To Zoom: scroll button or shift + left drag
::To Translate: ctrl + right drag
::Right click to bring up an options menu

==Helices==

In helices, the polypeptide mainchain twists into a path that resembles a spiral staircase. Just like spiral staircases, helices come in different forms, depending on how tightly twisted the mainchain is. The form of a helix can be described by parameters such as the number of steps (amino acids) it takes to complete a turn (a 360o rotation around the long axis of the helix), and how far you travel along the helix axis in one complete turn. Helices can also be left-handed or right-handed. For proteins composed of L-amino acids, helices are almost always right-handed (a notable exception is the type I poly-proline helix). Although several types of helix form are possible, two regular helices are very common in proteins: the α-helix and the 310-helix.

==The α-helix==

α-helices are the most common type of regular helix found in proteins. They are characterized by the following helix parameters:
::Dihedral angles: Φ ~ -60o, φ ~ -45o
::Repeat (number of residues per turn) = 3.6
::Rise (translation along axis per amino acid residue) = 1.5 Angstroms (0.15 nm)
::Twist (rotation around axis per amino acid residue) = 100o (= 360o/repeat)
::Pitch (translation along axis per turn) = 5.4 Angstroms (= 0.54 nm = Repeat x Rise)

The helix shown below is a 19 amino acid chain in α-helical conformation.
<Structure load='Tut_alpha_helix.pdb' size='500' frame='true' align='left' caption='' scene='User:Robert_Dutnall/Sandbox_1_alpha_helix/A_helix_load/1'/>

All the atoms are shown in this initial orientation (C = green; N = blue; O = red; S = yellow; H = white). The helix axis runs vertically, approximately parallel to the plane of the screen.

<scene name='User:Robert_Dutnall/Sandbox_1_alpha_helix/A_helix_mainchain/3'>Click here</scene> to show only the polypeptide mainchain (NH, Cα, and C=O).

Identify the N- and C-termini. <scene name='User:Robert_Dutnall/Sandbox_1_alpha_helix/A_helix_mainchain_label/4'>Click here to see if you were correct.</scene>

<scene name='User:Robert_Dutnall/Sandbox_1_alpha_helix/A_helix_mainchain_label_ribbon/3'>Click here to add a ribbon that will help show the path of the mainchain. </scene> You should be able to see that it is helical with a right-handed twist (you rotate to the right as you move along the helix axis).

Click the "toggle spin" button in the box to stop the structure from rotating. Now use your mouse to rotate the structure to look down the helix axis. If you have any problems with finding this view, <scene name='User:Robert_Dutnall/Sandbox_1_alpha_helix/A_helix_mainchain_label_axis/3'>click here </scene>to zoom in and look down the helix axis from the N-terminal end.

<scene name='User:Robert_Dutnall/Sandbox_1_alpha_helix/A_helix_mainchain_label/4'>Click here to zoom out again.</scene> Look at the structure carefully and identify the mainchain NH and C=O groups. What is the orientation of these groups with respect to the helix axis?

<scene name='User:Robert_Dutnall/Sandbox_1_alpha_helix/A_helix_mainchain_label_hbonds/10'>Click here to zoom in a little and add hydrogen bonds for the mainchain (dashed lines).</scene> The hydrogen bonds connect backbone NH groups and C=O groups. The N-H group is the hydrogen bond donor, the oxygen in the C=O group is the acceptor (N-H--->O=C). Each hydrogen bond is approximately 3.0 Angstroms (0.3 nm) in length (measured between the N and the O). These hydrogen bonds connect amino acids that are spaced 4 residues apart in the primary sequence. The NH group is from amino acid X and the O is from amino acid X-4 (where X is the number of the amino acid in the sequence).

<scene name='User:Robert_Dutnall/Sandbox_1_alpha_helix/A_helix_mainchain_label_hbonds/9'>Click here to zoom out again.</scene> You should be able to see that all of the mainchain NH and C=O groups are involved in hydrogen bonds. This is possible because 1) all the mainchain NH groups and C=O groups are parallel to the helix axis, 2) all the NH groups point toward the N-terminus of the helix, and 3) all the C=O groups point toward the C-terminus. Only the NH groups in the first (N-terminal) turn, and the C=O groups in the last (C-terminal) turn of the helix do not have hydrogen bonding partners. However, if this helix were part of a larger protein, these groups would participate in hydrogen bonds with other parts of the protein. This is called 'helix capping' and the other groups involved are typically from amino acid side chains (that are called 'helix capping residues').

<scene name='User:Robert_Dutnall/Sandbox_1_alpha_helix/A_helix_sidechains/3'>Click here to show the side chains again.</scene> The atoms of each amino side chain have been colored light blue to show them more clearly. <scene name='User:Robert_Dutnall/Sandbox_1_alpha_helix/A_helix_sidechains_axis/1'>Click here to change the view to look down the helix axis.</scene>

What is the general orientation of the side chains with respect to the helix axis? You should observe that each side chain points away from the helix axis, but points down toward the N-terminus of the helix (this is clearer if you only show the first bond of each side chain: <scene name='User:Robert_Dutnall/Sandbox_1_alpha_helix/A_helix_sidechains_cropped/1'>click here</scene> or <scene name='User:Robert_Dutnall/Sandbox_1_alpha_helix/A_helix_sidechains_cropped/2'>click here</scene>).

==The 310-helix==

310-helices are also found in proteins but are less common than α-helices. They are characterized by the following helix parameters:
::Dihedral angles: Φ ~ -49o, φ ~ -26o
::Repeat (number of residues per turn) = 3.0
::Rise (translation along axis per amino acid residue) = 2.0 Angstroms (0.2 nm)
::Twist (rotation around axis per amino acid residue) = 120o (= 360o/repeat)
::Pitch (translation along axis per turn) = 6.0 Angstroms (= 0.6 nm = Repeat x Rise)

The helix shown below is a 19 amino acid chain in 310-helical conformation.
<Structure load='Tut_3-10_helix.pdb' size='500' frame='true' align='left' caption='' scene='User:Robert_Dutnall/Sandbox_1_alpha_helix/310_helix_load/4'/>

All the atoms are shown in this initial orientation (C = green; N = blue; O = red; S = yellow; H = white). The helix axis runs vertically, approximately parallel to the plane of the screen.

<scene name='User:Robert_Dutnall/Sandbox_1_alpha_helix/310_helix_mainchain/2'>Click here</scene> to show only the polypeptide mainchain (NH, Cα, and C=O). The N- and C-termini are labeled.

<scene name='User:Robert_Dutnall/Sandbox_1_alpha_helix/310_helix_mainchain_ribbon/2'>Click here to add a ribbon that will help show the path of the mainchain. </scene> You should be able to see that just like the α-helix, it is helical with a right-handed twist, and again, all the mainchain NH groups point toward the N-terminus, and all the mainchain C=O groups point toward the C-terminus.

The difference between an α-helix and a 310-helix lies in the helix parameters. A 310-helix is more tightly twisted so that the mainchain completes one turn every 3 amino acids (instead of 3.6 for the α-helix). This also results in a larger rise and pitch so that the 310-helix is longer than an α-helix (of the same number of residues).

<scene name='User:Robert_Dutnall/Sandbox_1_alpha_helix/310_helix_mainchain_axis/1'>Click here </scene>to zoom in and look down the helix axis from the N-terminal end. You'll be able to see the triangular shape of the mainchain.

<scene name='User:Robert_Dutnall/Sandbox_1_alpha_helix/310_helix_mainchain_hbonds/1'>Click here to zoom out again and display hydrogen bonds for the mainchain.</scene> Once again, all of the mainchain NH and C=O groups are involved in hydrogen bonds. However, now the hydrogen bonds connect amino acids that are spaced 3 residues apart in the primary sequence. The NH group is from amino acid X and the O is from amino acid X-3 (where X is the number of the amino acid in the sequence). <scene name='User:Robert_Dutnall/Sandbox_1_alpha_helix/310_helix_mainchain_hbonds/2'>Click here</scene> to zoom in and you should be able to see this more clearly.

<scene name='User:Robert_Dutnall/Sandbox_1_alpha_helix/310_helix_sidechains/1'>Click here to zoom out and show the side chains again.</scene> The atoms of each amino side chain have been colored light blue to show them more clearly. <scene name='User:Robert_Dutnall/Sandbox_1_alpha_helix/310_helix_sidechains_axis/2'>Click here to change the view to look down the helix axis.</scene>

As for the α-helix, each side chain points away from the helix axis, and points down toward the N-terminus of the helix. However, because the 310-helix repeat parameter is an integer (= 3.0), the side chains are spaced 120o apart and form 3 distinct sides to the helix. You'll see this more clearly if the side chains are colored in groups to show this (residues 1,4,7,10 etc are blue; residues 2,5,8,11 etc are purple; residues 3,6,9,12 etc are yellow): <scene name='User:Robert_Dutnall/Sandbox_1_alpha_helix/310_helix_sidechains_tricolor/1'>click here to look from the side</scene> or <scene name='User:Robert_Dutnall/Sandbox_1_alpha_helix/310_helix_sidechains_tricol_ax/1'>click here to view down the helix axis</scene>.

<scene name='User:Robert_Dutnall/Sandbox_1_alpha_helix/310_helix_load/4'>Click here to reset the view of the helix.</scene>

'''What is the identity of the N-terminal amino acid?'''

'''What is the identity of the C-terminal amino acid?'''

'''Write down these answers so that you can submit them to your instructor.'''

= =
[[User:Robert Dutnall/Sandbox_1_sheets|Click here to go on to part 2 of this tutorial.]]

User:Robert Dutnall/Sandbox 1 alpha helix

2011-08-29T18:11:41Z

Robert Dutnall:

== Biochemistry Tutorial #2 - Secondary Structure (Part 1) ==

The secondary structure of a protein is defined by the local conformation of its backbone (polypeptide mainchain). There are two major types of regular secondary structures in proteins: helices and sheets. There are also regular turn structures. Turns often connect one element of secondary structure to another in the overall fold of the protein. Other parts of the protein mainchain may adopt more irregularly defined loops. This tutorial will focus mainly on helices and sheets.

''Note: in these tutorials, the images are 3D interactive images. You can manipulate them as you wish to get a better view of the molecules.''

You can rotate the structures by holding down the right mouse button and dragging. At any time you can click the 'toggle spin' button in box to stop/start the structure spinning.

Other things you can do:
::To rotate: left drag
::To Zoom: scroll button or shift + left drag
::To Translate: ctrl + right drag
::Right click to bring up an options menu

==Helices==

In helices, the polypeptide mainchain twists into a path that resembles a spiral staircase. Just like spiral staircases, helices come in different forms, depending on how tightly twisted the mainchain is. The form of a helix can be described by parameters such as the number of steps (amino acids) it takes to complete a turn (a 360o rotation around the long axis of the helix), and how far you travel along the helix axis in one complete turn. Helices can also be left-handed or right-handed. For proteins composed of L-amino acids, helices are almost always right-handed (a notable exception is the type I poly-proline helix). Although several types of helix form are possible, two regular helices are very common in proteins: the α-helix and the 310-helix.

==The α-helix==

α-helices are the most common type of regular helix found in proteins. They are characterized by the following helix parameters:
::Dihedral angles: Φ ~ -60o, φ ~ -45o
::Repeat (number of residues per turn) = 3.6
::Rise (translation along axis per amino acid residue) = 1.5 Angstroms (0.15 nm)
::Twist (rotation around axis per amino acid residue) = 100o (= 360o/repeat)
::Pitch (translation along axis per turn) = 5.4 Angstroms (= 0.54 nm = Repeat x Rise)

The helix shown below is a 19 amino acid chain in α-helical conformation.
<Structure load='Tut_alpha_helix.pdb' size='500' frame='true' align='left' caption='' scene='User:Robert_Dutnall/Sandbox_1_alpha_helix/A_helix_load/1'/>

All the atoms are shown in this initial orientation (C = green; N = blue; O = red; S = yellow; H = white). The helix axis runs vertically, approximately parallel to the plane of the screen.

<scene name='User:Robert_Dutnall/Sandbox_1_alpha_helix/A_helix_mainchain/3'>Click here</scene> to show only the polypeptide mainchain (NH, Cα, and C=O).

Identify the N- and C-termini. <scene name='User:Robert_Dutnall/Sandbox_1_alpha_helix/A_helix_mainchain_label/4'>Click here to see if you were correct.</scene>

<scene name='User:Robert_Dutnall/Sandbox_1_alpha_helix/A_helix_mainchain_label_ribbon/3'>Click here to add a ribbon that will help show the path of the mainchain. </scene> You should be able to see that it is helical with a right-handed twist (you rotate to the right as you move along the helix axis).

Click the "toggle spin" button in the box to stop the structure from rotating. Now use your mouse to rotate the structure to look down the helix axis. If you have any problems with finding this view, <scene name='User:Robert_Dutnall/Sandbox_1_alpha_helix/A_helix_mainchain_label_axis/3'>click here </scene>to zoom in and look down the helix axis from the N-terminal end.

<scene name='User:Robert_Dutnall/Sandbox_1_alpha_helix/A_helix_mainchain_label/4'>Click here to zoom out again.</scene> Look at the structure carefully and identify the mainchain NH and C=O groups. What is the orientation of these groups with respect to the helix axis?

<scene name='User:Robert_Dutnall/Sandbox_1_alpha_helix/A_helix_mainchain_label_hbonds/10'>Click here to zoom in a little and add hydrogen bonds for the mainchain (dashed lines).</scene> The hydrogen bonds connect backbone NH groups and C=O groups. The N-H group is the hydrogen bond donor, the oxygen in the C=O group is the acceptor (N-H--->O=C). Each hydrogen bond is approximately 3.0 Angstroms (0.3 nm) in length (measured between the N and the O). These hydrogen bonds connect amino acids that are spaced 4 residues apart in the primary sequence. The NH group is from amino acid X and the O is from amino acid X-4 (where X is the number of the amino acid in the sequence).

<scene name='User:Robert_Dutnall/Sandbox_1_alpha_helix/A_helix_mainchain_label_hbonds/9'>Click here to zoom out again.</scene> You should be able to see that all of the mainchain NH and C=O groups are involved in hydrogen bonds. This is possible because 1) all the mainchain NH groups and C=O groups are parallel to the helix axis, 2) all the NH groups point toward the N-terminus of the helix, and 3) all the C=O groups point toward the C-terminus. Only the NH groups in the first (N-terminal) turn, and the C=O groups in the last (C-terminal) turn of the helix do not have hydrogen bonding partners. However, if this helix were part of a larger protein, these groups would participate in hydrogen bonds with other parts of the protein. This is called 'helix capping' and the other groups involved are typically from amino acid side chains (that are called 'helix capping residues').

<scene name='User:Robert_Dutnall/Sandbox_1_alpha_helix/A_helix_sidechains/3'>Click here to show the side chains again.</scene> The atoms of each amino side chain have been colored light blue to show them more clearly. <scene name='User:Robert_Dutnall/Sandbox_1_alpha_helix/A_helix_sidechains_axis/1'>Click here to change the view to look down the helix axis.</scene>

What is the general orientation of the side chains with respect to the helix axis? You should observe that each side chain points away from the helix axis, but points down toward the N-terminus of the helix (this is clearer if you only show the first bond of each side chain: <scene name='User:Robert_Dutnall/Sandbox_1_alpha_helix/A_helix_sidechains_cropped/1'>click here</scene> or <scene name='User:Robert_Dutnall/Sandbox_1_alpha_helix/A_helix_sidechains_cropped/2'>click here</scene>).

==The 310-helix==

310-helices are also found in proteins but are less common than α-helices. They are characterized by the following helix parameters:
::Dihedral angles: Φ ~ -49o, φ ~ -26o
::Repeat (number of residues per turn) = 3.0
::Rise (translation along axis per amino acid residue) = 2.0 Angstroms (0.2 nm)
::Twist (rotation around axis per amino acid residue) = 120o (= 360o/repeat)
::Pitch (translation along axis per turn) = 6.0 Angstroms (= 0.6 nm = Repeat x Rise)

The helix shown below is a 19 amino acid chain in 310-helical conformation.
<Structure load='Tut_3-10_helix.pdb' size='500' frame='true' align='left' caption='' scene='User:Robert_Dutnall/Sandbox_1_alpha_helix/310_helix_load/4'/>

All the atoms are shown in this initial orientation (C = green; N = blue; O = red; S = yellow; H = white). The helix axis runs vertically, approximately parallel to the plane of the screen.

<scene name='User:Robert_Dutnall/Sandbox_1_alpha_helix/310_helix_mainchain/2'>Click here</scene> to show only the polypeptide mainchain (NH, Cα, and C=O). The N- and C-termini are labeled.

<scene name='User:Robert_Dutnall/Sandbox_1_alpha_helix/310_helix_mainchain_ribbon/2'>Click here to add a ribbon that will help show the path of the mainchain. </scene> You should be able to see that just like the α-helix, it is helical with a right-handed twist, and again, all the mainchain NH groups point toward the N-terminus, and all the mainchain C=O groups point toward the C-terminus.

The difference between an α-helix and a 310-helix lies in the helix parameters. A 310-helix is more tightly twisted so that the mainchain completes one turn every 3 amino acids (instead of 3.6 for the α-helix). This also results in a larger rise and pitch so that the 310-helix is longer than an α-helix (of the same number of residues).

<scene name='User:Robert_Dutnall/Sandbox_1_alpha_helix/310_helix_mainchain_axis/1'>Click here </scene>to zoom in and look down the helix axis from the N-terminal end. You'll be able to see the triangular shape of the mainchain.

<scene name='User:Robert_Dutnall/Sandbox_1_alpha_helix/310_helix_mainchain_hbonds/1'>Click here to zoom out again and display hydrogen bonds for the mainchain.</scene> Once again, all of the mainchain NH and C=O groups are involved in hydrogen bonds. However, now the hydrogen bonds connect amino acids that are spaced 3 residues apart in the primary sequence. The NH group is from amino acid X and the O is from amino acid X-3 (where X is the number of the amino acid in the sequence). <scene name='User:Robert_Dutnall/Sandbox_1_alpha_helix/310_helix_mainchain_hbonds/2'>Click here</scene> to zoom in and you should be able to see this more clearly.

<scene name='User:Robert_Dutnall/Sandbox_1_alpha_helix/310_helix_sidechains/1'>Click here to zoom out and show the side chains again.</scene> The atoms of each amino side chain have been colored light blue to show them more clearly. <scene name='User:Robert_Dutnall/Sandbox_1_alpha_helix/310_helix_sidechains_axis/2'>Click here to change the view to look down the helix axis.</scene>

As for the α-helix, each side chain points away from the helix axis, and points down toward the N-terminus of the helix. However, because the 310-helix repeat parameter is an integer (= 3.0), the side chains are spaced 120o apart and form 3 distinct sides to the helix. You'll see this more clearly if the side chains are colored in groups to show this (residues 1,4,7,10 etc are blue; residues 2,5,8,11 etc are purple; residues 3,6,9,12 etc are yellow): <scene name='User:Robert_Dutnall/Sandbox_1_alpha_helix/310_helix_sidechains_tricolor/1'>click here to look from the side</scene> or <scene name='User:Robert_Dutnall/Sandbox_1_alpha_helix/310_helix_sidechains_tricol_ax/1'>click here to view down the helix axis</scene>.

<scene name='User:Robert_Dutnall/Sandbox_1_alpha_helix/310_helix_load/4'>click here to reset the view of the helix.</scene>

'''What is the identity of the N-terminal amino acid?'''
'''What is the identity of the C-terminal amino acid?'''
'''Write down these answers so that you can submit them to your instructor.'''

= =
[[User:Robert Dutnall/Sandbox_1_sheets|Click here to go on to part 2 of this tutorial.]]

User:Robert Dutnall/Sandbox 1 alpha helix

2011-08-29T18:04:39Z

Robert Dutnall:

== Biochemistry Tutorial #2 - Secondary Structure (Part 1) ==

The secondary structure of a protein is defined by the local conformation of its backbone (polypeptide mainchain). There are two major types of regular secondary structures in proteins: helices and sheets. There are also regular turn structures. Turns often connect one element of secondary structure to another in the overall fold of the protein. Other parts of the protein mainchain may adopt more irregularly defined loops. This tutorial will focus mainly on helices and sheets.

''Note: in these tutorials, the images are 3D interactive images. You can manipulate them as you wish to get a better view of the molecules.''

You can rotate the structures by holding down the right mouse button and dragging. At any time you can click the 'toggle spin' button in box to stop/start the structure spinning.

Other things you can do:
::To rotate: left drag
::To Zoom: scroll button or shift + left drag
::To Translate: ctrl + right drag
::Right click to bring up an options menu

==Helices==

In helices, the polypeptide mainchain twists into a path that resembles a spiral staircase. Just like spiral staircases, helices come in different forms, depending on how tightly twisted the mainchain is. The form of a helix can be described by parameters such as the number of steps (amino acids) it takes to complete a turn (a 360o rotation around the long axis of the helix), and how far you travel along the helix axis in one complete turn. Helices can also be left-handed or right-handed. For proteins composed of L-amino acids, helices are almost always right-handed (a notable exception is the type I poly-proline helix). Although several types of helix form are possible, two regular helices are very common in proteins: the α-helix and the 310-helix.

==The α-helix==

α-helices are the most common type of regular helix found in proteins. They are characterized by the following helix parameters:
::Dihedral angles: Φ ~ -60o, φ ~ -45o
::Repeat (number of residues per turn) = 3.6
::Rise (translation along axis per amino acid residue) = 1.5 Angstroms (0.15 nm)
::Twist (rotation around axis per amino acid residue) = 100o (= 360o/repeat)
::Pitch (translation along axis per turn) = 5.4 Angstroms (= 0.54 nm = Repeat x Rise)

The helix shown below is a 19 amino acid chain in α-helical conformation.
<Structure load='Tut_alpha_helix.pdb' size='500' frame='true' align='left' caption='' scene='User:Robert_Dutnall/Sandbox_1_alpha_helix/A_helix_load/1'/>

All the atoms are shown in this initial orientation (C = green; N = blue; O = red; S = yellow; H = white). The helix axis runs vertically, approximately parallel to the plane of the screen.

<scene name='User:Robert_Dutnall/Sandbox_1_alpha_helix/A_helix_mainchain/3'>Click here</scene> to show only the polypeptide mainchain (NH, Cα, and C=O).

Identify the N- and C-termini. <scene name='User:Robert_Dutnall/Sandbox_1_alpha_helix/A_helix_mainchain_label/4'>Click here to see if you were correct.</scene>

<scene name='User:Robert_Dutnall/Sandbox_1_alpha_helix/A_helix_mainchain_label_ribbon/3'>Click here to add a ribbon that will help show the path of the mainchain. </scene> You should be able to see that it is helical with a right-handed twist (you rotate to the right as you move along the helix axis).

Click the "toggle spin" button in the box to stop the structure from rotating. Now use your mouse to rotate the structure to look down the helix axis. If you have any problems with finding this view, <scene name='User:Robert_Dutnall/Sandbox_1_alpha_helix/A_helix_mainchain_label_axis/3'>click here </scene>to zoom in and look down the helix axis from the N-terminal end.

<scene name='User:Robert_Dutnall/Sandbox_1_alpha_helix/A_helix_mainchain_label/4'>Click here to zoom out again.</scene> Look at the structure carefully and identify the mainchain NH and C=O groups. What is the orientation of these groups with respect to the helix axis?

<scene name='User:Robert_Dutnall/Sandbox_1_alpha_helix/A_helix_mainchain_label_hbonds/10'>Click here to zoom in a little and add hydrogen bonds for the mainchain (dashed lines).</scene> The hydrogen bonds connect backbone NH groups and C=O groups. The N-H group is the hydrogen bond donor, the oxygen in the C=O group is the acceptor (N-H--->O=C). Each hydrogen bond is approximately 3.0 Angstroms (0.3 nm) in length (measured between the N and the O). These hydrogen bonds connect amino acids that are spaced 4 residues apart in the primary sequence. The NH group is from amino acid X and the O is from amino acid X-4 (where X is the number of the amino acid in the sequence).

<scene name='User:Robert_Dutnall/Sandbox_1_alpha_helix/A_helix_mainchain_label_hbonds/9'>Click here to zoom out again.</scene> You should be able to see that all of the mainchain NH and C=O groups are involved in hydrogen bonds. This is possible because 1) all the mainchain NH groups and C=O groups are parallel to the helix axis, 2) all the NH groups point toward the N-terminus of the helix, and 3) all the C=O groups point toward the C-terminus. Only the NH groups in the first (N-terminal) turn, and the C=O groups in the last (C-terminal) turn of the helix do not have hydrogen bonding partners. However, if this helix were part of a larger protein, these groups would participate in hydrogen bonds with other parts of the protein. This is called 'helix capping' and the other groups involved are typically from amino acid side chains (that are called 'helix capping residues').

<scene name='User:Robert_Dutnall/Sandbox_1_alpha_helix/A_helix_sidechains/3'>Click here to show the side chains again.</scene> The atoms of each amino side chain have been colored light blue to show them more clearly. <scene name='User:Robert_Dutnall/Sandbox_1_alpha_helix/A_helix_sidechains_axis/1'>Click here to change the view to look down the helix axis.</scene>

What is the general orientation of the side chains with respect to the helix axis? You should observe that each side chain points away from the helix axis, but points down toward the N-terminus of the helix (this is clearer if you only show the first bond of each side chain: <scene name='User:Robert_Dutnall/Sandbox_1_alpha_helix/A_helix_sidechains_cropped/1'>click here</scene> or <scene name='User:Robert_Dutnall/Sandbox_1_alpha_helix/A_helix_sidechains_cropped/2'>click here</scene>).

==The 310-helix==

310-helices are also found in proteins but are less common than α-helices. They are characterized by the following helix parameters:
::Dihedral angles: Φ ~ -49o, φ ~ -26o
::Repeat (number of residues per turn) = 3.0
::Rise (translation along axis per amino acid residue) = 2.0 Angstroms (0.2 nm)
::Twist (rotation around axis per amino acid residue) = 120o (= 360o/repeat)
::Pitch (translation along axis per turn) = 6.0 Angstroms (= 0.6 nm = Repeat x Rise)

The helix shown below is a 19 amino acid chain in 310-helical conformation.
<Structure load='Tut_3-10_helix.pdb' size='500' frame='true' align='left' caption='' scene='User:Robert_Dutnall/Sandbox_1_alpha_helix/310_helix_load/4'/>

All the atoms are shown in this initial orientation (C = green; N = blue; O = red; S = yellow; H = white). The helix axis runs vertically, approximately parallel to the plane of the screen.

<scene name='User:Robert_Dutnall/Sandbox_1_alpha_helix/310_helix_mainchain/2'>Click here</scene> to show only the polypeptide mainchain (NH, Cα, and C=O). The N- and C-termini are labeled.

<scene name='User:Robert_Dutnall/Sandbox_1_alpha_helix/310_helix_mainchain_ribbon/2'>Click here to add a ribbon that will help show the path of the mainchain. </scene> You should be able to see that just like the α-helix, it is helical with a right-handed twist, and again, all the mainchain NH groups point toward the N-terminus, and all the mainchain C=O groups point toward the C-terminus.

The difference between an α-helix and a 310-helix lies in the helix parameters. A 310-helix is more tightly twisted so that the mainchain completes one turn every 3 amino acids (instead of 3.6 for the α-helix). This also results in a larger rise and pitch so that the 310-helix is longer than an α-helix (of the same number of residues).

<scene name='User:Robert_Dutnall/Sandbox_1_alpha_helix/310_helix_mainchain_axis/1'>Click here </scene>to zoom in and look down the helix axis from the N-terminal end. You'll be able to see the triangular shape of the mainchain.

<scene name='User:Robert_Dutnall/Sandbox_1_alpha_helix/310_helix_mainchain_hbonds/1'>Click here to zoom out again and display hydrogen bonds for the mainchain.</scene> Once again, all of the mainchain NH and C=O groups are involved in hydrogen bonds. However, now the hydrogen bonds connect amino acids that are spaced 3 residues apart in the primary sequence. The NH group is from amino acid X and the O is from amino acid X-3 (where X is the number of the amino acid in the sequence). <scene name='User:Robert_Dutnall/Sandbox_1_alpha_helix/310_helix_mainchain_hbonds/2'>Click here</scene> to zoom in and you should be able to see this more clearly.

<scene name='User:Robert_Dutnall/Sandbox_1_alpha_helix/310_helix_sidechains/1'>Click here to zoom out and show the side chains again.</scene> The atoms of each amino side chain have been colored light blue to show them more clearly. <scene name='User:Robert_Dutnall/Sandbox_1_alpha_helix/310_helix_sidechains_axis/2'>Click here to change the view to look down the helix axis.</scene>

As for the α-helix, each side chain points away from the helix axis, and points down toward the N-terminus of the helix. However, because the 310-helix repeat parameter is an integer (= 3.0), the side chains are spaced 120o apart and form 3 distinct sides to the helix. You'll see this more clearly if the side chains are colored in groups to show this (residues 1,4,7,10 etc are blue; residues 2,5,8,11 etc are purple; residues 3,6,9,12 etc are yellow): <scene name='User:Robert_Dutnall/Sandbox_1_alpha_helix/310_helix_sidechains_tricolor/1'>click here to look from the side</scene> or <scene name='User:Robert_Dutnall/Sandbox_1_alpha_helix/310_helix_sidechains_tricol_ax/1'>click here to view down the helix axis</scene>.

= =
[[User:Robert Dutnall/Sandbox_1_sheets|Click here to go on to part 2 of this tutorial.]]

User:Robert Dutnall/Sandbox 1 sheets

2011-08-29T18:04:10Z

Robert Dutnall:

User:Robert Dutnall/Sandbox 1 alpha helix

2011-08-29T18:02:55Z

Robert Dutnall:

== Biochemistry Tutorial #2 - Secondary Structure (Part 1) ==

The secondary structure of a protein is defined by the local conformation of its backbone (polypeptide mainchain). There are two major types of regular secondary structures in proteins: helices and sheets. There are also regular turn structures. Turns often connect one element of secondary structure to another in the overall fold of the protein. Other parts of the protein mainchain may adopt more irregularly defined loops. This tutorial will focus mainly on helices and sheets.

''Note: in these tutorials, the images are 3D interactive images. You can manipulate them as you wish to get a better view of the molecules.''

You can rotate the structures by holding down the right mouse button and dragging. At any time you can click the 'toggle spin' button in box to stop/start the structure spinning.

Other things you can do:
::To rotate: left drag
::To Zoom: scroll button or shift + left drag
::To Translate: ctrl + right drag
::Right click to bring up an options menu

=Helices=

In helices, the polypeptide mainchain twists into a path that resembles a spiral staircase. Just like spiral staircases, helices come in different forms, depending on how tightly twisted the mainchain is. The form of a helix can be described by parameters such as the number of steps (amino acids) it takes to complete a turn (a 360o rotation around the long axis of the helix), and how far you travel along the helix axis in one complete turn. Helices can also be left-handed or right-handed. For proteins composed of L-amino acids, helices are almost always right-handed (a notable exception is the type I poly-proline helix). Although several types of helix form are possible, two regular helices are very common in proteins: the α-helix and the 310-helix.

==The α-helix==

α-helices are the most common type of regular helix found in proteins. They are characterized by the following helix parameters:
::Dihedral angles: Φ ~ -60o, φ ~ -45o
::Repeat (number of residues per turn) = 3.6
::Rise (translation along axis per amino acid residue) = 1.5 Angstroms (0.15 nm)
::Twist (rotation around axis per amino acid residue) = 100o (= 360o/repeat)
::Pitch (translation along axis per turn) = 5.4 Angstroms (= 0.54 nm = Repeat x Rise)

The helix shown below is a 19 amino acid chain in α-helical conformation.
<Structure load='Tut_alpha_helix.pdb' size='500' frame='true' align='left' caption='' scene='User:Robert_Dutnall/Sandbox_1_alpha_helix/A_helix_load/1'/>

All the atoms are shown in this initial orientation (C = green; N = blue; O = red; S = yellow; H = white). The helix axis runs vertically, approximately parallel to the plane of the screen.

<scene name='User:Robert_Dutnall/Sandbox_1_alpha_helix/A_helix_mainchain/3'>Click here</scene> to show only the polypeptide mainchain (NH, Cα, and C=O).

Identify the N- and C-termini. <scene name='User:Robert_Dutnall/Sandbox_1_alpha_helix/A_helix_mainchain_label/4'>Click here to see if you were correct.</scene>

<scene name='User:Robert_Dutnall/Sandbox_1_alpha_helix/A_helix_mainchain_label_ribbon/3'>Click here to add a ribbon that will help show the path of the mainchain. </scene> You should be able to see that it is helical with a right-handed twist (you rotate to the right as you move along the helix axis).

Click the "toggle spin" button in the box to stop the structure from rotating. Now use your mouse to rotate the structure to look down the helix axis. If you have any problems with finding this view, <scene name='User:Robert_Dutnall/Sandbox_1_alpha_helix/A_helix_mainchain_label_axis/3'>click here </scene>to zoom in and look down the helix axis from the N-terminal end.

<scene name='User:Robert_Dutnall/Sandbox_1_alpha_helix/A_helix_mainchain_label/4'>Click here to zoom out again.</scene> Look at the structure carefully and identify the mainchain NH and C=O groups. What is the orientation of these groups with respect to the helix axis?

<scene name='User:Robert_Dutnall/Sandbox_1_alpha_helix/A_helix_mainchain_label_hbonds/10'>Click here to zoom in a little and add hydrogen bonds for the mainchain (dashed lines).</scene> The hydrogen bonds connect backbone NH groups and C=O groups. The N-H group is the hydrogen bond donor, the oxygen in the C=O group is the acceptor (N-H--->O=C). Each hydrogen bond is approximately 3.0 Angstroms (0.3 nm) in length (measured between the N and the O). These hydrogen bonds connect amino acids that are spaced 4 residues apart in the primary sequence. The NH group is from amino acid X and the O is from amino acid X-4 (where X is the number of the amino acid in the sequence).

<scene name='User:Robert_Dutnall/Sandbox_1_alpha_helix/A_helix_mainchain_label_hbonds/9'>Click here to zoom out again.</scene> You should be able to see that all of the mainchain NH and C=O groups are involved in hydrogen bonds. This is possible because 1) all the mainchain NH groups and C=O groups are parallel to the helix axis, 2) all the NH groups point toward the N-terminus of the helix, and 3) all the C=O groups point toward the C-terminus. Only the NH groups in the first (N-terminal) turn, and the C=O groups in the last (C-terminal) turn of the helix do not have hydrogen bonding partners. However, if this helix were part of a larger protein, these groups would participate in hydrogen bonds with other parts of the protein. This is called 'helix capping' and the other groups involved are typically from amino acid side chains (that are called 'helix capping residues').

<scene name='User:Robert_Dutnall/Sandbox_1_alpha_helix/A_helix_sidechains/3'>Click here to show the side chains again.</scene> The atoms of each amino side chain have been colored light blue to show them more clearly. <scene name='User:Robert_Dutnall/Sandbox_1_alpha_helix/A_helix_sidechains_axis/1'>Click here to change the view to look down the helix axis.</scene>

What is the general orientation of the side chains with respect to the helix axis? You should observe that each side chain points away from the helix axis, but points down toward the N-terminus of the helix (this is clearer if you only show the first bond of each side chain: <scene name='User:Robert_Dutnall/Sandbox_1_alpha_helix/A_helix_sidechains_cropped/1'>click here</scene> or <scene name='User:Robert_Dutnall/Sandbox_1_alpha_helix/A_helix_sidechains_cropped/2'>click here</scene>).

==The 310-helix==

310-helices are also found in proteins but are less common than α-helices. They are characterized by the following helix parameters:
::Dihedral angles: Φ ~ -49o, φ ~ -26o
::Repeat (number of residues per turn) = 3.0
::Rise (translation along axis per amino acid residue) = 2.0 Angstroms (0.2 nm)
::Twist (rotation around axis per amino acid residue) = 120o (= 360o/repeat)
::Pitch (translation along axis per turn) = 6.0 Angstroms (= 0.6 nm = Repeat x Rise)

The helix shown below is a 19 amino acid chain in 310-helical conformation.
<Structure load='Tut_3-10_helix.pdb' size='500' frame='true' align='left' caption='' scene='User:Robert_Dutnall/Sandbox_1_alpha_helix/310_helix_load/4'/>

All the atoms are shown in this initial orientation (C = green; N = blue; O = red; S = yellow; H = white). The helix axis runs vertically, approximately parallel to the plane of the screen.

<scene name='User:Robert_Dutnall/Sandbox_1_alpha_helix/310_helix_mainchain/2'>Click here</scene> to show only the polypeptide mainchain (NH, Cα, and C=O). The N- and C-termini are labeled.

<scene name='User:Robert_Dutnall/Sandbox_1_alpha_helix/310_helix_mainchain_ribbon/2'>Click here to add a ribbon that will help show the path of the mainchain. </scene> You should be able to see that just like the α-helix, it is helical with a right-handed twist, and again, all the mainchain NH groups point toward the N-terminus, and all the mainchain C=O groups point toward the C-terminus.

The difference between an α-helix and a 310-helix lies in the helix parameters. A 310-helix is more tightly twisted so that the mainchain completes one turn every 3 amino acids (instead of 3.6 for the α-helix). This also results in a larger rise and pitch so that the 310-helix is longer than an α-helix (of the same number of residues).

<scene name='User:Robert_Dutnall/Sandbox_1_alpha_helix/310_helix_mainchain_axis/1'>Click here </scene>to zoom in and look down the helix axis from the N-terminal end. You'll be able to see the triangular shape of the mainchain.

<scene name='User:Robert_Dutnall/Sandbox_1_alpha_helix/310_helix_mainchain_hbonds/1'>Click here to zoom out again and display hydrogen bonds for the mainchain.</scene> Once again, all of the mainchain NH and C=O groups are involved in hydrogen bonds. However, now the hydrogen bonds connect amino acids that are spaced 3 residues apart in the primary sequence. The NH group is from amino acid X and the O is from amino acid X-3 (where X is the number of the amino acid in the sequence). <scene name='User:Robert_Dutnall/Sandbox_1_alpha_helix/310_helix_mainchain_hbonds/2'>Click here</scene> to zoom in and you should be able to see this more clearly.

<scene name='User:Robert_Dutnall/Sandbox_1_alpha_helix/310_helix_sidechains/1'>Click here to zoom out and show the side chains again.</scene> The atoms of each amino side chain have been colored light blue to show them more clearly. <scene name='User:Robert_Dutnall/Sandbox_1_alpha_helix/310_helix_sidechains_axis/2'>Click here to change the view to look down the helix axis.</scene>

As for the α-helix, each side chain points away from the helix axis, and points down toward the N-terminus of the helix. However, because the 310-helix repeat parameter is an integer (= 3.0), the side chains are spaced 120o apart and form 3 distinct sides to the helix. You'll see this more clearly if the side chains are colored in groups to show this (residues 1,4,7,10 etc are blue; residues 2,5,8,11 etc are purple; residues 3,6,9,12 etc are yellow): <scene name='User:Robert_Dutnall/Sandbox_1_alpha_helix/310_helix_sidechains_tricolor/1'>click here to look from the side</scene> or <scene name='User:Robert_Dutnall/Sandbox_1_alpha_helix/310_helix_sidechains_tricol_ax/1'>click here to view down the helix axis</scene>.

= =
[[User:Robert Dutnall/Sandbox_1_sheets|Click here to go on to part 2 of this tutorial.]]

User:Robert Dutnall/Sandbox 1 sheets

2011-08-29T18:01:09Z

Robert Dutnall:

== Biochemistry Tutorial #2 - Secondary Structure ==

Part Two

=β-strands and β-sheets=

The second major secondary structure element is the β-sheet. β-sheets are composed of two or more segments of polypeptide mainchain in β-strand conformation. In a β-strand, the polypeptide mainchain is in a mostly extended conformation. As their name implies, β-sheets are relatively flat, planar-like structures made up of β-strands arranged side-by-side. They come in three flavors: parallel, anti-parallel and mixed, which differ in terms of the orientation of each component strand (with respect to the direction of the mainchain from N-terminus to C-terminus).

Note that the mainchain of a β-strand is not perfectly fully extended (Φ ≠ φ ≠ 180o) and that the mainchain actually slowly twists (this is more obvious if you look at a long segment of β-strand). Thus β-sheets are not completely flat and also exhibit some twisting (this is also more obvious if you look at sheets made of many β-strands).

==Parallel β-sheet==

Parallel β-sheets are composed of β-strands that all point in the same direction. Each β-strand has mainchain dihedral angles as follows: Φ ~ -120o, φ ~ +105o.

The sheet shown below is composed of three strands in parallel orientation. All the atoms are shown (C = green; N = blue; O = red; S = yellow; H = white).
<Structure load='Tut_parallel_bsheet.pdb' size='500' frame='true' align='left' caption='' scene='User:Robert_Dutnall/Sandbox_1_sheets/Parallel_load/2'/>

<scene name='User:Robert_Dutnall/Sandbox_1_sheets/Parallel_mainchain/2'>Click here</scene> to show only the polypeptide mainchain (NH, Cα, and C=O).

Identify the N- and C-termini of each strand. <scene name='User:Robert_Dutnall/Sandbox_1_sheets/Parallel_mainchain_labels/6'>Click here to see if you were correct.</scene>

As the structure rotates you should be able to see the extended nature of each strand and the parallel orientation of the three strands.

<scene name='User:Robert_Dutnall/Sandbox_1_sheets/Parallel_mainchain_labels_face/2'>Click here</scene> to stop the structure spinning and view the sheet from roughly perpendicular to its flat plane, with each strand running left-to-right (N- to C-terminus).

<scene name='User:Robert_Dutnall/Sandbox_1_sheets/Parallel_mainchain_labels_side/2'>Click here</scene> to stop the structure spinning and view the sheet from roughly edge-on to its flat plane.

<scene name='User:Robert_Dutnall/Sandbox_1_sheets/Parallel_mainchain_labels/6'>Click here to start the structure spinning again.</scene> Look at the structure carefully and identify the mainchain NH and C=O groups. What is the orientation of these groups with respect to the long axis of each strand? What the orientation of these groups with respect to the flat plane of the sheet?

<scene name='User:Robert_Dutnall/Sandbox_1_sheets/Parallel_mainchain_labels_hb/5'>Click here to add hydrogen bonds for the mainchain (dashed lines).</scene> The hydrogen bonds connect backbone NH groups and C=O groups. The N-H group is the hydrogen bond donor, the oxygen in the C=O group is the acceptor (N-H--->O=C). Each hydrogen bond is approximately 3.0 Angstroms (0.3 nm) in length (measured between the N and the O).

You should be able to see that the mainchain NH and C=O groups are involved in hydrogen bonds. In each strand the mainchain NH and C=O groups point to opposite sides of the mainchain (because of the almost fully extended conformation). The strands line up in the sheet so that the NH and C=O groups are parallel to plane of the sheet and lie opposite each other in pairs. This means that hydrogen bonds can be made between the strands of the sheet. <scene name='User:Robert_Dutnall/Sandbox_1_sheets/Parallel_mainchain_labels_hb_z/5'>Click here to zoom in to show some of the hydrogen bonds more clearly.</scene>

<scene name='User:Robert_Dutnall/Sandbox_1_sheets/Parallel_mainchain_labels_hb/5'>Click here to zoom out again.</scene> You should also notice that all of the NH and C=O groups that lie between strands are involved in hydrogen bonds. Only the groups on the edges of the sheet do not have hydrogen bond partners. However, as with helix capping, if this sheet were part of a larger protein, other residues would supply groups to hydrogen bond to most if not all of these.

<scene name='User:Robert_Dutnall/Sandbox_1_sheets/Parallel_sidechains/2'>Click here to show the side chains again.</scene> You are looking roughly edge-on to the flat plane of the sheet and the atoms of each amino side chain have been colored light blue to show them more clearly.

What is the general orientation of the side chains with respect to each strand and the sheet? You should observe that the side chains are approximately perpendicular to the flat plane of the sheet. Along each strand, the side chains alternate direction. You can see this more clearly if we color the side chains in one strand alternately. <scene name='User:Robert_Dutnall/Sandbox_1_sheets/Parallel_strand_alt/3'>Click here</scene> to freeze the view and color the side chains along one strand blue-purple-blue-purple...etc.

If we apply this to all the strands (<scene name='User:Robert_Dutnall/Sandbox_1_sheets/Parallel_sidechains_alt/2'>click here</scene>) you can see that all the sidechains above the plane of the sheet are purple, and all those below are blue.

==Anti-Parallel β-sheet==

Anti-parallel β-sheets are composed of β-strands that alternate in direction. Each β-strand has mainchain dihedral angles as follows: Φ ~ -150o, φ ~ +135o.

The sheet shown below is composed of three strands in anti-parallel orientation. All the atoms are shown (C = green; N = blue; O = red; S = yellow; H = white).
<Structure load='Tut_antiparallel_bsheet.pdb' size='500' frame='true' align='left' caption='' scene='User:Robert_Dutnall/Sandbox_1_sheets/Antiparallel_load/3'/>

<scene name='User:Robert_Dutnall/Sandbox_1_sheets/Antiparallel_mainchain/3'>Click here</scene> to show only the polypeptide mainchain of each strand (NH, Cα, and C=O).

Identify the N- and C-termini of each strand. <scene name='User:Robert_Dutnall/Sandbox_1_sheets/Antiparallel_mainchain_labels/1'>Click here to see if you were correct.</scene>

As the structure rotates you should be able to see the extended nature of each strand and the parallel orientation of the three strands.

<scene name='User:Robert_Dutnall/Sandbox_1_sheets/Antipara_mainchain_labels_face/1'>Click here</scene> to stop the structure spinning and view the sheet from roughly perpendicular to its flat plane.

<scene name='User:Robert_Dutnall/Sandbox_1_sheets/Antipara_mainchain_labels_side/1'>Click here</scene> to stop the structure spinning and view the sheet from roughly edge-on to its flat plane.

<scene name='User:Robert_Dutnall/Sandbox_1_sheets/Antiparallel_mainchain_labels/1'>Click here to start the structure spinning again.</scene> Look at the structure carefully and identify the mainchain NH and C=O groups. In each strand the mainchain NH and C=O groups point to opposite sides of the mainchain. The strands line up in the sheet so that these NH and C=O groups are parallel to plane of the sheet and lie opposite each other so that they can make hydrogen bonds.

<scene name='User:Robert_Dutnall/Sandbox_1_sheets/Antipara_mainchain_hbonds/1'>Click here to add hydrogen bonds for the mainchain (dashed lines).</scene> The hydrogen bonds connect backbone NH groups and C=O groups. The N-H group is the hydrogen bond donor, the oxygen in the C=O group is the acceptor (N-H--->O=C). Each hydrogen bond is approximately 3.0 Angstroms (0.3 nm) in length (measured between the N and the O).

You should be able to see that the mainchain NH and C=O groups are involved in hydrogen bonds between the strands of the sheet. <scene name='User:Robert_Dutnall/Sandbox_1_sheets/Antipara_mainchain_hbonds_z/1'>Click here to zoom in to show some of the hydrogen bonds more clearly.</scene>

<scene name='User:Robert_Dutnall/Sandbox_1_sheets/Antipara_mainchain_hbonds/1'>Click here to zoom out again.</scene> You should notice that all of the NH and C=O groups that lie between strands are involved in hydrogen bonds. Only the groups on the edges of the sheet do not have hydrogen bond partners, but if this sheet were part of a larger protein, other residues would supply groups to hydrogen bond to most if not all of these.

Two of the strands in this sheet are connected by a β-turn. <scene name='User:Robert_Dutnall/Sandbox_1_sheets/Antipara_mainchain_turn/2'>Click here</scene> to show the β-turn. The carbon atoms of the amino acids that define the turn have been colored dark orange. The turn allows a segment of polypeptide to reverse direction in a short distance. In this case it also allows two strands to interact in an antiparallel fashion. <scene name='User:Robert_Dutnall/Sandbox_1_sheets/Antipara_mainchain_turn_zoom/3'>Click here to zoom in on the turn and reorient it to show more clearly.</scene> Is this a Type I or Type II β-turn?

<scene name='User:Robert_Dutnall/Sandbox_1_sheets/Antipara_mainchain_sidechains/1'>Click here to zoom out again.</scene> In this view, some of the residues at the turn have been omitted and you are looking roughly edge-on to the flat plane of the sheet. Sidechains have been added and the atoms of each amino side chain have been colored blue or purple in an alternating fashion.

The side chains are approximately perpendicular to the flat plane of the sheet. Along each strand, the side chains alternate direction (above the plane, below the plane, above the plane...) so you should be able to see that all the sidechains above the plane of the sheet are purple, and all those below are blue.

= =
[[User:Robert Dutnall/Sandbox_1_alpha_helix|Click here to go on to back to the first part of this tutorial.]]

File:Tut antiparallel bsheet2.pdb

2011-08-29T16:18:59Z

Robert Dutnall:

== Licensing ==
{{self|cc-by-sa-3.0}}

File:Tut antiparallel bsheet.pdb

2011-08-29T16:16:17Z

Robert Dutnall: uploaded a new version of "Image:Tut antiparallel bsheet.pdb"

== Licensing ==
{{self|cc-by-sa-3.0}}

User:Robert Dutnall/Sandbox 1 sheets

2011-08-28T22:12:03Z

Robert Dutnall:

== Biochemistry Tutorial #2 - Secondary Structure ==

Part Two

=β-strands and β-sheets=

The second major secondary structure element is the β-sheet. β-sheets are composed of two or more segments of polypeptide mainchain in β-strand conformation. In a β-strand, the polypeptide mainchain is in a mostly extended conformation. As their name implies, β-sheets are relatively flat, planar-like structures made up of β-strands arranged side-by-side. They come in three flavors: parallel, anti-parallel and mixed, which differ in terms of the orientation of each component strand (with respect to the direction of the mainchain from N-terminus to C-terminus).

Note that the mainchain of a β-strand is not perfectly fully extended (Φ ≠ φ ≠ 180o) and that the mainchain actually slowly twists (this is more obvious if you look at a long segment of β-strand). Thus β-sheets are not completely flat and also exhibit some twisting (this is also more obvious if you look at sheets made of many β-strands).

==Parallel β-sheet==

Parallel β-sheets are composed of β-strands that all point in the same direction. Each β-strand has mainchain dihedral angles as follows: Φ ~ -120o, φ ~ +105o.

The sheet shown below is composed of three strands in parallel orientation. All the atoms are shown (C = green; N = blue; O = red; S = yellow; H = white).
<Structure load='Tut_parallel_bsheet.pdb' size='500' frame='true' align='left' caption='' scene='User:Robert_Dutnall/Sandbox_1_sheets/Parallel_load/2'/>

<scene name='User:Robert_Dutnall/Sandbox_1_sheets/Parallel_mainchain/2'>Click here</scene> to show only the polypeptide mainchain (NH, Cα, and C=O).

Identify the N- and C-termini of each strand. <scene name='User:Robert_Dutnall/Sandbox_1_sheets/Parallel_mainchain_labels/6'>Click here to see if you were correct.</scene>

As the structure rotates you should be able to see the extended nature of each strand and the parallel orientation of the three strands.

<scene name='User:Robert_Dutnall/Sandbox_1_sheets/Parallel_mainchain_labels_face/2'>Click here</scene> to stop the structure spinning and view the sheet from roughly perpendicular to its flat plane, with each strand running left-to-right (N- to C-terminus).

<scene name='User:Robert_Dutnall/Sandbox_1_sheets/Parallel_mainchain_labels_side/2'>Click here</scene> to stop the structure spinning and view the sheet from roughly edge-on to its flat plane.

<scene name='User:Robert_Dutnall/Sandbox_1_sheets/Parallel_mainchain_labels/6'>Click here to start the structure spinning again.</scene> Look at the structure carefully and identify the mainchain NH and C=O groups. What is the orientation of these groups with respect to the long axis of each strand? What the orientation of these groups with respect to the flat plane of the sheet?

<scene name='User:Robert_Dutnall/Sandbox_1_sheets/Parallel_mainchain_labels_hb/5'>Click here to add hydrogen bonds for the mainchain (dashed lines).</scene> The hydrogen bonds connect backbone NH groups and C=O groups. The N-H group is the hydrogen bond donor, the oxygen in the C=O group is the acceptor (N-H--->O=C). Each hydrogen bond is approximately 3.0 Angstroms (0.3 nm) in length (measured between the N and the O).

You should be able to see that the mainchain NH and C=O groups are involved in hydrogen bonds. In each strand the mainchain NH and C=O groups point to opposite sides of the mainchain (because of the almost fully extended conformation). The strands line up in the sheet so that these NH and C=O groups are parallel to plane of the sheet. This means that hydrogen bonds can be made between the strands of the sheet. <scene name='User:Robert_Dutnall/Sandbox_1_sheets/Parallel_mainchain_labels_hb_z/5'>Click here to zoom in to show some of the hydrogen bonds more clearly.</scene>

<scene name='User:Robert_Dutnall/Sandbox_1_sheets/Parallel_mainchain_labels_hb/5'>Click here to zoom out again.</scene> You should also notice that all of the NH and C=O groups that lie between strands are involved in hydrogen bonds. Only the groups on the edges of the sheet do not have hydrogen bond partners. However, as with helix capping, if this sheet were part of a larger protein, other residues would supply groups to hydrogen bond to most if not all of these.

<scene name='User:Robert_Dutnall/Sandbox_1_sheets/Parallel_sidechains/2'>Click here to show the side chains again.</scene> You are looking roughly edge-on to the flat plane of the sheet and the atoms of each amino side chain have been colored light blue to show them more clearly.

What is the general orientation of the side chains with respect to each strand and the sheet? You should observe that the side chains are approximately perpendicular to the flat plane of the sheet. Along each strand, the side chains alternate direction. You can see this more clearly if we color the side chains in one strand alternately. <scene name='User:Robert_Dutnall/Sandbox_1_sheets/Parallel_strand_alt/3'>Click here</scene> to freeze the view and color the side chains along one strand blue-purple-blue-purple...etc.

If we apply this to all the strands (<scene name='User:Robert_Dutnall/Sandbox_1_sheets/Parallel_sidechains_alt/2'>click here</scene>) you can see that all the sidechains above the plane of the sheet are purple, and all those below are blue.

==Anti-Parallel β-sheet==

Anti-parallel β-sheets are composed of β-strands that alternate in direction. Each β-strand has mainchain dihedral angles as follows: Φ ~ -120o, φ ~ +105o.

The sheet shown below is composed of three strands in anti-parallel orientation. All the atoms are shown (C = green; N = blue; O = red; S = yellow; H = white).
<Structure load='Tut_antiparallel_bsheet.pdb' size='500' frame='true' align='left' caption='' scene='User:Robert_Dutnall/Sandbox_1_sheets/Antiparallel_load/2'/>

<scene name='User:Robert_Dutnall/Sandbox_1_sheets/Parallel_mainchain/2'>Click here</scene> to show only the polypeptide mainchain (NH, Cα, and C=O).

Identify the N- and C-termini of each strand. <scene name='User:Robert_Dutnall/Sandbox_1_sheets/Parallel_mainchain_labels/6'>Click here to see if you were correct.</scene>

As the structure rotates you should be able to see the extended nature of each strand and the parallel orientation of the three strands.

<scene name='User:Robert_Dutnall/Sandbox_1_sheets/Parallel_mainchain_labels_face/2'>Click here</scene> to stop the structure spinning and view the sheet from roughly perpendicular to its flat plane, with each strand running left-to-right (N- to C-terminus).

<scene name='User:Robert_Dutnall/Sandbox_1_sheets/Parallel_mainchain_labels_side/2'>Click here</scene> to stop the structure spinning and view the sheet from roughly edge-on to its flat plane.

<scene name='User:Robert_Dutnall/Sandbox_1_sheets/Parallel_mainchain_labels/6'>Click here to start the structure spinning again.</scene> Look at the structure carefully and identify the mainchain NH and C=O groups. What is the orientation of these groups with respect to the long axis of each strand? What the orientation of these groups with respect to the flat plane of the sheet?

<scene name='User:Robert_Dutnall/Sandbox_1_sheets/Parallel_mainchain_labels_hb/5'>Click here to add hydrogen bonds for the mainchain (dashed lines).</scene> The hydrogen bonds connect backbone NH groups and C=O groups. The N-H group is the hydrogen bond donor, the oxygen in the C=O group is the acceptor (N-H--->O=C). Each hydrogen bond is approximately 3.0 Angstroms (0.3 nm) in length (measured between the N and the O).

You should be able to see that the mainchain NH and C=O groups are involved in hydrogen bonds. In each strand the mainchain NH and C=O groups point to opposite sides of the mainchain (because of the almost fully extended conformation). The strands line up in the sheet so that these NH and C=O groups are parallel to plane of the sheet. This means that hydrogen bonds can be made between the strands of the sheet. <scene name='User:Robert_Dutnall/Sandbox_1_sheets/Parallel_mainchain_labels_hb_z/5'>Click here to zoom in to show some of the hydrogen bonds more clearly.</scene>

<scene name='User:Robert_Dutnall/Sandbox_1_sheets/Parallel_mainchain_labels_hb/5'>Click here to zoom out again.</scene> You should also notice that all of the NH and C=O groups that lie between strands are involved in hydrogen bonds. Only the groups on the edges of the sheet do not have hydrogen bond partners. However, as with helix capping, if this sheet were part of a larger protein, other residues would supply groups to hydrogen bond to most if not all of these.

<scene name='User:Robert_Dutnall/Sandbox_1_sheets/Parallel_sidechains/2'>Click here to show the side chains again.</scene> You are looking roughly edge-on to the flat plane of the sheet and the atoms of each amino side chain have been colored light blue to show them more clearly.

What is the general orientation of the side chains with respect to each strand and the sheet? You should observe that the side chains are approximately perpendicular to the flat plane of the sheet. Along each strand, the side chains alternate direction. You can see this more clearly if we color the side chains in one strand alternately. <scene name='User:Robert_Dutnall/Sandbox_1_sheets/Parallel_strand_alt/3'>Click here</scene> to freeze the view and color the side chains along one strand blue-purple-blue-purple...etc.

If we apply this to all the strands (<scene name='User:Robert_Dutnall/Sandbox_1_sheets/Parallel_sidechains_alt/2'>click here</scene>) you can see that all the sidechains above the plane of the sheet are purple, and all those below are blue.

= =
[[User:Robert Dutnall/Sandbox_1_alpha_helix|Click here to go on to back to the first part of this tutorial.]]

File:Tut antiparallel bsheet.pdb

2011-08-28T22:09:15Z

Robert Dutnall:

== Licensing ==
{{self|cc-by-sa-3.0}}

User:Robert Dutnall/Sandbox 1 sheets

2011-08-28T22:08:56Z

Robert Dutnall:

== Biochemistry Tutorial #2 - Secondary Structure ==

Part Two

=β-strands and β-sheets=

The second major secondary structure element is the β-sheet. β-sheets are composed of two or more segments of polypeptide mainchain in β-strand conformation. In a β-strand, the polypeptide mainchain is in a mostly extended conformation. As their name implies, β-sheets are relatively flat, planar-like structures made up of β-strands arranged side-by-side. They come in three flavors: parallel, anti-parallel and mixed, which differ in terms of the orientation of each component strand (with respect to the direction of the mainchain from N-terminus to C-terminus).

Note that the mainchain of a β-strand is not perfectly fully extended (Φ ≠ φ ≠ 180o) and that the mainchain actually slowly twists (this is more obvious if you look at a long segment of β-strand). Thus β-sheets are not completely flat and also exhibit some twisting (this is also more obvious if you look at sheets made of many β-strands).

==Parallel β-sheet==

Parallel β-sheets are composed of β-strands that all point in the same direction. Each β-strand has mainchain dihedral angles as follows: Φ ~ -120o, φ ~ +105o.

The sheet shown below is composed of three strands in parallel orientation. All the atoms are shown (C = green; N = blue; O = red; S = yellow; H = white).
<Structure load='Tut_parallel_bsheet.pdb' size='500' frame='true' align='left' caption='' scene='User:Robert_Dutnall/Sandbox_1_sheets/Parallel_load/2'/>

<scene name='User:Robert_Dutnall/Sandbox_1_sheets/Parallel_mainchain/2'>Click here</scene> to show only the polypeptide mainchain (NH, Cα, and C=O).

Identify the N- and C-termini of each strand. <scene name='User:Robert_Dutnall/Sandbox_1_sheets/Parallel_mainchain_labels/6'>Click here to see if you were correct.</scene>

As the structure rotates you should be able to see the extended nature of each strand and the parallel orientation of the three strands.

<scene name='User:Robert_Dutnall/Sandbox_1_sheets/Parallel_mainchain_labels_face/2'>Click here</scene> to stop the structure spinning and view the sheet from roughly perpendicular to its flat plane, with each strand running left-to-right (N- to C-terminus).

<scene name='User:Robert_Dutnall/Sandbox_1_sheets/Parallel_mainchain_labels_side/2'>Click here</scene> to stop the structure spinning and view the sheet from roughly edge-on to its flat plane.

<scene name='User:Robert_Dutnall/Sandbox_1_sheets/Parallel_mainchain_labels/6'>Click here to start the structure spinning again.</scene> Look at the structure carefully and identify the mainchain NH and C=O groups. What is the orientation of these groups with respect to the long axis of each strand? What the orientation of these groups with respect to the flat plane of the sheet?

<scene name='User:Robert_Dutnall/Sandbox_1_sheets/Parallel_mainchain_labels_hb/5'>Click here to add hydrogen bonds for the mainchain (dashed lines).</scene> The hydrogen bonds connect backbone NH groups and C=O groups. The N-H group is the hydrogen bond donor, the oxygen in the C=O group is the acceptor (N-H--->O=C). Each hydrogen bond is approximately 3.0 Angstroms (0.3 nm) in length (measured between the N and the O).

You should be able to see that the mainchain NH and C=O groups are involved in hydrogen bonds. In each strand the mainchain NH and C=O groups point to opposite sides of the mainchain (because of the almost fully extended conformation). The strands line up in the sheet so that these NH and C=O groups are parallel to plane of the sheet. This means that hydrogen bonds can be made between the strands of the sheet. <scene name='User:Robert_Dutnall/Sandbox_1_sheets/Parallel_mainchain_labels_hb_z/5'>Click here to zoom in to show some of the hydrogen bonds more clearly.</scene>

<scene name='User:Robert_Dutnall/Sandbox_1_sheets/Parallel_mainchain_labels_hb/5'>Click here to zoom out again.</scene> You should also notice that all of the NH and C=O groups that lie between strands are involved in hydrogen bonds. Only the groups on the edges of the sheet do not have hydrogen bond partners. However, as with helix capping, if this sheet were part of a larger protein, other residues would supply groups to hydrogen bond to most if not all of these.

<scene name='User:Robert_Dutnall/Sandbox_1_sheets/Parallel_sidechains/2'>Click here to show the side chains again.</scene> You are looking roughly edge-on to the flat plane of the sheet and the atoms of each amino side chain have been colored light blue to show them more clearly.

What is the general orientation of the side chains with respect to each strand and the sheet? You should observe that the side chains are approximately perpendicular to the flat plane of the sheet. Along each strand, the side chains alternate direction. You can see this more clearly if we color the side chains in one strand alternately. <scene name='User:Robert_Dutnall/Sandbox_1_sheets/Parallel_strand_alt/3'>Click here</scene> to freeze the view and color the side chains along one strand blue-purple-blue-purple...etc.

If we apply this to all the strands (<scene name='User:Robert_Dutnall/Sandbox_1_sheets/Parallel_sidechains_alt/2'>click here</scene>) you can see that all the sidechains above the plane of the sheet are purple, and all those below are blue.

==Anti-Parallel β-sheet==

Anti-parallel β-sheets are composed of β-strands that alternate in direction. Each β-strand has mainchain dihedral angles as follows: Φ ~ -120o, φ ~ +105o.

The sheet shown below is composed of three strands in anti-parallel orientation. All the atoms are shown (C = green; N = blue; O = red; S = yellow; H = white).
<Structure load='Tut_parallel_bsheet.pdb' size='500' frame='true' align='left' caption='' scene='User:Robert_Dutnall/Sandbox_1_sheets/Parallel_load/2'/>

<scene name='User:Robert_Dutnall/Sandbox_1_sheets/Parallel_mainchain/2'>Click here</scene> to show only the polypeptide mainchain (NH, Cα, and C=O).

Identify the N- and C-termini of each strand. <scene name='User:Robert_Dutnall/Sandbox_1_sheets/Parallel_mainchain_labels/6'>Click here to see if you were correct.</scene>

As the structure rotates you should be able to see the extended nature of each strand and the parallel orientation of the three strands.

<scene name='User:Robert_Dutnall/Sandbox_1_sheets/Parallel_mainchain_labels_face/2'>Click here</scene> to stop the structure spinning and view the sheet from roughly perpendicular to its flat plane, with each strand running left-to-right (N- to C-terminus).

<scene name='User:Robert_Dutnall/Sandbox_1_sheets/Parallel_mainchain_labels_side/2'>Click here</scene> to stop the structure spinning and view the sheet from roughly edge-on to its flat plane.

<scene name='User:Robert_Dutnall/Sandbox_1_sheets/Parallel_mainchain_labels/6'>Click here to start the structure spinning again.</scene> Look at the structure carefully and identify the mainchain NH and C=O groups. What is the orientation of these groups with respect to the long axis of each strand? What the orientation of these groups with respect to the flat plane of the sheet?

<scene name='User:Robert_Dutnall/Sandbox_1_sheets/Parallel_mainchain_labels_hb/5'>Click here to add hydrogen bonds for the mainchain (dashed lines).</scene> The hydrogen bonds connect backbone NH groups and C=O groups. The N-H group is the hydrogen bond donor, the oxygen in the C=O group is the acceptor (N-H--->O=C). Each hydrogen bond is approximately 3.0 Angstroms (0.3 nm) in length (measured between the N and the O).

You should be able to see that the mainchain NH and C=O groups are involved in hydrogen bonds. In each strand the mainchain NH and C=O groups point to opposite sides of the mainchain (because of the almost fully extended conformation). The strands line up in the sheet so that these NH and C=O groups are parallel to plane of the sheet. This means that hydrogen bonds can be made between the strands of the sheet. <scene name='User:Robert_Dutnall/Sandbox_1_sheets/Parallel_mainchain_labels_hb_z/5'>Click here to zoom in to show some of the hydrogen bonds more clearly.</scene>

<scene name='User:Robert_Dutnall/Sandbox_1_sheets/Parallel_mainchain_labels_hb/5'>Click here to zoom out again.</scene> You should also notice that all of the NH and C=O groups that lie between strands are involved in hydrogen bonds. Only the groups on the edges of the sheet do not have hydrogen bond partners. However, as with helix capping, if this sheet were part of a larger protein, other residues would supply groups to hydrogen bond to most if not all of these.

<scene name='User:Robert_Dutnall/Sandbox_1_sheets/Parallel_sidechains/2'>Click here to show the side chains again.</scene> You are looking roughly edge-on to the flat plane of the sheet and the atoms of each amino side chain have been colored light blue to show them more clearly.

What is the general orientation of the side chains with respect to each strand and the sheet? You should observe that the side chains are approximately perpendicular to the flat plane of the sheet. Along each strand, the side chains alternate direction. You can see this more clearly if we color the side chains in one strand alternately. <scene name='User:Robert_Dutnall/Sandbox_1_sheets/Parallel_strand_alt/3'>Click here</scene> to freeze the view and color the side chains along one strand blue-purple-blue-purple...etc.

If we apply this to all the strands (<scene name='User:Robert_Dutnall/Sandbox_1_sheets/Parallel_sidechains_alt/2'>click here</scene>) you can see that all the sidechains above the plane of the sheet are purple, and all those below are blue.

= =
[[User:Robert Dutnall/Sandbox_1_alpha_helix|Click here to go on to back to the first part of this tutorial.]]

User:Robert Dutnall/Sandbox 1 sheets

2011-08-26T21:39:46Z

Robert Dutnall:

== Biochemistry Tutorial #2 - Secondary Structure ==

Part Two

=β-strands and β-sheets=

The second major secondary structure element is the β-sheet. β-sheets are composed of two or more segments of polypeptide mainchain in β-strand conformation. In a β-strand, the polypeptide mainchain is in a mostly extended conformation. As their name implies, β-sheets are relatively flat, planar-like structures made up of β-strands arranged side-by-side. They come in three flavors: parallel, anti-parallel and mixed, which differ in terms of the orientation of each component strand (with respect to the direction of the mainchain from N-terminus to C-terminus).

Note that the mainchain of a β-strand is not perfectly fully extended (Φ ≠ φ ≠ 180o) and that the mainchain actually slowly twists (this is more obvious if you look at a long segment of β-strand). Thus β-sheets are not completely flat and also exhibit some twisting (this is also more obvious if you look at sheets made of many β-strands).

==Parallel β-sheet==

Parallel β-sheets are composed of β-strand that all point in the same direction. Each β-strand has mainchain dihedral angles as follows: Φ ~ -120o, φ ~ +105o.

The sheet shown below is composed of three strands in parallel orientation.
<Structure load='Tut_parallel_bsheet.pdb' size='500' frame='true' align='left' caption='' scene='User:Robert_Dutnall/Sandbox_1_sheets/Parallel_load/1'/>

All the atoms are shown in this initial orientation (C = green; N = blue; O = red; S = yellow; H = white).

<scene name='User:Robert_Dutnall/Sandbox_1_sheets/Parallel_mainchain/1'>Click here</scene> to show only the polypeptide mainchain (NH, Cα, and C=O).

Identify the N- and C-termini of each strand. <scene name='User:Robert_Dutnall/Sandbox_1_sheets/Parallel_mainchain_labels/5'>Click here to see if you were correct.</scene>

As the structure rotates you should be able to see the extended nature of each strand and the parallel orientation of the three strands.

<scene name='User:Robert_Dutnall/Sandbox_1_sheets/Parallel_mainchain_labels_face/1'>Click here</scene> to stop the structure spinning and view the sheet from roughly perpendicular to its flat plane.
<scene name='User:Robert_Dutnall/Sandbox_1_sheets/Parallel_mainchain_labels_side/1'>Click here</scene> to stop the structure spinning and view the sheet from roughly edge-on to its flat plane.

<scene name='User:Robert_Dutnall/Sandbox_1_sheets/Parallel_mainchain_labels/5'>Click here to start the structure spinning again.</scene> Look at the structure carefully and identify the mainchain NH and C=O groups. What is the orientation of these groups with respect to the long axis of each strand? What the orientation of these groups with respect to the flat plane of the sheet?

<scene name='User:Robert_Dutnall/Sandbox_1_sheets/Parallel_mainchain_labels_hb/4'>Click here to add hydrogen bonds for the mainchain (dashed lines).</scene> The hydrogen bonds connect backbone NH groups and C=O groups. The N-H group is the hydrogen bond donor, the oxygen in the C=O group is the acceptor (N-H--->O=C). Each hydrogen bond is approximately 3.0 Angstroms (0.3 nm) in length (measured between the N and the O).

You should be able to see that the mainchain NH and C=O groups are involved in hydrogen bonds. In each strand the mainchain NH and C=O groups point to opposite sides of the mainchain (because of the almost fully extended conformation). The strands line up in the sheet so that these NH and C=O groups are parallel to plane of the sheet. This means that hydrogen bonds can be made between the strands of the sheet. <scene name='User:Robert_Dutnall/Sandbox_1_sheets/Parallel_mainchain_labels_hb_z/4'>Click here to zoom in to show some of the hydrogen bonds more clearly.</scene>

<scene name='User:Robert_Dutnall/Sandbox_1_sheets/Parallel_mainchain_labels_hb/4'>Click here to zoom out again.</scene>

You should also notice that all of the NH and C=O groups that lie between strands are involved in hydrogen bonds. Only the groups on the edges of the sheet do not have hydrogen bond partners. However, as with helix capping, if this sheet were part of a larger protein, other residues would supply groups to hydrogen bond to most if not all of these.

<scene name='User:Robert_Dutnall/Sandbox_1_sheets/Parallel_sidechains/1'>Click here to show the side chains again.</scene> The atoms of each amino side chain have been colored light blue to show them more clearly.

What is the general orientation of the side chains with respect to each strand and the sheet? You should observe that the side chains are approximately perpendicular to the flat plane of the sheet. Along each strand, the side chains alternate direction. You can see this more clearly if we color the side chains in one strand alternately. <scene name='User:Robert_Dutnall/Sandbox_1_sheets/Parallel_strand_alt/1'>Click here</scene> to color the side chains along one strand blue-purple-blue-purple...etc. If we apply this to all the sheets (<scene name='User:Robert_Dutnall/Sandbox_1_sheets/Parallel_sidechains_alt/1'>click here</scene>) you can see that all the amino acids on one face of the sheet are blue, and on the other are purple.

==The 310-helix==

310-helices are also found in proteins but are less common than α-helices. They are characterized by the following helix parameters:
::Dihedral angles: Φ ~ -49o, φ ~ -26o
::Repeat (number of residues per turn) = 3.0
::Rise (translation along axis per amino acid residue) = 2.0 Angstroms (0.2 nm)
::Twist (rotation around axis per amino acid residue) = 120o (= 360o/repeat)
::Pitch (translation along axis per turn) = 6.0 Angstroms (= 0.6 nm = Repeat x Rise)

The helix shown below is a 19 amino acid chain in 310-helical conformation.
<Structure load='Tut_3-10_helix.pdb' size='500' frame='true' align='left' caption='' scene='User:Robert_Dutnall/Sandbox_1_alpha_helix/310_helix_load/4'/>

All the atoms are shown in this initial orientation (C = green; N = blue; O = red; S = yellow; H = white). The helix axis runs vertically, approximately parallel to the plane of the screen.

<scene name='User:Robert_Dutnall/Sandbox_1_alpha_helix/310_helix_mainchain/2'>Click here</scene> to show only the polypeptide mainchain (NH, Cα, and C=O). The N- and C-termini are labeled.

<scene name='User:Robert_Dutnall/Sandbox_1_alpha_helix/310_helix_mainchain_ribbon/2'>Click here to add a ribbon that will help show the path of the mainchain. </scene> You should be able to see that just like the α-helix, it is helical with a right-handed twist, and again, all the mainchain NH groups point toward the N-terminus, and all the mainchain C=O groups point toward the C-terminus.

The difference between an α-helix and a 310-helix lies in the helix parameters. A 310-helix is more tightly twisted so that the mainchain completes one turn every 3 amino acids (instead of 3.6 for the α-helix). This also results in a larger rise and pitch so that the 310-helix is longer than an α-helix (of the same number of residues).

<scene name='User:Robert_Dutnall/Sandbox_1_alpha_helix/310_helix_mainchain_axis/1'>Click here </scene>to zoom in and look down the helix axis from the N-terminal end. You'll be able to see the triangular shape of the mainchain.

<scene name='User:Robert_Dutnall/Sandbox_1_alpha_helix/310_helix_mainchain_hbonds/1'>Click here to zoom out again and display hydrogen bonds for the mainchain.</scene> Once again, all of the mainchain NH and C=O groups are involved in hydrogen bonds. However, now the hydrogen bonds connect amino acids that are spaced 3 residues apart in the primary sequence. The NH group is from amino acid X and the O is from amino acid X-3 (where X is the number of the amino acid in the sequence). <scene name='User:Robert_Dutnall/Sandbox_1_alpha_helix/310_helix_mainchain_hbonds/2'>Click here</scene> to zoom in and you should be able to see this more clearly.

<scene name='User:Robert_Dutnall/Sandbox_1_alpha_helix/310_helix_sidechains/1'>Click here to zoom out and show the side chains again.</scene> The atoms of each amino side chain have been colored light blue to show them more clearly. <scene name='User:Robert_Dutnall/Sandbox_1_alpha_helix/310_helix_sidechains_axis/2'>Click here to change the view to look down the helix axis.</scene>

As for the α-helix, each side chain points away from the helix axis, and points down toward the N-terminus of the helix. However, because the 310-helix repeat parameter is an integer (= 3.0), the side chains are spaced 120o apart and form 3 distinct sides to the helix. You'll see this more clearly if the side chains are colored in groups to show this (residues 1,4,7,10 etc are blue; residues 2,5,8,11 etc are purple; residues 3,6,9,12 etc are yellow): <scene name='User:Robert_Dutnall/Sandbox_1_alpha_helix/310_helix_sidechains_tricolor/1'>click here to look from the side</scene> or <scene name='User:Robert_Dutnall/Sandbox_1_alpha_helix/310_helix_sidechains_tricol_ax/1'>click here to view down the helix axis</scene>.

= =
[[User:Robert Dutnall/Sandbox_1_alpha_helix|Click here to go on to back to the first part of this tutorial.]]

User:Robert Dutnall/Sandbox 1 sheets

2011-08-26T21:14:36Z

Robert Dutnall:

== Biochemistry Tutorial #2 - Secondary Structure ==

Part Two

=β-strands and β-sheets=

The second major secondary structure element is the β-sheet. β-sheets are composed of two or more segments of polypeptide mainchain in β-strand conformation. In a β-strand, the polypeptide mainchain is in a mostly extended conformation. As their name implies, β-sheets are relatively flat, planar-like structures made up of β-strands arranged side-by-side. They come in three flavors: parallel, anti-parallel and mixed, which differ in terms of the orientation of each component strand (with respect to the direction of the mainchain from N-terminus to C-terminus).

Note that the mainchain of a β-strand is not perfectly fully extended (Φ ≠ φ ≠ 180o) and that the mainchain actually slowly twists (this is more obvious if you look at a long segment of β-strand). Thus β-sheets are not completely flat and also exhibit some twisting (this is also more obvious if you look at sheets made of many β-strands).

==Parallel β-sheet==

Parallel β-sheets are composed of β-strand that all point in the same direction. Each β-strand has mainchain dihedral angles as follows: Φ ~ -120o, φ ~ +105o.

The sheet shown below is composed of three strands in parallel orientation.
<Structure load='Tut_parallel_bsheet.pdb' size='500' frame='true' align='left' caption='' scene='User:Robert_Dutnall/Sandbox_1_sheets/Parallel_load/1'/>

All the atoms are shown in this initial orientation (C = green; N = blue; O = red; S = yellow; H = white).

<scene name='User:Robert_Dutnall/Sandbox_1_sheets/Parallel_mainchain/1'>Click here</scene> to show only the polypeptide mainchain (NH, Cα, and C=O).

Identify the N- and C-termini of each strand. <scene name='User:Robert_Dutnall/Sandbox_1_sheets/Parallel_mainchain_labels/5'>Click here to see if you were correct.</scene>

As the structure rotates you should be able to see the extended nature of each strand and the parallel orientation of the three strands.

<scene name='User:Robert_Dutnall/Sandbox_1_sheets/Parallel_mainchain_labels_face/1'>Click here to stop the structure spinning and view the sheet from roughly perpendicular to its flat plane.</scene>

<scene name='User:Robert_Dutnall/Sandbox_1_sheets/Parallel_mainchain_labels_side/1'>Click here to stop the structure spinning and view the sheet from roughly edge-on to its flat plane.</scene>

<scene name='User:Robert_Dutnall/Sandbox_1_sheets/Parallel_mainchain_labels/5'>Click here to start the structure spinning again.</scene>

Look at the structure carefully and identify the mainchain NH and C=O groups. What is the orientation of these groups with respect to the long axis of each strand? What the orientation of these groups with respect to the flat plane of the sheet?

<scene name='User:Robert_Dutnall/Sandbox_1_sheets/Parallel_mainchain_labels_hb/4'>Click here to add hydrogen bonds for the mainchain (dashed lines).</scene> The hydrogen bonds connect backbone NH groups and C=O groups. The N-H group is the hydrogen bond donor, the oxygen in the C=O group is the acceptor (N-H--->O=C). Each hydrogen bond is approximately 3.0 Angstroms (0.3 nm) in length (measured between the N and the O).

You should be able to see that the mainchain NH and C=O groups are involved in hydrogen bonds. In each strand the mainchain NH and C=O groups point to opposite sides of the mainchain (because of the almost fully extended conformation). The strands line up in the sheet so that these NH and C=O groups are parallel to plane of the sheet. This means that hydrogen bonds can be made between the strands of the sheet. <scene name='User:Robert_Dutnall/Sandbox_1_sheets/Parallel_mainchain_labels_hb_z/4'>Click here to zoom in to show some of the hydrogen bonds more clearly.</scene>

<scene name='User:Robert_Dutnall/Sandbox_1_sheets/Parallel_mainchain_labels_hb/4'>Click here to zoom out again.</scene>

You should also notice that all of the NH and C=O groups that lie between strands are involved in hydrogen bonds. Only the groups on the edges of the sheet do not have hydrogen bond partners. However, as with helix capping, if this sheet were part of a larger protein, other residues would supply groups to hydrogen bond to most if not all of these.

<scene name='User:Robert_Dutnall/Sandbox_1_alpha_helix/A_helix_sidechains/3'>Click here to show the side chains again.</scene> The atoms of each amino side chain have been colored light blue to show them more clearly. <scene name='User:Robert_Dutnall/Sandbox_1_alpha_helix/A_helix_sidechains_axis/1'>Click here to change the view to look down the helix axis.</scene>

What is the general orientation of the side chains with respect to the helix axis? You should observe that each side chain points away from the helix axis, but points down toward the N-terminus of the helix (this is clearer if you only show the first bond of each side chain: <scene name='User:Robert_Dutnall/Sandbox_1_alpha_helix/A_helix_sidechains_cropped/1'>click here</scene> or <scene name='User:Robert_Dutnall/Sandbox_1_alpha_helix/A_helix_sidechains_cropped/2'>click here</scene>).

==The 310-helix==

310-helices are also found in proteins but are less common than α-helices. They are characterized by the following helix parameters:
::Dihedral angles: Φ ~ -49o, φ ~ -26o
::Repeat (number of residues per turn) = 3.0
::Rise (translation along axis per amino acid residue) = 2.0 Angstroms (0.2 nm)
::Twist (rotation around axis per amino acid residue) = 120o (= 360o/repeat)
::Pitch (translation along axis per turn) = 6.0 Angstroms (= 0.6 nm = Repeat x Rise)

The helix shown below is a 19 amino acid chain in 310-helical conformation.
<Structure load='Tut_3-10_helix.pdb' size='500' frame='true' align='left' caption='' scene='User:Robert_Dutnall/Sandbox_1_alpha_helix/310_helix_load/4'/>

All the atoms are shown in this initial orientation (C = green; N = blue; O = red; S = yellow; H = white). The helix axis runs vertically, approximately parallel to the plane of the screen.

<scene name='User:Robert_Dutnall/Sandbox_1_alpha_helix/310_helix_mainchain/2'>Click here</scene> to show only the polypeptide mainchain (NH, Cα, and C=O). The N- and C-termini are labeled.

<scene name='User:Robert_Dutnall/Sandbox_1_alpha_helix/310_helix_mainchain_ribbon/2'>Click here to add a ribbon that will help show the path of the mainchain. </scene> You should be able to see that just like the α-helix, it is helical with a right-handed twist, and again, all the mainchain NH groups point toward the N-terminus, and all the mainchain C=O groups point toward the C-terminus.

The difference between an α-helix and a 310-helix lies in the helix parameters. A 310-helix is more tightly twisted so that the mainchain completes one turn every 3 amino acids (instead of 3.6 for the α-helix). This also results in a larger rise and pitch so that the 310-helix is longer than an α-helix (of the same number of residues).

<scene name='User:Robert_Dutnall/Sandbox_1_alpha_helix/310_helix_mainchain_axis/1'>Click here </scene>to zoom in and look down the helix axis from the N-terminal end. You'll be able to see the triangular shape of the mainchain.

<scene name='User:Robert_Dutnall/Sandbox_1_alpha_helix/310_helix_mainchain_hbonds/1'>Click here to zoom out again and display hydrogen bonds for the mainchain.</scene> Once again, all of the mainchain NH and C=O groups are involved in hydrogen bonds. However, now the hydrogen bonds connect amino acids that are spaced 3 residues apart in the primary sequence. The NH group is from amino acid X and the O is from amino acid X-3 (where X is the number of the amino acid in the sequence). <scene name='User:Robert_Dutnall/Sandbox_1_alpha_helix/310_helix_mainchain_hbonds/2'>Click here</scene> to zoom in and you should be able to see this more clearly.

<scene name='User:Robert_Dutnall/Sandbox_1_alpha_helix/310_helix_sidechains/1'>Click here to zoom out and show the side chains again.</scene> The atoms of each amino side chain have been colored light blue to show them more clearly. <scene name='User:Robert_Dutnall/Sandbox_1_alpha_helix/310_helix_sidechains_axis/2'>Click here to change the view to look down the helix axis.</scene>

As for the α-helix, each side chain points away from the helix axis, and points down toward the N-terminus of the helix. However, because the 310-helix repeat parameter is an integer (= 3.0), the side chains are spaced 120o apart and form 3 distinct sides to the helix. You'll see this more clearly if the side chains are colored in groups to show this (residues 1,4,7,10 etc are blue; residues 2,5,8,11 etc are purple; residues 3,6,9,12 etc are yellow): <scene name='User:Robert_Dutnall/Sandbox_1_alpha_helix/310_helix_sidechains_tricolor/1'>click here to look from the side</scene> or <scene name='User:Robert_Dutnall/Sandbox_1_alpha_helix/310_helix_sidechains_tricol_ax/1'>click here to view down the helix axis</scene>.

= =
[[User:Robert Dutnall/Sandbox_1_alpha_helix|Click here to go on to back to the first part of this tutorial.]]

User:Robert Dutnall/Sandbox 1 sheets

2011-08-26T20:43:31Z

Robert Dutnall:

== Biochemistry Tutorial #2 - Secondary Structure ==

Part Two

=β-strands and β-sheets=

The second major secondary structure element is the β-sheet. β-sheets are composed of two or more segments of polypeptide mainchain in β-strand conformation. In a β-strand, the polypeptide mainchain is in a mostly extended conformation. As their name implies, β-sheets are relatively flat, planar-like structures made up of β-strands arranged side-by-side. They come in three flavors: parallel, anti-parallel and mixed, which differ in terms of the orientation of each component strand (with respect to the direction of the mainchain from N-terminus to C-terminus).

Note that the mainchain of a β-strand is not perfectly fully extended (Φ ≠ φ ≠ 180o) and that the mainchain actually slowly twists (this is more obvious if you look at a long segment of β-strand). Thus β-sheets are not completely flat and also exhibit some twisting (this is also more obvious if you look at sheets made of many β-strands).

==Parallel β-sheet==

Parallel β-sheets are composed of β-strand that all point in the same direction. Each β-strand has mainchain dihedral angles as follows: Φ ~ -120o, φ ~ +105o.

The sheet shown below is composed of three strands in parallel orientation.
<Structure load='Tut_parallel_bsheet.pdb' size='500' frame='true' align='left' caption='' scene='User:Robert_Dutnall/Sandbox_1_sheets/Parallel_load/1'/>

All the atoms are shown in this initial orientation (C = green; N = blue; O = red; S = yellow; H = white).

<scene name='User:Robert_Dutnall/Sandbox_1_sheets/Parallel_mainchain/1'>Click here</scene> to show only the polypeptide mainchain (NH, Cα, and C=O).

Identify the N- and C-termini of each strand. <scene name='User:Robert_Dutnall/Sandbox_1_sheets/Parallel_mainchain_labels/4'>Click here to see if you were correct.</scene>

<scene name='User:Robert_Dutnall/Sandbox_1_alpha_helix/A_helix_mainchain_label_ribbon/3'>Click here to add a ribbon that will help show the path of the mainchain. </scene> You should be able to see that it is helical with a right-handed twist (you rotate to the right as you move along the helix axis).

Click the "toggle spin" button in the box to stop the structure from rotating. Now use your mouse to rotate the structure to look down the helix axis. If you have any problems with finding this view, <scene name='User:Robert_Dutnall/Sandbox_1_alpha_helix/A_helix_mainchain_label_axis/3'>click here </scene>to zoom in and look down the helix axis from the N-terminal end.

<scene name='User:Robert_Dutnall/Sandbox_1_alpha_helix/A_helix_mainchain_label/4'>Click here to zoom out again.</scene> Look at the structure carefully and identify the mainchain NH and C=O groups. What is the orientation of these groups with respect to the helix axis?

<scene name='User:Robert_Dutnall/Sandbox_1_alpha_helix/A_helix_mainchain_label_hbonds/10'>Click here to zoom in a little and add hydrogen bonds for the mainchain (dashed lines).</scene> The hydrogen bonds connect backbone NH groups and C=O groups. The N-H group is the hydrogen bond donor, the oxygen in the C=O group is the acceptor (N-H--->O=C). Each hydrogen bond is approximately 3.0 Angstroms (0.3 nm) in length (measured between the N and the O). These hydrogen bonds connect amino acids that are spaced 4 residues apart in the primary sequence. The NH group is from amino acid X and the O is from amino acid X-4 (where X is the number of the amino acid in the sequence).

<scene name='User:Robert_Dutnall/Sandbox_1_alpha_helix/A_helix_mainchain_label_hbonds/9'>Click here to zoom out again.</scene> You should be able to see that all of the mainchain NH and C=O groups are involved in hydrogen bonds. This is possible because 1) all the mainchain NH groups and C=O groups are parallel to the helix axis, 2) all the NH groups point toward the N-terminus of the helix, and 3) all the C=O groups point toward the C-terminus. Only the NH groups in the first (N-terminal) turn, and the C=O groups in the last (C-terminal) turn of the helix do not have hydrogen bonding partners. However, if this helix were part of a larger protein, these groups would participate in hydrogen bonds with other parts of the protein. This is called 'helix capping' and the other groups involved are typically from amino acid side chains (that are called 'helix capping residues').

<scene name='User:Robert_Dutnall/Sandbox_1_alpha_helix/A_helix_sidechains/3'>Click here to show the side chains again.</scene> The atoms of each amino side chain have been colored light blue to show them more clearly. <scene name='User:Robert_Dutnall/Sandbox_1_alpha_helix/A_helix_sidechains_axis/1'>Click here to change the view to look down the helix axis.</scene>

What is the general orientation of the side chains with respect to the helix axis? You should observe that each side chain points away from the helix axis, but points down toward the N-terminus of the helix (this is clearer if you only show the first bond of each side chain: <scene name='User:Robert_Dutnall/Sandbox_1_alpha_helix/A_helix_sidechains_cropped/1'>click here</scene> or <scene name='User:Robert_Dutnall/Sandbox_1_alpha_helix/A_helix_sidechains_cropped/2'>click here</scene>).

==The 310-helix==

310-helices are also found in proteins but are less common than α-helices. They are characterized by the following helix parameters:
::Dihedral angles: Φ ~ -49o, φ ~ -26o
::Repeat (number of residues per turn) = 3.0
::Rise (translation along axis per amino acid residue) = 2.0 Angstroms (0.2 nm)
::Twist (rotation around axis per amino acid residue) = 120o (= 360o/repeat)
::Pitch (translation along axis per turn) = 6.0 Angstroms (= 0.6 nm = Repeat x Rise)

The helix shown below is a 19 amino acid chain in 310-helical conformation.
<Structure load='Tut_3-10_helix.pdb' size='500' frame='true' align='left' caption='' scene='User:Robert_Dutnall/Sandbox_1_alpha_helix/310_helix_load/4'/>

All the atoms are shown in this initial orientation (C = green; N = blue; O = red; S = yellow; H = white). The helix axis runs vertically, approximately parallel to the plane of the screen.

<scene name='User:Robert_Dutnall/Sandbox_1_alpha_helix/310_helix_mainchain/2'>Click here</scene> to show only the polypeptide mainchain (NH, Cα, and C=O). The N- and C-termini are labeled.

<scene name='User:Robert_Dutnall/Sandbox_1_alpha_helix/310_helix_mainchain_ribbon/2'>Click here to add a ribbon that will help show the path of the mainchain. </scene> You should be able to see that just like the α-helix, it is helical with a right-handed twist, and again, all the mainchain NH groups point toward the N-terminus, and all the mainchain C=O groups point toward the C-terminus.

The difference between an α-helix and a 310-helix lies in the helix parameters. A 310-helix is more tightly twisted so that the mainchain completes one turn every 3 amino acids (instead of 3.6 for the α-helix). This also results in a larger rise and pitch so that the 310-helix is longer than an α-helix (of the same number of residues).

<scene name='User:Robert_Dutnall/Sandbox_1_alpha_helix/310_helix_mainchain_axis/1'>Click here </scene>to zoom in and look down the helix axis from the N-terminal end. You'll be able to see the triangular shape of the mainchain.

<scene name='User:Robert_Dutnall/Sandbox_1_alpha_helix/310_helix_mainchain_hbonds/1'>Click here to zoom out again and display hydrogen bonds for the mainchain.</scene> Once again, all of the mainchain NH and C=O groups are involved in hydrogen bonds. However, now the hydrogen bonds connect amino acids that are spaced 3 residues apart in the primary sequence. The NH group is from amino acid X and the O is from amino acid X-3 (where X is the number of the amino acid in the sequence). <scene name='User:Robert_Dutnall/Sandbox_1_alpha_helix/310_helix_mainchain_hbonds/2'>Click here</scene> to zoom in and you should be able to see this more clearly.

<scene name='User:Robert_Dutnall/Sandbox_1_alpha_helix/310_helix_sidechains/1'>Click here to zoom out and show the side chains again.</scene> The atoms of each amino side chain have been colored light blue to show them more clearly. <scene name='User:Robert_Dutnall/Sandbox_1_alpha_helix/310_helix_sidechains_axis/2'>Click here to change the view to look down the helix axis.</scene>

As for the α-helix, each side chain points away from the helix axis, and points down toward the N-terminus of the helix. However, because the 310-helix repeat parameter is an integer (= 3.0), the side chains are spaced 120o apart and form 3 distinct sides to the helix. You'll see this more clearly if the side chains are colored in groups to show this (residues 1,4,7,10 etc are blue; residues 2,5,8,11 etc are purple; residues 3,6,9,12 etc are yellow): <scene name='User:Robert_Dutnall/Sandbox_1_alpha_helix/310_helix_sidechains_tricolor/1'>click here to look from the side</scene> or <scene name='User:Robert_Dutnall/Sandbox_1_alpha_helix/310_helix_sidechains_tricol_ax/1'>click here to view down the helix axis</scene>.

= =
[[User:Robert Dutnall/Sandbox_1_alpha_helix|Click here to go on to back to the first part of this tutorial.]]

User:Robert Dutnall/Sandbox 1 sheets

2011-08-26T20:25:28Z

Robert Dutnall:

== Biochemistry Tutorial #2 - Secondary Structure ==

Part Two

=β-strands and β-sheets=

The second major secondary structure element is the β-sheet. β-sheets are composed of two or more segments of polypeptide mainchain in β-strand conformation. In a β-strand, the polypeptide mainchain is in a mostly extended conformation. As their name implies, β-sheets are relatively flat, planar-like structures made up of β-strands arranged side-by-side. They come in three flavors: parallel, anti-parallel and mixed, which differ in terms of the orientation of each component strand (with respect to the direction of the mainchain from N-terminus to C-terminus).

Note that the mainchain of a β-strand is not perfectly fully extended (Φ ≠ φ ≠ 180o) and that the mainchain actually slowly twists (this is more obvious if you look at a long segment of β-strand). Thus β-sheets are not completely flat and also exhibit some twisting (this is also more obvious if you look at sheets made of many β-strands).

==Parallel β-sheet==

Parallel β-sheets are composed of β-strand that all point in the same direction. Each β-strand has mainchain dihedral angles as follows: Φ ~ -120o, φ ~ +105o.

The sheet shown below is composed of three strands in parallel orientation.
<Structure load='Tut_parallel_bsheet.pdb' size='500' frame='true' align='left' caption='' scene='User:Robert_Dutnall/Sandbox_1_sheets/parallel_load/1'/>

All the atoms are shown in this initial orientation (C = green; N = blue; O = red; S = yellow; H = white). The helix axis runs vertically, approximately parallel to the plane of the screen.

<scene name='User:Robert_Dutnall/Sandbox_1_sheets/parallel_mainchain/1'>Click here</scene> to show only the polypeptide mainchain (NH, Cα, and C=O).

Identify the N- and C-termini of each strand. <scene name='User:Robert_Dutnall/Sandbox_1_alpha_helix/parallel_mainchain_labels/1'>Click here to see if you were correct.</scene>

<scene name='User:Robert_Dutnall/Sandbox_1_alpha_helix/A_helix_mainchain_label_ribbon/3'>Click here to add a ribbon that will help show the path of the mainchain. </scene> You should be able to see that it is helical with a right-handed twist (you rotate to the right as you move along the helix axis).

Click the "toggle spin" button in the box to stop the structure from rotating. Now use your mouse to rotate the structure to look down the helix axis. If you have any problems with finding this view, <scene name='User:Robert_Dutnall/Sandbox_1_alpha_helix/A_helix_mainchain_label_axis/3'>click here </scene>to zoom in and look down the helix axis from the N-terminal end.

<scene name='User:Robert_Dutnall/Sandbox_1_alpha_helix/A_helix_mainchain_label/4'>Click here to zoom out again.</scene> Look at the structure carefully and identify the mainchain NH and C=O groups. What is the orientation of these groups with respect to the helix axis?

<scene name='User:Robert_Dutnall/Sandbox_1_alpha_helix/A_helix_mainchain_label_hbonds/10'>Click here to zoom in a little and add hydrogen bonds for the mainchain (dashed lines).</scene> The hydrogen bonds connect backbone NH groups and C=O groups. The N-H group is the hydrogen bond donor, the oxygen in the C=O group is the acceptor (N-H--->O=C). Each hydrogen bond is approximately 3.0 Angstroms (0.3 nm) in length (measured between the N and the O). These hydrogen bonds connect amino acids that are spaced 4 residues apart in the primary sequence. The NH group is from amino acid X and the O is from amino acid X-4 (where X is the number of the amino acid in the sequence).

<scene name='User:Robert_Dutnall/Sandbox_1_alpha_helix/A_helix_mainchain_label_hbonds/9'>Click here to zoom out again.</scene> You should be able to see that all of the mainchain NH and C=O groups are involved in hydrogen bonds. This is possible because 1) all the mainchain NH groups and C=O groups are parallel to the helix axis, 2) all the NH groups point toward the N-terminus of the helix, and 3) all the C=O groups point toward the C-terminus. Only the NH groups in the first (N-terminal) turn, and the C=O groups in the last (C-terminal) turn of the helix do not have hydrogen bonding partners. However, if this helix were part of a larger protein, these groups would participate in hydrogen bonds with other parts of the protein. This is called 'helix capping' and the other groups involved are typically from amino acid side chains (that are called 'helix capping residues').

<scene name='User:Robert_Dutnall/Sandbox_1_alpha_helix/A_helix_sidechains/3'>Click here to show the side chains again.</scene> The atoms of each amino side chain have been colored light blue to show them more clearly. <scene name='User:Robert_Dutnall/Sandbox_1_alpha_helix/A_helix_sidechains_axis/1'>Click here to change the view to look down the helix axis.</scene>

What is the general orientation of the side chains with respect to the helix axis? You should observe that each side chain points away from the helix axis, but points down toward the N-terminus of the helix (this is clearer if you only show the first bond of each side chain: <scene name='User:Robert_Dutnall/Sandbox_1_alpha_helix/A_helix_sidechains_cropped/1'>click here</scene> or <scene name='User:Robert_Dutnall/Sandbox_1_alpha_helix/A_helix_sidechains_cropped/2'>click here</scene>).

==The 310-helix==

310-helices are also found in proteins but are less common than α-helices. They are characterized by the following helix parameters:
::Dihedral angles: Φ ~ -49o, φ ~ -26o
::Repeat (number of residues per turn) = 3.0
::Rise (translation along axis per amino acid residue) = 2.0 Angstroms (0.2 nm)
::Twist (rotation around axis per amino acid residue) = 120o (= 360o/repeat)
::Pitch (translation along axis per turn) = 6.0 Angstroms (= 0.6 nm = Repeat x Rise)

The helix shown below is a 19 amino acid chain in 310-helical conformation.
<Structure load='Tut_3-10_helix.pdb' size='500' frame='true' align='left' caption='' scene='User:Robert_Dutnall/Sandbox_1_alpha_helix/310_helix_load/4'/>

All the atoms are shown in this initial orientation (C = green; N = blue; O = red; S = yellow; H = white). The helix axis runs vertically, approximately parallel to the plane of the screen.

<scene name='User:Robert_Dutnall/Sandbox_1_alpha_helix/310_helix_mainchain/2'>Click here</scene> to show only the polypeptide mainchain (NH, Cα, and C=O). The N- and C-termini are labeled.

<scene name='User:Robert_Dutnall/Sandbox_1_alpha_helix/310_helix_mainchain_ribbon/2'>Click here to add a ribbon that will help show the path of the mainchain. </scene> You should be able to see that just like the α-helix, it is helical with a right-handed twist, and again, all the mainchain NH groups point toward the N-terminus, and all the mainchain C=O groups point toward the C-terminus.

The difference between an α-helix and a 310-helix lies in the helix parameters. A 310-helix is more tightly twisted so that the mainchain completes one turn every 3 amino acids (instead of 3.6 for the α-helix). This also results in a larger rise and pitch so that the 310-helix is longer than an α-helix (of the same number of residues).

<scene name='User:Robert_Dutnall/Sandbox_1_alpha_helix/310_helix_mainchain_axis/1'>Click here </scene>to zoom in and look down the helix axis from the N-terminal end. You'll be able to see the triangular shape of the mainchain.

<scene name='User:Robert_Dutnall/Sandbox_1_alpha_helix/310_helix_mainchain_hbonds/1'>Click here to zoom out again and display hydrogen bonds for the mainchain.</scene> Once again, all of the mainchain NH and C=O groups are involved in hydrogen bonds. However, now the hydrogen bonds connect amino acids that are spaced 3 residues apart in the primary sequence. The NH group is from amino acid X and the O is from amino acid X-3 (where X is the number of the amino acid in the sequence). <scene name='User:Robert_Dutnall/Sandbox_1_alpha_helix/310_helix_mainchain_hbonds/2'>Click here</scene> to zoom in and you should be able to see this more clearly.

<scene name='User:Robert_Dutnall/Sandbox_1_alpha_helix/310_helix_sidechains/1'>Click here to zoom out and show the side chains again.</scene> The atoms of each amino side chain have been colored light blue to show them more clearly. <scene name='User:Robert_Dutnall/Sandbox_1_alpha_helix/310_helix_sidechains_axis/2'>Click here to change the view to look down the helix axis.</scene>

As for the α-helix, each side chain points away from the helix axis, and points down toward the N-terminus of the helix. However, because the 310-helix repeat parameter is an integer (= 3.0), the side chains are spaced 120o apart and form 3 distinct sides to the helix. You'll see this more clearly if the side chains are colored in groups to show this (residues 1,4,7,10 etc are blue; residues 2,5,8,11 etc are purple; residues 3,6,9,12 etc are yellow): <scene name='User:Robert_Dutnall/Sandbox_1_alpha_helix/310_helix_sidechains_tricolor/1'>click here to look from the side</scene> or <scene name='User:Robert_Dutnall/Sandbox_1_alpha_helix/310_helix_sidechains_tricol_ax/1'>click here to view down the helix axis</scene>.

= =
[[User:Robert Dutnall/Sandbox_1_alpha_helix|Click here to go on to back to the first part of this tutorial.]]

File:Tut parallel bsheet.pdb

2011-08-26T19:30:40Z

Robert Dutnall:

== Licensing ==
{{self|cc-by-sa-3.0}}

File:Tut parallel sheet.pdb

2011-08-26T19:25:30Z

Robert Dutnall: uploaded a new version of "Image:Tut parallel sheet.pdb": Parallel sheet from thioredoxin

== Summary ==
Parallel sheet from Thioredoxin
== Licensing ==
{{self|cc-by-sa-3.0}}

User:Robert Dutnall/Sandbox 1 sheets

2011-08-26T19:24:48Z

Robert Dutnall:

== Biochemistry Tutorial #2 - Secondary Structure ==

Part Two

=β-strands and β-sheets=

The second major secondary structure element is the β-sheet. β-shees are composed of two or more segments of polypeptide mainchain in β-strand conformation. In a β-strand, the polypeptide mainchain is in a mostly extended conformation. As their name implies, β-sheets are relatively flat, planar structures made up of β-strands arranged side-by-side. They come in three flavors: parallel, anti-parallel and mixed, which differ in terms of the orientation of each component strand (with respect to the direction of the mainchain from N-terminus to C-terminus).

==Parallel β-sheet==

Parallel β-sheets are composed of β-strand that all point in the same direction. Each β-strand has mainchain dihedral angles as follows: Φ ~ -120o, φ ~ +105o. Note that the mainchain of each β-strand is not fully extended (Φ = φ = 180o) so that the chain will actually slowly twist to the right

The helix shown below is a 19 amino acid chain in α-helical conformation.
<Structure load='Tut_antiparallel_sheet.pdb' size='500' frame='true' align='left' caption='' scene='User:Robert_Dutnall/Sandbox_1_sheets/Antiparallel_load/1'/>

All the atoms are shown in this initial orientation (C = green; N = blue; O = red; S = yellow; H = white). The helix axis runs vertically, approximately parallel to the plane of the screen.

<scene name='User:Robert_Dutnall/Sandbox_1_sheets/Antiparallel_mainchain/1'>Click here</scene> to show only the polypeptide mainchain (NH, Cα, and C=O).

Identify the N- and C-termini. <scene name='User:Robert_Dutnall/Sandbox_1_alpha_helix/A_helix_mainchain_label/4'>Click here to see if you were correct.</scene>

<scene name='User:Robert_Dutnall/Sandbox_1_alpha_helix/A_helix_mainchain_label_ribbon/3'>Click here to add a ribbon that will help show the path of the mainchain. </scene> You should be able to see that it is helical with a right-handed twist (you rotate to the right as you move along the helix axis).

Click the "toggle spin" button in the box to stop the structure from rotating. Now use your mouse to rotate the structure to look down the helix axis. If you have any problems with finding this view, <scene name='User:Robert_Dutnall/Sandbox_1_alpha_helix/A_helix_mainchain_label_axis/3'>click here </scene>to zoom in and look down the helix axis from the N-terminal end.

<scene name='User:Robert_Dutnall/Sandbox_1_alpha_helix/A_helix_mainchain_label/4'>Click here to zoom out again.</scene> Look at the structure carefully and identify the mainchain NH and C=O groups. What is the orientation of these groups with respect to the helix axis?

<scene name='User:Robert_Dutnall/Sandbox_1_alpha_helix/A_helix_mainchain_label_hbonds/10'>Click here to zoom in a little and add hydrogen bonds for the mainchain (dashed lines).</scene> The hydrogen bonds connect backbone NH groups and C=O groups. The N-H group is the hydrogen bond donor, the oxygen in the C=O group is the acceptor (N-H--->O=C). Each hydrogen bond is approximately 3.0 Angstroms (0.3 nm) in length (measured between the N and the O). These hydrogen bonds connect amino acids that are spaced 4 residues apart in the primary sequence. The NH group is from amino acid X and the O is from amino acid X-4 (where X is the number of the amino acid in the sequence).

<scene name='User:Robert_Dutnall/Sandbox_1_alpha_helix/A_helix_mainchain_label_hbonds/9'>Click here to zoom out again.</scene> You should be able to see that all of the mainchain NH and C=O groups are involved in hydrogen bonds. This is possible because 1) all the mainchain NH groups and C=O groups are parallel to the helix axis, 2) all the NH groups point toward the N-terminus of the helix, and 3) all the C=O groups point toward the C-terminus. Only the NH groups in the first (N-terminal) turn, and the C=O groups in the last (C-terminal) turn of the helix do not have hydrogen bonding partners. However, if this helix were part of a larger protein, these groups would participate in hydrogen bonds with other parts of the protein. This is called 'helix capping' and the other groups involved are typically from amino acid side chains (that are called 'helix capping residues').

<scene name='User:Robert_Dutnall/Sandbox_1_alpha_helix/A_helix_sidechains/3'>Click here to show the side chains again.</scene> The atoms of each amino side chain have been colored light blue to show them more clearly. <scene name='User:Robert_Dutnall/Sandbox_1_alpha_helix/A_helix_sidechains_axis/1'>Click here to change the view to look down the helix axis.</scene>

What is the general orientation of the side chains with respect to the helix axis? You should observe that each side chain points away from the helix axis, but points down toward the N-terminus of the helix (this is clearer if you only show the first bond of each side chain: <scene name='User:Robert_Dutnall/Sandbox_1_alpha_helix/A_helix_sidechains_cropped/1'>click here</scene> or <scene name='User:Robert_Dutnall/Sandbox_1_alpha_helix/A_helix_sidechains_cropped/2'>click here</scene>).

==The 310-helix==

310-helices are also found in proteins but are less common than α-helices. They are characterized by the following helix parameters:
::Dihedral angles: Φ ~ -49o, φ ~ -26o
::Repeat (number of residues per turn) = 3.0
::Rise (translation along axis per amino acid residue) = 2.0 Angstroms (0.2 nm)
::Twist (rotation around axis per amino acid residue) = 120o (= 360o/repeat)
::Pitch (translation along axis per turn) = 6.0 Angstroms (= 0.6 nm = Repeat x Rise)

The helix shown below is a 19 amino acid chain in 310-helical conformation.
<Structure load='Tut_3-10_helix.pdb' size='500' frame='true' align='left' caption='' scene='User:Robert_Dutnall/Sandbox_1_alpha_helix/310_helix_load/4'/>

All the atoms are shown in this initial orientation (C = green; N = blue; O = red; S = yellow; H = white). The helix axis runs vertically, approximately parallel to the plane of the screen.

<scene name='User:Robert_Dutnall/Sandbox_1_alpha_helix/310_helix_mainchain/2'>Click here</scene> to show only the polypeptide mainchain (NH, Cα, and C=O). The N- and C-termini are labeled.

<scene name='User:Robert_Dutnall/Sandbox_1_alpha_helix/310_helix_mainchain_ribbon/2'>Click here to add a ribbon that will help show the path of the mainchain. </scene> You should be able to see that just like the α-helix, it is helical with a right-handed twist, and again, all the mainchain NH groups point toward the N-terminus, and all the mainchain C=O groups point toward the C-terminus.

The difference between an α-helix and a 310-helix lies in the helix parameters. A 310-helix is more tightly twisted so that the mainchain completes one turn every 3 amino acids (instead of 3.6 for the α-helix). This also results in a larger rise and pitch so that the 310-helix is longer than an α-helix (of the same number of residues).

<scene name='User:Robert_Dutnall/Sandbox_1_alpha_helix/310_helix_mainchain_axis/1'>Click here </scene>to zoom in and look down the helix axis from the N-terminal end. You'll be able to see the triangular shape of the mainchain.

<scene name='User:Robert_Dutnall/Sandbox_1_alpha_helix/310_helix_mainchain_hbonds/1'>Click here to zoom out again and display hydrogen bonds for the mainchain.</scene> Once again, all of the mainchain NH and C=O groups are involved in hydrogen bonds. However, now the hydrogen bonds connect amino acids that are spaced 3 residues apart in the primary sequence. The NH group is from amino acid X and the O is from amino acid X-3 (where X is the number of the amino acid in the sequence). <scene name='User:Robert_Dutnall/Sandbox_1_alpha_helix/310_helix_mainchain_hbonds/2'>Click here</scene> to zoom in and you should be able to see this more clearly.

<scene name='User:Robert_Dutnall/Sandbox_1_alpha_helix/310_helix_sidechains/1'>Click here to zoom out and show the side chains again.</scene> The atoms of each amino side chain have been colored light blue to show them more clearly. <scene name='User:Robert_Dutnall/Sandbox_1_alpha_helix/310_helix_sidechains_axis/2'>Click here to change the view to look down the helix axis.</scene>

As for the α-helix, each side chain points away from the helix axis, and points down toward the N-terminus of the helix. However, because the 310-helix repeat parameter is an integer (= 3.0), the side chains are spaced 120o apart and form 3 distinct sides to the helix. You'll see this more clearly if the side chains are colored in groups to show this (residues 1,4,7,10 etc are blue; residues 2,5,8,11 etc are purple; residues 3,6,9,12 etc are yellow): <scene name='User:Robert_Dutnall/Sandbox_1_alpha_helix/310_helix_sidechains_tricolor/1'>click here to look from the side</scene> or <scene name='User:Robert_Dutnall/Sandbox_1_alpha_helix/310_helix_sidechains_tricol_ax/1'>click here to view down the helix axis</scene>.

= =
[[User:Robert Dutnall/Sandbox_1_alpha_helix|Click here to go on to back to the first part of this tutorial.]]

User:Robert Dutnall/Sandbox 1 sheets

2011-08-26T19:01:33Z

Robert Dutnall:

== Biochemistry Tutorial #2 - Secondary Structure ==

Part Two

=β-strands and β-sheets=

The second major secondary structure element is the β-sheet. β-shees are composed of two or more segments of polypeptide mainchain in β-strand conformation. In a β-strand, the polypeptide mainchain is in a mostly extended conformation. As their name implies, β-sheets are relatively flat, planar structures made up of β-strands arranged side-by-side. They come in three flavors: parallel, anti-parallel and mixed, which differ in terms of the orientation of each component strand (with respect to the direction of the mainchain from N-terminus to C-terminus).

==Parallel β-sheet==

Parallel β-sheets are composed of β-strand that all point in the same direction. Each β-strand has mainchain dihedral angles as follows: Φ ~ -120o, φ ~ +105o. Note that the mainchain of each β-strand is not fully extended (Φ = φ = 180o) so that the chain will actually slowly twist to the right

The helix shown below is a 19 amino acid chain in α-helical conformation.
<Structure load='Tut_antiparallel_sheet.pdb' size='500' frame='true' align='left' caption='' scene='User:Robert_Dutnall/Sandbox_1_sheets/Antiparallel_load/1'/>

All the atoms are shown in this initial orientation (C = green; N = blue; O = red; S = yellow; H = white). The helix axis runs vertically, approximately parallel to the plane of the screen.

<scene name='User:Robert_Dutnall/Sandbox_1_alpha_helix/A_helix_mainchain/3'>Click here</scene> to show only the polypeptide mainchain (NH, Cα, and C=O).

Identify the N- and C-termini. <scene name='User:Robert_Dutnall/Sandbox_1_alpha_helix/A_helix_mainchain_label/4'>Click here to see if you were correct.</scene>

<scene name='User:Robert_Dutnall/Sandbox_1_alpha_helix/A_helix_mainchain_label_ribbon/3'>Click here to add a ribbon that will help show the path of the mainchain. </scene> You should be able to see that it is helical with a right-handed twist (you rotate to the right as you move along the helix axis).

Click the "toggle spin" button in the box to stop the structure from rotating. Now use your mouse to rotate the structure to look down the helix axis. If you have any problems with finding this view, <scene name='User:Robert_Dutnall/Sandbox_1_alpha_helix/A_helix_mainchain_label_axis/3'>click here </scene>to zoom in and look down the helix axis from the N-terminal end.

<scene name='User:Robert_Dutnall/Sandbox_1_alpha_helix/A_helix_mainchain_label/4'>Click here to zoom out again.</scene> Look at the structure carefully and identify the mainchain NH and C=O groups. What is the orientation of these groups with respect to the helix axis?

<scene name='User:Robert_Dutnall/Sandbox_1_alpha_helix/A_helix_mainchain_label_hbonds/10'>Click here to zoom in a little and add hydrogen bonds for the mainchain (dashed lines).</scene> The hydrogen bonds connect backbone NH groups and C=O groups. The N-H group is the hydrogen bond donor, the oxygen in the C=O group is the acceptor (N-H--->O=C). Each hydrogen bond is approximately 3.0 Angstroms (0.3 nm) in length (measured between the N and the O). These hydrogen bonds connect amino acids that are spaced 4 residues apart in the primary sequence. The NH group is from amino acid X and the O is from amino acid X-4 (where X is the number of the amino acid in the sequence).

<scene name='User:Robert_Dutnall/Sandbox_1_alpha_helix/A_helix_mainchain_label_hbonds/9'>Click here to zoom out again.</scene> You should be able to see that all of the mainchain NH and C=O groups are involved in hydrogen bonds. This is possible because 1) all the mainchain NH groups and C=O groups are parallel to the helix axis, 2) all the NH groups point toward the N-terminus of the helix, and 3) all the C=O groups point toward the C-terminus. Only the NH groups in the first (N-terminal) turn, and the C=O groups in the last (C-terminal) turn of the helix do not have hydrogen bonding partners. However, if this helix were part of a larger protein, these groups would participate in hydrogen bonds with other parts of the protein. This is called 'helix capping' and the other groups involved are typically from amino acid side chains (that are called 'helix capping residues').

<scene name='User:Robert_Dutnall/Sandbox_1_alpha_helix/A_helix_sidechains/3'>Click here to show the side chains again.</scene> The atoms of each amino side chain have been colored light blue to show them more clearly. <scene name='User:Robert_Dutnall/Sandbox_1_alpha_helix/A_helix_sidechains_axis/1'>Click here to change the view to look down the helix axis.</scene>

What is the general orientation of the side chains with respect to the helix axis? You should observe that each side chain points away from the helix axis, but points down toward the N-terminus of the helix (this is clearer if you only show the first bond of each side chain: <scene name='User:Robert_Dutnall/Sandbox_1_alpha_helix/A_helix_sidechains_cropped/1'>click here</scene> or <scene name='User:Robert_Dutnall/Sandbox_1_alpha_helix/A_helix_sidechains_cropped/2'>click here</scene>).

==The 310-helix==

310-helices are also found in proteins but are less common than α-helices. They are characterized by the following helix parameters:
::Dihedral angles: Φ ~ -49o, φ ~ -26o
::Repeat (number of residues per turn) = 3.0
::Rise (translation along axis per amino acid residue) = 2.0 Angstroms (0.2 nm)
::Twist (rotation around axis per amino acid residue) = 120o (= 360o/repeat)
::Pitch (translation along axis per turn) = 6.0 Angstroms (= 0.6 nm = Repeat x Rise)

The helix shown below is a 19 amino acid chain in 310-helical conformation.
<Structure load='Tut_3-10_helix.pdb' size='500' frame='true' align='left' caption='' scene='User:Robert_Dutnall/Sandbox_1_alpha_helix/310_helix_load/4'/>

All the atoms are shown in this initial orientation (C = green; N = blue; O = red; S = yellow; H = white). The helix axis runs vertically, approximately parallel to the plane of the screen.

<scene name='User:Robert_Dutnall/Sandbox_1_alpha_helix/310_helix_mainchain/2'>Click here</scene> to show only the polypeptide mainchain (NH, Cα, and C=O). The N- and C-termini are labeled.

<scene name='User:Robert_Dutnall/Sandbox_1_alpha_helix/310_helix_mainchain_ribbon/2'>Click here to add a ribbon that will help show the path of the mainchain. </scene> You should be able to see that just like the α-helix, it is helical with a right-handed twist, and again, all the mainchain NH groups point toward the N-terminus, and all the mainchain C=O groups point toward the C-terminus.

The difference between an α-helix and a 310-helix lies in the helix parameters. A 310-helix is more tightly twisted so that the mainchain completes one turn every 3 amino acids (instead of 3.6 for the α-helix). This also results in a larger rise and pitch so that the 310-helix is longer than an α-helix (of the same number of residues).

<scene name='User:Robert_Dutnall/Sandbox_1_alpha_helix/310_helix_mainchain_axis/1'>Click here </scene>to zoom in and look down the helix axis from the N-terminal end. You'll be able to see the triangular shape of the mainchain.

<scene name='User:Robert_Dutnall/Sandbox_1_alpha_helix/310_helix_mainchain_hbonds/1'>Click here to zoom out again and display hydrogen bonds for the mainchain.</scene> Once again, all of the mainchain NH and C=O groups are involved in hydrogen bonds. However, now the hydrogen bonds connect amino acids that are spaced 3 residues apart in the primary sequence. The NH group is from amino acid X and the O is from amino acid X-3 (where X is the number of the amino acid in the sequence). <scene name='User:Robert_Dutnall/Sandbox_1_alpha_helix/310_helix_mainchain_hbonds/2'>Click here</scene> to zoom in and you should be able to see this more clearly.

<scene name='User:Robert_Dutnall/Sandbox_1_alpha_helix/310_helix_sidechains/1'>Click here to zoom out and show the side chains again.</scene> The atoms of each amino side chain have been colored light blue to show them more clearly. <scene name='User:Robert_Dutnall/Sandbox_1_alpha_helix/310_helix_sidechains_axis/2'>Click here to change the view to look down the helix axis.</scene>

As for the α-helix, each side chain points away from the helix axis, and points down toward the N-terminus of the helix. However, because the 310-helix repeat parameter is an integer (= 3.0), the side chains are spaced 120o apart and form 3 distinct sides to the helix. You'll see this more clearly if the side chains are colored in groups to show this (residues 1,4,7,10 etc are blue; residues 2,5,8,11 etc are purple; residues 3,6,9,12 etc are yellow): <scene name='User:Robert_Dutnall/Sandbox_1_alpha_helix/310_helix_sidechains_tricolor/1'>click here to look from the side</scene> or <scene name='User:Robert_Dutnall/Sandbox_1_alpha_helix/310_helix_sidechains_tricol_ax/1'>click here to view down the helix axis</scene>.

= =
[[User:Robert Dutnall/Sandbox_1_alpha_helix|Click here to go on to back to the first part of this tutorial.]]

User:Robert Dutnall/Sandbox 1 sheets

2011-08-26T18:37:17Z

Robert Dutnall:

== Biochemistry Tutorial #2 - Secondary Structure ==

Part Two

=β-strands and β-sheets=

In helices, the polypeptide mainchain twists into a path that resembles a spiral staircase. Just like spiral staircases, helices come in different forms, depending on how tightly twisted the mainchain is. The form of a helix can be described by parameters such as the number of steps (amino acids) it takes to complete a turn (a 360o rotation around the long axis of the helix), and how far you travel along the helix axis in one complete turn. Helices can also be left-handed or right-handed. For proteins composed of L-amino acids, helices are almost always right-handed (a notable exception is the type I poly-proline helix). Although several types of helix form are possible, two regular helices are very common in proteins: the α-helix and the 310-helix.

==The α-helix==

α-helices are the most common type of regular helix found in proteins. They are characterized by the following helix parameters:
::Dihedral angles: Φ ~ -60o, φ ~ -45o
::Repeat (number of residues per turn) = 3.6
::Rise (translation along axis per amino acid residue) = 1.5 Angstroms (0.15 nm)
::Twist (rotation around axis per amino acid residue) = 100o (= 360o/repeat)
::Pitch (translation along axis per turn) = 5.4 Angstroms (= 0.54 nm = Repeat x Rise)

The helix shown below is a 19 amino acid chain in α-helical conformation.
<Structure load='Tut_antiparallel_sheet.pdb' size='500' frame='true' align='left' caption='' scene='User:Robert_Dutnall/Sandbox_1_sheets/Antiparallel_load/1'/>

All the atoms are shown in this initial orientation (C = green; N = blue; O = red; S = yellow; H = white). The helix axis runs vertically, approximately parallel to the plane of the screen.

<scene name='User:Robert_Dutnall/Sandbox_1_alpha_helix/A_helix_mainchain/3'>Click here</scene> to show only the polypeptide mainchain (NH, Cα, and C=O).

Identify the N- and C-termini. <scene name='User:Robert_Dutnall/Sandbox_1_alpha_helix/A_helix_mainchain_label/4'>Click here to see if you were correct.</scene>

<scene name='User:Robert_Dutnall/Sandbox_1_alpha_helix/A_helix_mainchain_label_ribbon/3'>Click here to add a ribbon that will help show the path of the mainchain. </scene> You should be able to see that it is helical with a right-handed twist (you rotate to the right as you move along the helix axis).

Click the "toggle spin" button in the box to stop the structure from rotating. Now use your mouse to rotate the structure to look down the helix axis. If you have any problems with finding this view, <scene name='User:Robert_Dutnall/Sandbox_1_alpha_helix/A_helix_mainchain_label_axis/3'>click here </scene>to zoom in and look down the helix axis from the N-terminal end.

<scene name='User:Robert_Dutnall/Sandbox_1_alpha_helix/A_helix_mainchain_label/4'>Click here to zoom out again.</scene> Look at the structure carefully and identify the mainchain NH and C=O groups. What is the orientation of these groups with respect to the helix axis?

<scene name='User:Robert_Dutnall/Sandbox_1_alpha_helix/A_helix_mainchain_label_hbonds/10'>Click here to zoom in a little and add hydrogen bonds for the mainchain (dashed lines).</scene> The hydrogen bonds connect backbone NH groups and C=O groups. The N-H group is the hydrogen bond donor, the oxygen in the C=O group is the acceptor (N-H--->O=C). Each hydrogen bond is approximately 3.0 Angstroms (0.3 nm) in length (measured between the N and the O). These hydrogen bonds connect amino acids that are spaced 4 residues apart in the primary sequence. The NH group is from amino acid X and the O is from amino acid X-4 (where X is the number of the amino acid in the sequence).

<scene name='User:Robert_Dutnall/Sandbox_1_alpha_helix/A_helix_mainchain_label_hbonds/9'>Click here to zoom out again.</scene> You should be able to see that all of the mainchain NH and C=O groups are involved in hydrogen bonds. This is possible because 1) all the mainchain NH groups and C=O groups are parallel to the helix axis, 2) all the NH groups point toward the N-terminus of the helix, and 3) all the C=O groups point toward the C-terminus. Only the NH groups in the first (N-terminal) turn, and the C=O groups in the last (C-terminal) turn of the helix do not have hydrogen bonding partners. However, if this helix were part of a larger protein, these groups would participate in hydrogen bonds with other parts of the protein. This is called 'helix capping' and the other groups involved are typically from amino acid side chains (that are called 'helix capping residues').

<scene name='User:Robert_Dutnall/Sandbox_1_alpha_helix/A_helix_sidechains/3'>Click here to show the side chains again.</scene> The atoms of each amino side chain have been colored light blue to show them more clearly. <scene name='User:Robert_Dutnall/Sandbox_1_alpha_helix/A_helix_sidechains_axis/1'>Click here to change the view to look down the helix axis.</scene>

What is the general orientation of the side chains with respect to the helix axis? You should observe that each side chain points away from the helix axis, but points down toward the N-terminus of the helix (this is clearer if you only show the first bond of each side chain: <scene name='User:Robert_Dutnall/Sandbox_1_alpha_helix/A_helix_sidechains_cropped/1'>click here</scene> or <scene name='User:Robert_Dutnall/Sandbox_1_alpha_helix/A_helix_sidechains_cropped/2'>click here</scene>).

==The 310-helix==

310-helices are also found in proteins but are less common than α-helices. They are characterized by the following helix parameters:
::Dihedral angles: Φ ~ -49o, φ ~ -26o
::Repeat (number of residues per turn) = 3.0
::Rise (translation along axis per amino acid residue) = 2.0 Angstroms (0.2 nm)
::Twist (rotation around axis per amino acid residue) = 120o (= 360o/repeat)
::Pitch (translation along axis per turn) = 6.0 Angstroms (= 0.6 nm = Repeat x Rise)

The helix shown below is a 19 amino acid chain in 310-helical conformation.
<Structure load='Tut_3-10_helix.pdb' size='500' frame='true' align='left' caption='' scene='User:Robert_Dutnall/Sandbox_1_alpha_helix/310_helix_load/4'/>

All the atoms are shown in this initial orientation (C = green; N = blue; O = red; S = yellow; H = white). The helix axis runs vertically, approximately parallel to the plane of the screen.

<scene name='User:Robert_Dutnall/Sandbox_1_alpha_helix/310_helix_mainchain/2'>Click here</scene> to show only the polypeptide mainchain (NH, Cα, and C=O). The N- and C-termini are labeled.

<scene name='User:Robert_Dutnall/Sandbox_1_alpha_helix/310_helix_mainchain_ribbon/2'>Click here to add a ribbon that will help show the path of the mainchain. </scene> You should be able to see that just like the α-helix, it is helical with a right-handed twist, and again, all the mainchain NH groups point toward the N-terminus, and all the mainchain C=O groups point toward the C-terminus.

The difference between an α-helix and a 310-helix lies in the helix parameters. A 310-helix is more tightly twisted so that the mainchain completes one turn every 3 amino acids (instead of 3.6 for the α-helix). This also results in a larger rise and pitch so that the 310-helix is longer than an α-helix (of the same number of residues).

<scene name='User:Robert_Dutnall/Sandbox_1_alpha_helix/310_helix_mainchain_axis/1'>Click here </scene>to zoom in and look down the helix axis from the N-terminal end. You'll be able to see the triangular shape of the mainchain.

<scene name='User:Robert_Dutnall/Sandbox_1_alpha_helix/310_helix_mainchain_hbonds/1'>Click here to zoom out again and display hydrogen bonds for the mainchain.</scene> Once again, all of the mainchain NH and C=O groups are involved in hydrogen bonds. However, now the hydrogen bonds connect amino acids that are spaced 3 residues apart in the primary sequence. The NH group is from amino acid X and the O is from amino acid X-3 (where X is the number of the amino acid in the sequence). <scene name='User:Robert_Dutnall/Sandbox_1_alpha_helix/310_helix_mainchain_hbonds/2'>Click here</scene> to zoom in and you should be able to see this more clearly.

<scene name='User:Robert_Dutnall/Sandbox_1_alpha_helix/310_helix_sidechains/1'>Click here to zoom out and show the side chains again.</scene> The atoms of each amino side chain have been colored light blue to show them more clearly. <scene name='User:Robert_Dutnall/Sandbox_1_alpha_helix/310_helix_sidechains_axis/2'>Click here to change the view to look down the helix axis.</scene>

As for the α-helix, each side chain points away from the helix axis, and points down toward the N-terminus of the helix. However, because the 310-helix repeat parameter is an integer (= 3.0), the side chains are spaced 120o apart and form 3 distinct sides to the helix. You'll see this more clearly if the side chains are colored in groups to show this (residues 1,4,7,10 etc are blue; residues 2,5,8,11 etc are purple; residues 3,6,9,12 etc are yellow): <scene name='User:Robert_Dutnall/Sandbox_1_alpha_helix/310_helix_sidechains_tricolor/1'>click here to look from the side</scene> or <scene name='User:Robert_Dutnall/Sandbox_1_alpha_helix/310_helix_sidechains_tricol_ax/1'>click here to view down the helix axis</scene>.

= =
[[User:Robert Dutnall/Sandbox_1_alpha_helix|Click here to go on to back to the first part of this tutorial.]]

File:Tut parallel sheet.pdb

2011-08-26T18:31:52Z

Robert Dutnall: Parallel sheet from Thioredoxin

== Summary ==
Parallel sheet from Thioredoxin
== Licensing ==
{{self|cc-by-sa-3.0}}

File:Tut antiparallel sheet.pdb

2011-08-26T18:31:25Z

Robert Dutnall: Antiparallel sheet from thioredoxin

== Summary ==
Antiparallel sheet from thioredoxin
== Licensing ==
{{self|cc-by-sa-3.0}}

User:Robert Dutnall/Sandbox 1 sheets

2011-08-26T17:46:49Z

Robert Dutnall: New page: == Biochemistry Tutorial #2 - Secondary Structure == Part Two =β-strands and β-sheets= In helices, the polypeptide mainchain twists into a path that resembles a spiral staircase. Just...

== Biochemistry Tutorial #2 - Secondary Structure ==

Part Two

=β-strands and β-sheets=

In helices, the polypeptide mainchain twists into a path that resembles a spiral staircase. Just like spiral staircases, helices come in different forms, depending on how tightly twisted the mainchain is. The form of a helix can be described by parameters such as the number of steps (amino acids) it takes to complete a turn (a 360o rotation around the long axis of the helix), and how far you travel along the helix axis in one complete turn. Helices can also be left-handed or right-handed. For proteins composed of L-amino acids, helices are almost always right-handed (a notable exception is the type I poly-proline helix). Although several types of helix form are possible, two regular helices are very common in proteins: the α-helix and the 310-helix.

==The α-helix==

α-helices are the most common type of regular helix found in proteins. They are characterized by the following helix parameters:
::Dihedral angles: Φ ~ -60o, φ ~ -45o
::Repeat (number of residues per turn) = 3.6
::Rise (translation along axis per amino acid residue) = 1.5 Angstroms (0.15 nm)
::Twist (rotation around axis per amino acid residue) = 100o (= 360o/repeat)
::Pitch (translation along axis per turn) = 5.4 Angstroms (= 0.54 nm = Repeat x Rise)

The helix shown below is a 19 amino acid chain in α-helical conformation.
<Structure load='Tut_alpha_helix.pdb' size='500' frame='true' align='left' caption='' scene='User:Robert_Dutnall/Sandbox_1_alpha_helix/A_helix_load/1'/>

All the atoms are shown in this initial orientation (C = green; N = blue; O = red; S = yellow; H = white). The helix axis runs vertically, approximately parallel to the plane of the screen.

<scene name='User:Robert_Dutnall/Sandbox_1_alpha_helix/A_helix_mainchain/3'>Click here</scene> to show only the polypeptide mainchain (NH, Cα, and C=O).

Identify the N- and C-termini. <scene name='User:Robert_Dutnall/Sandbox_1_alpha_helix/A_helix_mainchain_label/4'>Click here to see if you were correct.</scene>

<scene name='User:Robert_Dutnall/Sandbox_1_alpha_helix/A_helix_mainchain_label_ribbon/3'>Click here to add a ribbon that will help show the path of the mainchain. </scene> You should be able to see that it is helical with a right-handed twist (you rotate to the right as you move along the helix axis).

Click the "toggle spin" button in the box to stop the structure from rotating. Now use your mouse to rotate the structure to look down the helix axis. If you have any problems with finding this view, <scene name='User:Robert_Dutnall/Sandbox_1_alpha_helix/A_helix_mainchain_label_axis/3'>click here </scene>to zoom in and look down the helix axis from the N-terminal end.

<scene name='User:Robert_Dutnall/Sandbox_1_alpha_helix/A_helix_mainchain_label/4'>Click here to zoom out again.</scene> Look at the structure carefully and identify the mainchain NH and C=O groups. What is the orientation of these groups with respect to the helix axis?

<scene name='User:Robert_Dutnall/Sandbox_1_alpha_helix/A_helix_mainchain_label_hbonds/10'>Click here to zoom in a little and add hydrogen bonds for the mainchain (dashed lines).</scene> The hydrogen bonds connect backbone NH groups and C=O groups. The N-H group is the hydrogen bond donor, the oxygen in the C=O group is the acceptor (N-H--->O=C). Each hydrogen bond is approximately 3.0 Angstroms (0.3 nm) in length (measured between the N and the O). These hydrogen bonds connect amino acids that are spaced 4 residues apart in the primary sequence. The NH group is from amino acid X and the O is from amino acid X-4 (where X is the number of the amino acid in the sequence).

<scene name='User:Robert_Dutnall/Sandbox_1_alpha_helix/A_helix_mainchain_label_hbonds/9'>Click here to zoom out again.</scene> You should be able to see that all of the mainchain NH and C=O groups are involved in hydrogen bonds. This is possible because 1) all the mainchain NH groups and C=O groups are parallel to the helix axis, 2) all the NH groups point toward the N-terminus of the helix, and 3) all the C=O groups point toward the C-terminus. Only the NH groups in the first (N-terminal) turn, and the C=O groups in the last (C-terminal) turn of the helix do not have hydrogen bonding partners. However, if this helix were part of a larger protein, these groups would participate in hydrogen bonds with other parts of the protein. This is called 'helix capping' and the other groups involved are typically from amino acid side chains (that are called 'helix capping residues').

<scene name='User:Robert_Dutnall/Sandbox_1_alpha_helix/A_helix_sidechains/3'>Click here to show the side chains again.</scene> The atoms of each amino side chain have been colored light blue to show them more clearly. <scene name='User:Robert_Dutnall/Sandbox_1_alpha_helix/A_helix_sidechains_axis/1'>Click here to change the view to look down the helix axis.</scene>

What is the general orientation of the side chains with respect to the helix axis? You should observe that each side chain points away from the helix axis, but points down toward the N-terminus of the helix (this is clearer if you only show the first bond of each side chain: <scene name='User:Robert_Dutnall/Sandbox_1_alpha_helix/A_helix_sidechains_cropped/1'>click here</scene> or <scene name='User:Robert_Dutnall/Sandbox_1_alpha_helix/A_helix_sidechains_cropped/2'>click here</scene>).

==The 310-helix==

310-helices are also found in proteins but are less common than α-helices. They are characterized by the following helix parameters:
::Dihedral angles: Φ ~ -49o, φ ~ -26o
::Repeat (number of residues per turn) = 3.0
::Rise (translation along axis per amino acid residue) = 2.0 Angstroms (0.2 nm)
::Twist (rotation around axis per amino acid residue) = 120o (= 360o/repeat)
::Pitch (translation along axis per turn) = 6.0 Angstroms (= 0.6 nm = Repeat x Rise)

The helix shown below is a 19 amino acid chain in 310-helical conformation.
<Structure load='Tut_3-10_helix.pdb' size='500' frame='true' align='left' caption='' scene='User:Robert_Dutnall/Sandbox_1_alpha_helix/310_helix_load/4'/>

All the atoms are shown in this initial orientation (C = green; N = blue; O = red; S = yellow; H = white). The helix axis runs vertically, approximately parallel to the plane of the screen.

<scene name='User:Robert_Dutnall/Sandbox_1_alpha_helix/310_helix_mainchain/2'>Click here</scene> to show only the polypeptide mainchain (NH, Cα, and C=O). The N- and C-termini are labeled.

<scene name='User:Robert_Dutnall/Sandbox_1_alpha_helix/310_helix_mainchain_ribbon/2'>Click here to add a ribbon that will help show the path of the mainchain. </scene> You should be able to see that just like the α-helix, it is helical with a right-handed twist, and again, all the mainchain NH groups point toward the N-terminus, and all the mainchain C=O groups point toward the C-terminus.

The difference between an α-helix and a 310-helix lies in the helix parameters. A 310-helix is more tightly twisted so that the mainchain completes one turn every 3 amino acids (instead of 3.6 for the α-helix). This also results in a larger rise and pitch so that the 310-helix is longer than an α-helix (of the same number of residues).

<scene name='User:Robert_Dutnall/Sandbox_1_alpha_helix/310_helix_mainchain_axis/1'>Click here </scene>to zoom in and look down the helix axis from the N-terminal end. You'll be able to see the triangular shape of the mainchain.

<scene name='User:Robert_Dutnall/Sandbox_1_alpha_helix/310_helix_mainchain_hbonds/1'>Click here to zoom out again and display hydrogen bonds for the mainchain.</scene> Once again, all of the mainchain NH and C=O groups are involved in hydrogen bonds. However, now the hydrogen bonds connect amino acids that are spaced 3 residues apart in the primary sequence. The NH group is from amino acid X and the O is from amino acid X-3 (where X is the number of the amino acid in the sequence). <scene name='User:Robert_Dutnall/Sandbox_1_alpha_helix/310_helix_mainchain_hbonds/2'>Click here</scene> to zoom in and you should be able to see this more clearly.

<scene name='User:Robert_Dutnall/Sandbox_1_alpha_helix/310_helix_sidechains/1'>Click here to zoom out and show the side chains again.</scene> The atoms of each amino side chain have been colored light blue to show them more clearly. <scene name='User:Robert_Dutnall/Sandbox_1_alpha_helix/310_helix_sidechains_axis/2'>Click here to change the view to look down the helix axis.</scene>

As for the α-helix, each side chain points away from the helix axis, and points down toward the N-terminus of the helix. However, because the 310-helix repeat parameter is an integer (= 3.0), the side chains are spaced 120o apart and form 3 distinct sides to the helix. You'll see this more clearly if the side chains are colored in groups to show this (residues 1,4,7,10 etc are blue; residues 2,5,8,11 etc are purple; residues 3,6,9,12 etc are yellow): <scene name='User:Robert_Dutnall/Sandbox_1_alpha_helix/310_helix_sidechains_tricolor/1'>click here to look from the side</scene> or <scene name='User:Robert_Dutnall/Sandbox_1_alpha_helix/310_helix_sidechains_tricol_ax/1'>click here to view down the helix axis</scene>.

= =
[[User:Robert Dutnall/Sandbox_1_alpha_helix|Click here to go on to back to the first part of this tutorial.]]

User:Robert Dutnall/Sandbox 1 alpha helix

2011-08-26T17:43:45Z

Robert Dutnall:

== Biochemistry Tutorial #2 - Secondary Structure ==

The secondary structure of a protein is defined by the local conformation of its backbone (polypeptide mainchain). There are two major types of regular secondary structures in proteins: helices and sheets. There are also regular turn structures. Turns often connect one element of secondary structure to another in the overall fold of the protein. Other parts of the protein mainchain may adopt more irregularly defined loops. This tutorial will focus mainly on helices and sheets.

''Note: in these tutorials, the images are 3D interactive images. You can manipulate them as you wish to get a better view of the molecules.''

You can rotate the structures by holding down the right mouse button and dragging. At any time you can click the 'toggle spin' button in box to stop/start the structure spinning.

Other things you can do:
::To rotate: left drag
::To Zoom: scroll button or shift + left drag
::To Translate: ctrl + right drag
::Right click to bring up an options menu

=Helices=

In helices, the polypeptide mainchain twists into a path that resembles a spiral staircase. Just like spiral staircases, helices come in different forms, depending on how tightly twisted the mainchain is. The form of a helix can be described by parameters such as the number of steps (amino acids) it takes to complete a turn (a 360o rotation around the long axis of the helix), and how far you travel along the helix axis in one complete turn. Helices can also be left-handed or right-handed. For proteins composed of L-amino acids, helices are almost always right-handed (a notable exception is the type I poly-proline helix). Although several types of helix form are possible, two regular helices are very common in proteins: the α-helix and the 310-helix.

==The α-helix==

α-helices are the most common type of regular helix found in proteins. They are characterized by the following helix parameters:
::Dihedral angles: Φ ~ -60o, φ ~ -45o
::Repeat (number of residues per turn) = 3.6
::Rise (translation along axis per amino acid residue) = 1.5 Angstroms (0.15 nm)
::Twist (rotation around axis per amino acid residue) = 100o (= 360o/repeat)
::Pitch (translation along axis per turn) = 5.4 Angstroms (= 0.54 nm = Repeat x Rise)

The helix shown below is a 19 amino acid chain in α-helical conformation.
<Structure load='Tut_alpha_helix.pdb' size='500' frame='true' align='left' caption='' scene='User:Robert_Dutnall/Sandbox_1_alpha_helix/A_helix_load/1'/>

All the atoms are shown in this initial orientation (C = green; N = blue; O = red; S = yellow; H = white). The helix axis runs vertically, approximately parallel to the plane of the screen.

<scene name='User:Robert_Dutnall/Sandbox_1_alpha_helix/A_helix_mainchain/3'>Click here</scene> to show only the polypeptide mainchain (NH, Cα, and C=O).

Identify the N- and C-termini. <scene name='User:Robert_Dutnall/Sandbox_1_alpha_helix/A_helix_mainchain_label/4'>Click here to see if you were correct.</scene>

<scene name='User:Robert_Dutnall/Sandbox_1_alpha_helix/A_helix_mainchain_label_ribbon/3'>Click here to add a ribbon that will help show the path of the mainchain. </scene> You should be able to see that it is helical with a right-handed twist (you rotate to the right as you move along the helix axis).

Click the "toggle spin" button in the box to stop the structure from rotating. Now use your mouse to rotate the structure to look down the helix axis. If you have any problems with finding this view, <scene name='User:Robert_Dutnall/Sandbox_1_alpha_helix/A_helix_mainchain_label_axis/3'>click here </scene>to zoom in and look down the helix axis from the N-terminal end.

<scene name='User:Robert_Dutnall/Sandbox_1_alpha_helix/A_helix_mainchain_label/4'>Click here to zoom out again.</scene> Look at the structure carefully and identify the mainchain NH and C=O groups. What is the orientation of these groups with respect to the helix axis?

<scene name='User:Robert_Dutnall/Sandbox_1_alpha_helix/A_helix_mainchain_label_hbonds/10'>Click here to zoom in a little and add hydrogen bonds for the mainchain (dashed lines).</scene> The hydrogen bonds connect backbone NH groups and C=O groups. The N-H group is the hydrogen bond donor, the oxygen in the C=O group is the acceptor (N-H--->O=C). Each hydrogen bond is approximately 3.0 Angstroms (0.3 nm) in length (measured between the N and the O). These hydrogen bonds connect amino acids that are spaced 4 residues apart in the primary sequence. The NH group is from amino acid X and the O is from amino acid X-4 (where X is the number of the amino acid in the sequence).

<scene name='User:Robert_Dutnall/Sandbox_1_alpha_helix/A_helix_mainchain_label_hbonds/9'>Click here to zoom out again.</scene> You should be able to see that all of the mainchain NH and C=O groups are involved in hydrogen bonds. This is possible because 1) all the mainchain NH groups and C=O groups are parallel to the helix axis, 2) all the NH groups point toward the N-terminus of the helix, and 3) all the C=O groups point toward the C-terminus. Only the NH groups in the first (N-terminal) turn, and the C=O groups in the last (C-terminal) turn of the helix do not have hydrogen bonding partners. However, if this helix were part of a larger protein, these groups would participate in hydrogen bonds with other parts of the protein. This is called 'helix capping' and the other groups involved are typically from amino acid side chains (that are called 'helix capping residues').

<scene name='User:Robert_Dutnall/Sandbox_1_alpha_helix/A_helix_sidechains/3'>Click here to show the side chains again.</scene> The atoms of each amino side chain have been colored light blue to show them more clearly. <scene name='User:Robert_Dutnall/Sandbox_1_alpha_helix/A_helix_sidechains_axis/1'>Click here to change the view to look down the helix axis.</scene>

What is the general orientation of the side chains with respect to the helix axis? You should observe that each side chain points away from the helix axis, but points down toward the N-terminus of the helix (this is clearer if you only show the first bond of each side chain: <scene name='User:Robert_Dutnall/Sandbox_1_alpha_helix/A_helix_sidechains_cropped/1'>click here</scene> or <scene name='User:Robert_Dutnall/Sandbox_1_alpha_helix/A_helix_sidechains_cropped/2'>click here</scene>).

==The 310-helix==

310-helices are also found in proteins but are less common than α-helices. They are characterized by the following helix parameters:
::Dihedral angles: Φ ~ -49o, φ ~ -26o
::Repeat (number of residues per turn) = 3.0
::Rise (translation along axis per amino acid residue) = 2.0 Angstroms (0.2 nm)
::Twist (rotation around axis per amino acid residue) = 120o (= 360o/repeat)
::Pitch (translation along axis per turn) = 6.0 Angstroms (= 0.6 nm = Repeat x Rise)

The helix shown below is a 19 amino acid chain in 310-helical conformation.
<Structure load='Tut_3-10_helix.pdb' size='500' frame='true' align='left' caption='' scene='User:Robert_Dutnall/Sandbox_1_alpha_helix/310_helix_load/4'/>

All the atoms are shown in this initial orientation (C = green; N = blue; O = red; S = yellow; H = white). The helix axis runs vertically, approximately parallel to the plane of the screen.

<scene name='User:Robert_Dutnall/Sandbox_1_alpha_helix/310_helix_mainchain/2'>Click here</scene> to show only the polypeptide mainchain (NH, Cα, and C=O). The N- and C-termini are labeled.

<scene name='User:Robert_Dutnall/Sandbox_1_alpha_helix/310_helix_mainchain_ribbon/2'>Click here to add a ribbon that will help show the path of the mainchain. </scene> You should be able to see that just like the α-helix, it is helical with a right-handed twist, and again, all the mainchain NH groups point toward the N-terminus, and all the mainchain C=O groups point toward the C-terminus.

The difference between an α-helix and a 310-helix lies in the helix parameters. A 310-helix is more tightly twisted so that the mainchain completes one turn every 3 amino acids (instead of 3.6 for the α-helix). This also results in a larger rise and pitch so that the 310-helix is longer than an α-helix (of the same number of residues).

<scene name='User:Robert_Dutnall/Sandbox_1_alpha_helix/310_helix_mainchain_axis/1'>Click here </scene>to zoom in and look down the helix axis from the N-terminal end. You'll be able to see the triangular shape of the mainchain.

<scene name='User:Robert_Dutnall/Sandbox_1_alpha_helix/310_helix_mainchain_hbonds/1'>Click here to zoom out again and display hydrogen bonds for the mainchain.</scene> Once again, all of the mainchain NH and C=O groups are involved in hydrogen bonds. However, now the hydrogen bonds connect amino acids that are spaced 3 residues apart in the primary sequence. The NH group is from amino acid X and the O is from amino acid X-3 (where X is the number of the amino acid in the sequence). <scene name='User:Robert_Dutnall/Sandbox_1_alpha_helix/310_helix_mainchain_hbonds/2'>Click here</scene> to zoom in and you should be able to see this more clearly.

<scene name='User:Robert_Dutnall/Sandbox_1_alpha_helix/310_helix_sidechains/1'>Click here to zoom out and show the side chains again.</scene> The atoms of each amino side chain have been colored light blue to show them more clearly. <scene name='User:Robert_Dutnall/Sandbox_1_alpha_helix/310_helix_sidechains_axis/2'>Click here to change the view to look down the helix axis.</scene>

As for the α-helix, each side chain points away from the helix axis, and points down toward the N-terminus of the helix. However, because the 310-helix repeat parameter is an integer (= 3.0), the side chains are spaced 120o apart and form 3 distinct sides to the helix. You'll see this more clearly if the side chains are colored in groups to show this (residues 1,4,7,10 etc are blue; residues 2,5,8,11 etc are purple; residues 3,6,9,12 etc are yellow): <scene name='User:Robert_Dutnall/Sandbox_1_alpha_helix/310_helix_sidechains_tricolor/1'>click here to look from the side</scene> or <scene name='User:Robert_Dutnall/Sandbox_1_alpha_helix/310_helix_sidechains_tricol_ax/1'>click here to view down the helix axis</scene>.

= =
[[User:Robert Dutnall/Sandbox_1_sheets|Click here to go on to the next part of this tutorial.]]

User:Robert Dutnall/Sandbox 1 alpha helix

2011-08-26T17:35:28Z

Robert Dutnall:

User:Robert Dutnall/Sandbox 1 alpha helix

2011-08-26T17:33:53Z

Robert Dutnall:

== Biochemistry Tutorial #2 - Secondary Structure ==

The secondary structure of a protein is defined by the local conformation of its backbone (polypeptide mainchain). There are two major types of regular secondary structures in proteins: helices and sheets. There are also regular turn structures. Turns often connect one element of secondary structure to another in the overall fold of the protein. Other parts of the protein mainchain may adopt more irregularly defined loops. This tutorial will focus mainly on helices and sheets.

''Note: in these tutorials, the images are 3D interactive images. You can manipulate them as you wish to get a better view of the molecules.''

You can rotate the structures by holding down the right mouse button and dragging. At any time you can click the 'toggle spin' button in box to stop/start the structure spinning.

Other things you can do:
::To rotate: left drag
::To Zoom: scroll button or shift + left drag
::To Translate: ctrl + right drag
::Right click to bring up an options menu

=Helices=

In helices, the polypeptide mainchain twists into a path that resembles a spiral staircase. Just like spiral staircases, helices come in different forms, depending on how tightly twisted the mainchain is. The form of a helix can be described by parameters such as the number of steps (amino acids) it takes to complete a turn (a 360o rotation around the long axis of the helix), and how far you travel along the helix axis in one complete turn. Helices can also be left-handed or right-handed. For proteins composed of L-amino acids, helices are almost always right-handed (a notable exception is the type I poly-proline helix). Although several types of helix form are possible, two regular helices are very common in proteins: the α-helix and the 310-helix.

==The α-helix==

α-helices are the most common type of regular helix found in proteins. They are characterized by the following helix parameters:
::Dihedral angles: Φ ~ -60o, φ ~ -45o
::Repeat (number of residues per turn) = 3.6
::Rise (translation along axis per amino acid residue) = 1.5 Angstroms (0.15 nm)
::Twist (rotation around axis per amino acid residue) = 100o (= 360o/repeat)
::Pitch (translation along axis per turn) = 5.4 Angstroms (= Repeat x Rise)

The helix shown below is a 19 amino acid chain in α-helical conformation.
<Structure load='Tut_alpha_helix.pdb' size='500' frame='true' align='left' caption='' scene='User:Robert_Dutnall/Sandbox_1_alpha_helix/A_helix_load/1'/>

All the atoms are shown in this initial orientation (C = green; N = blue; O = red; S = yellow; H = white). The helix axis runs vertically, approximately parallel to the plane of the screen.

<scene name='User:Robert_Dutnall/Sandbox_1_alpha_helix/A_helix_mainchain/3'>Click here</scene> to show only the polypeptide mainchain (NH, Cα, and C=O).

Identify the N- and C-termini. <scene name='User:Robert_Dutnall/Sandbox_1_alpha_helix/A_helix_mainchain_label/4'>Click here to see if you were correct.</scene>

<scene name='User:Robert_Dutnall/Sandbox_1_alpha_helix/A_helix_mainchain_label_ribbon/3'>Click here to add a ribbon that will help show the path of the mainchain. </scene> You should be able to see that it is helical with a right-handed twist (you rotate to the right as you move along the helix axis).

Click the "toggle spin" button in the box to stop the structure from rotating. Now use your mouse to rotate the structure to look down the helix axis. If you have any problems with finding this view, <scene name='User:Robert_Dutnall/Sandbox_1_alpha_helix/A_helix_mainchain_label_axis/3'>click here </scene>to zoom in and look down the helix axis from the N-terminal end.

<scene name='User:Robert_Dutnall/Sandbox_1_alpha_helix/A_helix_mainchain_label/4'>Click here to zoom out again.</scene> Look at the structure carefully and identify the mainchain NH and C=O groups. What is the orientation of these groups with respect to the helix axis?

<scene name='User:Robert_Dutnall/Sandbox_1_alpha_helix/A_helix_mainchain_label_hbonds/10'>Click here to zoom in a little and add hydrogen bonds for the mainchain (dashed lines).</scene> The hydrogen bonds connect backbone NH groups and C=O groups. The N-H group is the hydrogen bond donor, the oxygen in the C=O group is the acceptor (N-H--->O=C). Each hydrogen bond is approximately 3.0 Angstroms (0.3 nm) in length (measured between the N and the O). These hydrogen bonds connect amino acids that are spaced 4 residues apart in the primary sequence. The NH group is from amino acid X and the O is from amino acid X-4 (where X is the number of the amino acid in the sequence).

<scene name='User:Robert_Dutnall/Sandbox_1_alpha_helix/A_helix_mainchain_label_hbonds/9'>Click here to zoom out again.</scene> You should be able to see that all of the mainchain NH and C=O groups are involved in hydrogen bonds. This is possible because 1) all the mainchain NH groups and C=O groups are parallel to the helix axis, 2) all the NH groups point toward the N-terminus of the helix, and 3) all the C=O groups point toward the C-terminus. Only the NH groups in the first (N-terminal) turn, and the C=O groups in the last (C-terminal) turn of the helix do not have hydrogen bonding partners. However, if this helix were part of a larger protein, these groups would participate in hydrogen bonds with other parts of the protein. This is called 'helix capping' and the other groups involved are typically from amino acid side chains (that are called 'helix capping residues').

<scene name='User:Robert_Dutnall/Sandbox_1_alpha_helix/A_helix_sidechains/3'>Click here to show the side chains again.</scene> The atoms of each amino side chain have been colored light blue to show them more clearly. <scene name='User:Robert_Dutnall/Sandbox_1_alpha_helix/A_helix_sidechains_axis/1'>Click here to change the view to look down the helix axis.</scene>

What is the general orientation of the side chains with respect to the helix axis? You should observe that each side chain points away from the helix axis, but points down toward the N-terminus of the helix (this is clearer if you only show the first bond of each side chain: <scene name='User:Robert_Dutnall/Sandbox_1_alpha_helix/A_helix_sidechains_cropped/1'>click here</scene> or <scene name='User:Robert_Dutnall/Sandbox_1_alpha_helix/A_helix_sidechains_cropped/2'>click here</scene>).

==The 310-helix==

310-helices are also found in proteins but are less common than α-helices. They are characterized by the following helix parameters:
::Dihedral angles: Φ ~ -49o, φ ~ -26o
::Repeat (number of residues per turn) = 3.0
::Rise (translation along axis per amino acid residue) = 2.0 Angstroms (0.15 nm)
::Twist (rotation around axis per amino acid residue) = 120o (= 360o/repeat)
::Pitch (translation along axis per turn) = 6.0 Angstroms (= Repeat x Rise)

The helix shown below is a 19 amino acid chain in 310-helical conformation.
<Structure load='Tut_3-10_helix.pdb' size='500' frame='true' align='left' caption='' scene='User:Robert_Dutnall/Sandbox_1_alpha_helix/310_helix_load/4'/>

All the atoms are shown in this initial orientation (C = green; N = blue; O = red; S = yellow; H = white). The helix axis runs vertically, approximately parallel to the plane of the screen.

<scene name='User:Robert_Dutnall/Sandbox_1_alpha_helix/310_helix_mainchain/2'>Click here</scene> to show only the polypeptide mainchain (NH, Cα, and C=O). The N- and C-termini are labeled.

<scene name='User:Robert_Dutnall/Sandbox_1_alpha_helix/310_helix_mainchain_ribbon/2'>Click here to add a ribbon that will help show the path of the mainchain. </scene> You should be able to see that just like the α-helix, it is helical with a right-handed twist, and again, all the mainchain NH groups point toward the N-terminus, and all the mainchain C=O groups point toward the C-terminus.

The difference between an α-helix and a 310-helix lies in the helix parameters. A 310-helix is more tightly twisted so that the mainchain completes one turn every 3 amino acids (instead of 3.6 for the α-helix). This also results in a larger rise and pitch so that the 310-helix is longer than an α-helix (of the same number of residues).

<scene name='User:Robert_Dutnall/Sandbox_1_alpha_helix/310_helix_mainchain_axis/1'>Click here </scene>to zoom in and look down the helix axis from the N-terminal end. You'll be able to see the triangular shape of the mainchain.

<scene name='User:Robert_Dutnall/Sandbox_1_alpha_helix/310_helix_mainchain_hbonds/1'>Click here to zoom out again and display hydrogen bonds for the mainchain.</scene> Once again, all of the mainchain NH and C=O groups are involved in hydrogen bonds. However, now the hydrogen bonds connect amino acids that are spaced 3 residues apart in the primary sequence. The NH group is from amino acid X and the O is from amino acid X-3 (where X is the number of the amino acid in the sequence). <scene name='User:Robert_Dutnall/Sandbox_1_alpha_helix/310_helix_mainchain_hbonds/2'>Click here</scene> to zoom in and you should be able to see this more clearly.

<scene name='User:Robert_Dutnall/Sandbox_1_alpha_helix/310_helix_sidechains/1'>Click here to zoom out and show the side chains again.</scene> The atoms of each amino side chain have been colored light blue to show them more clearly. <scene name='User:Robert_Dutnall/Sandbox_1_alpha_helix/310_helix_sidechains_axis/2'>Click here to change the view to look down the helix axis.</scene>

As for the α-helix, each side chain points away from the helix axis, and points down toward the N-terminus of the helix. However, because the 310-helix repeat parameter is an integer (= 3.0), the side chains are spaced 120o apart and form 3 distinct sides to the helix. You'll see this more clearly if the side chains are colored in groups to show this (residues 1,4,7,10 etc are blue; residues 2,5,8,11 etc are purple; residues 3,6,9,12 etc are yellow): <scene name='User:Robert_Dutnall/Sandbox_1_alpha_helix/310_helix_sidechains_tricolor/1'>click here to look from the side</scene> or <scene name='User:Robert_Dutnall/Sandbox_1_alpha_helix/310_helix_sidechains_tricol_ax/1'>click here to view down the helix axis</scene>.

= =

User:Robert Dutnall/Sandbox 1 alpha helix

2011-08-26T17:32:28Z

Robert Dutnall:

== Biochemistry Tutorial #2 - Secondary Structure ==

The secondary structure of a protein is defined by the local conformation of its backbone (polypeptide mainchain). There are two major types of regular secondary structures in proteins: helices and sheets. There are also regular turn structures. Turns often connect one element of secondary structure to another in the overall fold of the protein. Other parts of the protein mainchain may adopt more irregularly defined loops. This tutorial will focus mainly on helices and sheets.

''Note: in these tutorials, the images are 3D interactive images. You can manipulate them as you wish to get a better view of the molecules.''

You can rotate the structures by holding down the right mouse button and dragging. At any time you can click the 'toggle spin' button in box to stop/start the structure spinning.

Other things you can do:
::To rotate: left drag
::To Zoom: scroll button or shift + left drag
::To Translate: ctrl + right drag
::Right click to bring up an options menu

=Helices=

In helices, the polypeptide mainchain twists into a path that resembles a spiral staircase. Just like spiral staircases, helices come in different forms, depending on how tightly twisted the mainchain is. The form of a helix can be described by parameters such as the number of steps (amino acids) it takes to complete a turn (a 360o rotation around the long axis of the helix), and how far you travel in one complete turn. Helices can also be left-handed or right-handed. For proteins composed of L-amino acids, helices are almost always right-handed (a noteable exception is the type I poly-proline helix). Although several types of helix are possible, two regular helices are very common in proteins: the α-helix and the 310-helix.

==The α-helix==

α-helices are the most common type of regular helix found in proteins. They are characterized by the following helix parameters:
::Dihedral angles: Φ ~ -60o, φ ~ -45o
::Repeat (number of residues per turn) = 3.6
::Rise (translation along axis per amino acid residue) = 1.5 Angstroms (0.15 nm)
::Twist (rotation around axis per amino acid residue) = 100o (= 360o/repeat)
::Pitch (translation along axis per turn) = 5.4 Angstroms (= Repeat x Rise)

The helix shown below is a 19 amino acid chain in α-helical conformation.
<Structure load='Tut_alpha_helix.pdb' size='500' frame='true' align='left' caption='' scene='User:Robert_Dutnall/Sandbox_1_alpha_helix/A_helix_load/1'/>

All the atoms are shown in this initial orientation (C = green; N = blue; O = red; S = yellow; H = white). The helix axis runs vertically, approximately parallel to the plane of the screen.

<scene name='User:Robert_Dutnall/Sandbox_1_alpha_helix/A_helix_mainchain/3'>Click here</scene> to show only the polypeptide mainchain (NH, Cα, and C=O).

Identify the N- and C-termini. <scene name='User:Robert_Dutnall/Sandbox_1_alpha_helix/A_helix_mainchain_label/4'>Click here to see if you were correct.</scene>

<scene name='User:Robert_Dutnall/Sandbox_1_alpha_helix/A_helix_mainchain_label_ribbon/3'>Click here to add a ribbon that will help show the path of the mainchain. </scene> You should be able to see that it is helical with a right-handed twist (you rotate to the right as you move along the helix axis).

Click the "toggle spin" button in the box to stop the structure from rotating. Now use your mouse to rotate the structure to look down the helix axis. If you have any problems with finding this view, <scene name='User:Robert_Dutnall/Sandbox_1_alpha_helix/A_helix_mainchain_label_axis/3'>click here </scene>to zoom in and look down the helix axis from the N-terminal end.

<scene name='User:Robert_Dutnall/Sandbox_1_alpha_helix/A_helix_mainchain_label/4'>Click here to zoom out again.</scene> Look at the structure carefully and identify the mainchain NH and C=O groups. What is the orientation of these groups with respect to the helix axis?

<scene name='User:Robert_Dutnall/Sandbox_1_alpha_helix/A_helix_mainchain_label_hbonds/10'>Click here to zoom in a little and add hydrogen bonds for the mainchain (dashed lines).</scene> The hydrogen bonds connect backbone NH groups and C=O groups. The N-H group is the hydrogen bond donor, the oxygen in the C=O group is the acceptor (N-H--->O=C). Each hydrogen bond is approximately 3.0 Angstroms (0.3 nm) in length (measured between the N and the O). These hydrogen bonds connect amino acids that are spaced 4 residues apart in the primary sequence. The NH group is from amino acid X and the O is from amino acid X-4 (where X is the number of the amino acid in the sequence).

<scene name='User:Robert_Dutnall/Sandbox_1_alpha_helix/A_helix_mainchain_label_hbonds/9'>Click here to zoom out again.</scene> You should be able to see that all of the mainchain NH and C=O groups are involved in hydrogen bonds. This is possible because 1) all the mainchain NH groups and C=O groups are parallel to the helix axis, 2) all the NH groups point toward the N-terminus of the helix, and 3) all the C=O groups point toward the C-terminus. Only the NH groups in the first (N-terminal) turn, and the C=O groups in the last (C-terminal) turn of the helix do not have hydrogen bonding partners. However, if this helix were part of a larger protein, these groups would participate in hydrogen bonds with other parts of the protein. This is called 'helix capping' and the other groups involved are typically from amino acid side chains (that are called 'helix capping residues').

<scene name='User:Robert_Dutnall/Sandbox_1_alpha_helix/A_helix_sidechains/3'>Click here to show the side chains again.</scene> The atoms of each amino side chain have been colored light blue to show them more clearly. <scene name='User:Robert_Dutnall/Sandbox_1_alpha_helix/A_helix_sidechains_axis/1'>Click here to change the view to look down the helix axis.</scene>

What is the general orientation of the side chains with respect to the helix axis? You should observe that each side chain points away from the helix axis, but points down toward the N-terminus of the helix (this is clearer if you only show the first bond of each side chain: <scene name='User:Robert_Dutnall/Sandbox_1_alpha_helix/A_helix_sidechains_cropped/1'>click here</scene> or <scene name='User:Robert_Dutnall/Sandbox_1_alpha_helix/A_helix_sidechains_cropped/2'>click here</scene>).

==The 310-helix==

310-helices are also found in proteins but are less common than α-helices. They are characterized by the following helix parameters:
::Dihedral angles: Φ ~ -49o, φ ~ -26o
::Repeat (number of residues per turn) = 3.0
::Rise (translation along axis per amino acid residue) = 2.0 Angstroms (0.15 nm)
::Twist (rotation around axis per amino acid residue) = 120o (= 360o/repeat)
::Pitch (translation along axis per turn) = 6.0 Angstroms (= Repeat x Rise)

The helix shown below is a 19 amino acid chain in 310-helical conformation.
<Structure load='Tut_3-10_helix.pdb' size='500' frame='true' align='left' caption='' scene='User:Robert_Dutnall/Sandbox_1_alpha_helix/310_helix_load/4'/>

All the atoms are shown in this initial orientation (C = green; N = blue; O = red; S = yellow; H = white). The helix axis runs vertically, approximately parallel to the plane of the screen.

<scene name='User:Robert_Dutnall/Sandbox_1_alpha_helix/310_helix_mainchain/2'>Click here</scene> to show only the polypeptide mainchain (NH, Cα, and C=O). The N- and C-termini are labeled.

<scene name='User:Robert_Dutnall/Sandbox_1_alpha_helix/310_helix_mainchain_ribbon/2'>Click here to add a ribbon that will help show the path of the mainchain. </scene> You should be able to see that just like the α-helix, it is helical with a right-handed twist, and again, all the mainchain NH groups point toward the N-terminus, and all the mainchain C=O groups point toward the C-terminus.

The difference between an α-helix and a 310-helix lies in the helix parameters. A 310-helix is more tightly twisted so that the mainchain completes one turn every 3 amino acids (instead of 3.6 for the α-helix). This also results in a larger rise and pitch so that the 310-helix is longer than an α-helix (of the same number of residues).

<scene name='User:Robert_Dutnall/Sandbox_1_alpha_helix/310_helix_mainchain_axis/1'>Click here </scene>to zoom in and look down the helix axis from the N-terminal end. You'll be able to see the triangular shape of the mainchain.

<scene name='User:Robert_Dutnall/Sandbox_1_alpha_helix/310_helix_mainchain_hbonds/1'>Click here to zoom out again and display hydrogen bonds for the mainchain.</scene> Once again, all of the mainchain NH and C=O groups are involved in hydrogen bonds. However, now the hydrogen bonds connect amino acids that are spaced 3 residues apart in the primary sequence. The NH group is from amino acid X and the O is from amino acid X-3 (where X is the number of the amino acid in the sequence). <scene name='User:Robert_Dutnall/Sandbox_1_alpha_helix/310_helix_mainchain_hbonds/2'>Click here</scene> to zoom in and you should be able to see this more clearly.

<scene name='User:Robert_Dutnall/Sandbox_1_alpha_helix/310_helix_sidechains/1'>Click here to zoom out and show the side chains again.</scene> The atoms of each amino side chain have been colored light blue to show them more clearly. <scene name='User:Robert_Dutnall/Sandbox_1_alpha_helix/310_helix_sidechains_axis/2'>Click here to change the view to look down the helix axis.</scene>

As for the α-helix, each side chain points away from the helix axis, and points down toward the N-terminus of the helix. However, because the 310-helix repeat parameter is an integer (= 3.0), the side chains are spaced 120o apart and form 3 distinct sides to the helix. You'll see this more clearly if the side chains are colored in groups to show this (residues 1,4,7,10 etc are blue; residues 2,5,8,11 etc are purple; residues 3,6,9,12 etc are yellow): <scene name='User:Robert_Dutnall/Sandbox_1_alpha_helix/310_helix_sidechains_tricolor/1'>click here to look from the side</scene> or <scene name='User:Robert_Dutnall/Sandbox_1_alpha_helix/310_helix_sidechains_tricol_ax/1'>click here to view down the helix axis</scene>.

= =

User:Robert Dutnall/Sandbox 1 alpha helix

2011-08-26T17:20:47Z

Robert Dutnall:

== Biochemistry Tutorial #2 - Secondary Structure ==

The secondary structure of a protein is defined by the local conformation of its backbone (polypeptide mainchain). There are two major types of regular secondary structures in proteins: helices and sheets. There are also regular turn structures. Turns often connect one element of secondary structure to another in the overall fold of the protein. Other parts of the protein mainchain may adopt more irregularly defined loops. This tutorial will focus mainly on

''Note: in these tutorials, the images are 3D interactive images. You can manipulate them as you wish to get a better view of the molecules.''

You can rotate the structures by holding down the right mouse button and dragging. At any time you can click the 'toggle spin' button in box to stop/start the structure spinning.

Other things you can do:
::To rotate: left drag
::To Zoom: scroll button or shift + left drag
::To Translate: ctrl + right drag
::Right click to bring up an options menu

=Helices=

==An α-helix==

α-helices are the most common type of regular helix found in proteins. They are characterized by the following helix parameters:
::Dihedral angles: Φ ~ -60o, φ ~ -45o
::Repeat (number of residues per turn) = 3.6
::Rise (translation along axis per amino acid residue) = 1.5 Angstroms (0.15 nm)
::Twist (rotation around axis per amino acid residue) = 100o (= 360o/repeat)
::Pitch (translation along axis per turn) = 5.4 Angstroms (= Repeat x Rise)

The helix shown below is a 19 amino acid chain in α-helical conformation.
<Structure load='Tut_alpha_helix.pdb' size='500' frame='true' align='left' caption='' scene='User:Robert_Dutnall/Sandbox_1_alpha_helix/A_helix_load/1'/>

All the atoms are shown in this initial orientation (C = green; N = blue; O = red; S = yellow; H = white). The helix axis runs vertically, approximately parallel to the plane of the screen.

<scene name='User:Robert_Dutnall/Sandbox_1_alpha_helix/A_helix_mainchain/3'>Click here</scene> to show only the polypeptide mainchain (NH, Cα, and C=O).

Identify the N- and C-termini. <scene name='User:Robert_Dutnall/Sandbox_1_alpha_helix/A_helix_mainchain_label/4'>Click here to see if you were correct.</scene>

<scene name='User:Robert_Dutnall/Sandbox_1_alpha_helix/A_helix_mainchain_label_ribbon/3'>Click here to add a ribbon that will help show the path of the mainchain. </scene> You should be able to see that it is helical with a right-handed twist (you rotate to the right as you move along the helix axis).

Click the "toggle spin" button in the box to stop the structure from rotating. Now use your mouse to rotate the structure to look down the helix axis. If you have any problems with finding this view, <scene name='User:Robert_Dutnall/Sandbox_1_alpha_helix/A_helix_mainchain_label_axis/3'>click here </scene>to zoom in and look down the helix axis from the N-terminal end.

<scene name='User:Robert_Dutnall/Sandbox_1_alpha_helix/A_helix_mainchain_label/4'>Click here to zoom out again.</scene> Look at the structure carefully and identify the mainchain NH and C=O groups. What is the orientation of these groups with respect to the helix axis?

<scene name='User:Robert_Dutnall/Sandbox_1_alpha_helix/A_helix_mainchain_label_hbonds/10'>Click here to zoom in a little and add hydrogen bonds for the mainchain (dashed lines).</scene> The hydrogen bonds connect backbone NH groups and C=O groups. The N-H group is the hydrogen bond donor, the oxygen in the C=O group is the acceptor (N-H--->O=C). Each hydrogen bond is approximately 3.0 Angstroms (0.3 nm) in length (measured between the N and the O). These hydrogen bonds connect amino acids that are spaced 4 residues apart in the primary sequence. The NH group is from amino acid X and the O is from amino acid X-4 (where X is the number of the amino acid in the sequence).

<scene name='User:Robert_Dutnall/Sandbox_1_alpha_helix/A_helix_mainchain_label_hbonds/9'>Click here to zoom out again.</scene> You should be able to see that all of the mainchain NH and C=O groups are involved in hydrogen bonds. This is possible because 1) all the mainchain NH groups and C=O groups are parallel to the helix axis, 2) all the NH groups point toward the N-terminus of the helix, and 3) all the C=O groups point toward the C-terminus. Only the NH groups in the first (N-terminal) turn, and the C=O groups in the last (C-terminal) turn of the helix do not have hydrogen bonding partners. However, if this helix were part of a larger protein, these groups would participate in hydrogen bonds with other parts of the protein. This is called 'helix capping' and the other groups involved are typically from amino acid side chains (that are called 'helix capping residues').

<scene name='User:Robert_Dutnall/Sandbox_1_alpha_helix/A_helix_sidechains/3'>Click here to show the side chains again.</scene> The atoms of each amino side chain have been colored light blue to show them more clearly. <scene name='User:Robert_Dutnall/Sandbox_1_alpha_helix/A_helix_sidechains_axis/1'>Click here to change the view to look down the helix axis.</scene>

What is the general orientation of the side chains with respect to the helix axis? You should observe that each side chain points away from the helix axis, but points down toward the N-terminus of the helix (this is clearer if you only show the first bond of each side chain: <scene name='User:Robert_Dutnall/Sandbox_1_alpha_helix/A_helix_sidechains_cropped/1'>click here</scene> or <scene name='User:Robert_Dutnall/Sandbox_1_alpha_helix/A_helix_sidechains_cropped/2'>click here</scene>).

==An 310-helix==

310-helices are also found in proteins but are less common than α-helices. They are characterized by the following helix parameters:
::Dihedral angles: Φ ~ -49o, φ ~ -26o
::Repeat (number of residues per turn) = 3.0
::Rise (translation along axis per amino acid residue) = 2.0 Angstroms (0.15 nm)
::Twist (rotation around axis per amino acid residue) = 120o (= 360o/repeat)
::Pitch (translation along axis per turn) = 6.0 Angstroms (= Repeat x Rise)

The helix shown below is a 19 amino acid chain in 310-helical conformation.
<Structure load='Tut_3-10_helix.pdb' size='500' frame='true' align='left' caption='' scene='User:Robert_Dutnall/Sandbox_1_alpha_helix/310_helix_load/4'/>

All the atoms are shown in this initial orientation (C = green; N = blue; O = red; S = yellow; H = white). The helix axis runs vertically, approximately parallel to the plane of the screen.

<scene name='User:Robert_Dutnall/Sandbox_1_alpha_helix/310_helix_mainchain/2'>Click here</scene> to show only the polypeptide mainchain (NH, Cα, and C=O). The N- and C-termini are labeled.

<scene name='User:Robert_Dutnall/Sandbox_1_alpha_helix/310_helix_mainchain_ribbon/2'>Click here to add a ribbon that will help show the path of the mainchain. </scene> You should be able to see that just like the α-helix, it is helical with a right-handed twist, and again, all the mainchain NH groups point toward the N-terminus, and all the mainchain C=O groups point toward the C-terminus.

The difference between an α-helix and a 310-helix lies in the helix parameters. A 310-helix is more tightly twisted so that the mainchain completes one turn every 3 amino acids (instead of 3.6 for the α-helix). This also results in a larger rise and pitch so that the 310-helix is longer than an α-helix (of the same number of residues).

<scene name='User:Robert_Dutnall/Sandbox_1_alpha_helix/310_helix_mainchain_axis/1'>Click here </scene>to zoom in and look down the helix axis from the N-terminal end. You'll be able to see the triangular shape of the mainchain.

<scene name='User:Robert_Dutnall/Sandbox_1_alpha_helix/310_helix_mainchain_hbonds/1'>Click here to zoom out again and display hydrogen bonds for the mainchain.</scene> Once again, all of the mainchain NH and C=O groups are involved in hydrogen bonds. However, now the hydrogen bonds connect amino acids that are spaced 3 residues apart in the primary sequence. The NH group is from amino acid X and the O is from amino acid X-3 (where X is the number of the amino acid in the sequence). <scene name='User:Robert_Dutnall/Sandbox_1_alpha_helix/310_helix_mainchain_hbonds/2'>Click here</scene> to zoom in and you should be able to see this more clearly.

<scene name='User:Robert_Dutnall/Sandbox_1_alpha_helix/310_helix_sidechains/1'>Click here to zoom out and show the side chains again.</scene> The atoms of each amino side chain have been colored light blue to show them more clearly. <scene name='User:Robert_Dutnall/Sandbox_1_alpha_helix/310_helix_sidechains_axis/2'>Click here to change the view to look down the helix axis.</scene>

As for the α-helix, each side chain points away from the helix axis, and points down toward the N-terminus of the helix. However, because the 310-helix repeat parameter is an integer (= 3.0), the side chains are spaced 120o apart and form 3 distinct sides to the helix. You'll see this more clearly if the side chains are colored in groups to show this (residues 1,4,7,10 etc are blue; residues 2,5,8,11 etc are purple; residues 3,6,9,12 etc are yellow): <scene name='User:Robert_Dutnall/Sandbox_1_alpha_helix/310_helix_sidechains_tricolor/1'>click here to look from the side</scene> or <scene name='User:Robert_Dutnall/Sandbox_1_alpha_helix/310_helix_sidechains_tricol_ax/1'>click here to view down the helix axis</scene>.

= =

User:Robert Dutnall/Sandbox 1 alpha helix

2011-08-26T00:23:35Z

Robert Dutnall:

== Biochemistry Tutorial #2 - Secondary Structure ==

The secondary structure of a protein is defined by the local conformation of its backbone (polypeptide mainchain). There are two major types of regular secondary structures in proteins: helices and sheets. There are also regular turn structures. Turns often connect one element of secondary structure to another in the overall fold of the protein. Other parts of the protein mainchain may adopt more irregularly defined loops. This tutorial will focus mainly on

''Note: in these tutorials, the images are 3D interactive images. You can manipulate them as you wish to get a better view of the molecules.''

You can rotate the structures by holding down the right mouse button and dragging. At any time you can click the 'toggle spin' button in box to stop/start the structure spinning.

Other things you can do:
::To rotate: left drag
::To Zoom: scroll button or shift + left drag
::To Translate: ctrl + right drag
::Right click to bring up an options menu

=Helices=

==An α-helix==

α-helices are the most common type of regular helix found in proteins. They are characterized by the following helix parameters:
::Dihedral angles: Φ ~ -60o, φ ~ -45o
::Repeat (number of residues per turn) = 3.6
::Rise (translation along axis per amino acid residue) = 1.5 Angstroms (0.15 nm)
::Twist (rotation around axis per amino acid residue) = 100o (= 360o/repeat)
::Pitch (translation along axis per turn) = 5.4 Angstroms (= Repeat x Rise)

The helix shown below is a 19 amino acid chain in α-helical conformation.
<Structure load='Tut_alpha_helix.pdb' size='500' frame='true' align='left' caption='' scene='User:Robert_Dutnall/Sandbox_1_alpha_helix/A_helix_load/1'/>

All the atoms are shown in this initial orientation (C = green; N = blue; O = red; S = yellow; H = white). The helix axis runs vertically, approximately parallel to the plane of the screen.

<scene name='User:Robert_Dutnall/Sandbox_1_alpha_helix/A_helix_mainchain/3'>Click here</scene> to show only the polypeptide mainchain (NH, Cα, and C=O).

Identify the N- and C-termini. <scene name='User:Robert_Dutnall/Sandbox_1_alpha_helix/A_helix_mainchain_label/4'>Click here to see if you were correct.</scene>

<scene name='User:Robert_Dutnall/Sandbox_1_alpha_helix/A_helix_mainchain_label_ribbon/3'>Click here to add a ribbon that will help show the path of the mainchain. </scene> You should be able to see that it is helical with a right-handed twist (you rotate to the right as you move along the helix axis).

Click the "toggle spin" button in the box to stop the structure from rotating. Now use your mouse to rotate the structure to look down the helix axis. If you have any problems with finding this view, <scene name='User:Robert_Dutnall/Sandbox_1_alpha_helix/A_helix_mainchain_label_axis/3'>click here </scene>to zoom in and look down the helix axis from the N-terminal end.

<scene name='User:Robert_Dutnall/Sandbox_1_alpha_helix/A_helix_mainchain_label/4'>Click here to zoom out again.</scene> Look at the structure carefully and identify the mainchain NH and C=O groups. What is the orientation of these groups with respect to the helix axis?

<scene name='User:Robert_Dutnall/Sandbox_1_alpha_helix/A_helix_mainchain_label_hbonds/10'>Click here to zoom in a little and add hydrogen bonds for the mainchain (dashed lines).</scene> The hydrogen bonds connect backbone NH groups and C=O groups. The N-H group is the hydrogen bond donor, the oxygen in the C=O group is the acceptor (N-H--->O=C). Each hydrogen bond is approximately 3.0 Angstroms (0.3 nm) in length (measured between the N and the O). These hydrogen bonds connect amino acids that are spaced 4 residues apart in the primary sequence. The NH group is from amino acid X and the O is from amino acid X-4 (where X is the number of the amino acid in the sequence).

<scene name='User:Robert_Dutnall/Sandbox_1_alpha_helix/A_helix_mainchain_label_hbonds/9'>Click here to zoom out again.</scene> You should be able to see that all of the mainchain NH and C=O groups are involved in hydrogen bonds. This is possible because 1) all the mainchain NH groups and C=O groups are parallel to the helix axis, 2) all the NH groups point toward the N-terminus of the helix, and 3) all the C=O groups point toward the C-terminus. Only the NH groups in the first (N-terminal) turn, and the C=O groups in the last (C-terminal) turn of the helix do not have hydrogen bonding partners. However, if this helix were part of a larger protein, these groups would participate in hydrogen bonds with other parts of the protein. This is called 'helix capping' and the other groups involved are typically from amino acid side chains (that are called 'helix capping residues').

<scene name='User:Robert_Dutnall/Sandbox_1_alpha_helix/A_helix_sidechains/3'>Click here to show the side chains again.</scene> The atoms of each amino side chain have been colored light blue to show them more clearly. <scene name='User:Robert_Dutnall/Sandbox_1_alpha_helix/A_helix_sidechains_axis/1'>Click here to change the view to look down the helix axis.</scene>

What is the general orientation of the side chains with respect to the helix axis? You should observe that each side chain points away from the helix axis, but points down toward the N-terminus of the helix (this is clearer if you only show the first bond of each side chain: <scene name='User:Robert_Dutnall/Sandbox_1_alpha_helix/A_helix_sidechains_cropped/1'>click here</scene> or <scene name='User:Robert_Dutnall/Sandbox_1_alpha_helix/A_helix_sidechains_cropped/2'>click here</scene>).

==An 310-helix==

310-helices are less common than α-helices. They are characterized by the following helix parameters:
::Dihedral angles: Φ ~ -49o, φ ~ -26o
::Repeat (number of residues per turn) = 3.0
::Rise (translation along axis per amino acid residue) = 2.0 Angstroms (0.15 nm)
::Twist (rotation around axis per amino acid residue) = 120o (= 360o/repeat)
::Pitch (translation along axis per turn) = 6.0 Angstroms (= Repeat x Rise)

The helix shown below is a 19 amino acid chain in α-helical conformation.
<Structure load='Tut_3-10_helix.pdb' size='500' frame='true' align='left' caption='' scene='User:Robert_Dutnall/Sandbox_1_alpha_helix/310_helix_load/3'/>

All the atoms are shown in this initial orientation (C = green; N = blue; O = red; S = yellow; H = white). The helix axis runs vertically, approximately parallel to the plane of the screen.

<scene name='User:Robert_Dutnall/Sandbox_1_alpha_helix/310_helix_mainchain_ribbons/1'>Click here</scene> to show only the polypeptide mainchain (NH, Cα, and C=O). A ribbon has been added and the N- and C-termini are labeled.

Identify the N- and C-termini. <scene name='User:Robert_Dutnall/Sandbox_1_alpha_helix/A_helix_mainchain_label/4'>Click here to see if you were correct.</scene>

<scene name='User:Robert_Dutnall/Sandbox_1_alpha_helix/A_helix_mainchain_label_ribbon/3'>Click here to add a ribbon that will help show the path of the mainchain. </scene> You should be able to see that it is helical with a right-handed twist (you rotate to the right as you move along the helix axis).

Click the "toggle spin" button in the box to stop the structure from rotating. Now use your mouse to rotate the structure to look down the helix axis. If you have any problems with finding this view, <scene name='User:Robert_Dutnall/Sandbox_1_alpha_helix/A_helix_mainchain_label_axis/3'>click here </scene>to zoom in and look down the helix axis from the N-terminal end.

<scene name='User:Robert_Dutnall/Sandbox_1_alpha_helix/A_helix_mainchain_label/4'>Click here to zoom out again.</scene> Look at the structure carefully and identify the mainchain NH and C=O groups. What is the orientation of these groups with respect to the helix axis?

<scene name='User:Robert_Dutnall/Sandbox_1_alpha_helix/A_helix_mainchain_label_hbonds/10'>Click here to zoom in a little and add hydrogen bonds for the mainchain (dashed lines).</scene> The hydrogen bonds connect backbone NH groups and C=O groups. The N-H group is the hydrogen bond donor, the oxygen in the C=O group is the acceptor (N-H--->O=C). Each hydrogen bond is approximately 3.0 Angstroms (0.3 nm) in length (measured between the N and the O). These hydrogen bonds connect amino acids that are spaced 4 residues apart in the primary sequence. The NH group is from amino acid X and the O is from amino acid X-4 (where X is the number of the amino acid in the sequence).

<scene name='User:Robert_Dutnall/Sandbox_1_alpha_helix/A_helix_mainchain_label_hbonds/9'>Click here to zoom out again.</scene> You should be able to see that all of the mainchain NH and C=O groups are involved in hydrogen bonds. This is possible because 1) all the mainchain NH groups and C=O groups are parallel to the helix axis, 2) all the NH groups point toward the N-terminus of the helix, and 3) all the C=O groups point toward the C-terminus. Only the NH groups in the first (N-terminal) turn, and the C=O groups in the last (C-terminal) turn of the helix do not have hydrogen bonding partners. However, if this helix were part of a larger protein, these groups would participate in hydrogen bonds with other parts of the protein. This is called 'helix capping' and the other groups involved are typically from amino acid side chains (that are called 'helix capping residues').

<scene name='User:Robert_Dutnall/Sandbox_1_alpha_helix/A_helix_sidechains/3'>Click here to show the side chains again.</scene> The atoms of each amino side chain have been colored light blue to show them more clearly. <scene name='User:Robert_Dutnall/Sandbox_1_alpha_helix/A_helix_sidechains_axis/1'>Click here to change the view to look down the helix axis.</scene>

What is the general orientation of the side chains with respect to the helix axis? You should observe that each side chain points away from the helix axis, but points down toward the N-terminus of the helix (this is clearer if you only show the first bond of each side chain: <scene name='User:Robert_Dutnall/Sandbox_1_alpha_helix/A_helix_sidechains_cropped/1'>click here</scene> or <scene name='User:Robert_Dutnall/Sandbox_1_alpha_helix/A_helix_sidechains_cropped/2'>click here</scene>).

= =

File:Tut 3-10 helix.pdb

2011-08-26T00:05:54Z

Robert Dutnall:

== Licensing ==
{{self|cc-by-sa-3.0}}

File:Tut 310 helix.pdb

2011-08-26T00:01:03Z

Robert Dutnall: uploaded a new version of "Image:Tut 310 helix.pdb"

== Summary ==
19 amino acid peptide in 3-10 conformation (phi = -49; psi = -26)
== Licensing ==
{{cc-by-sa-3.0}}

User:Robert Dutnall/Sandbox 1 alpha helix

2011-08-25T23:56:59Z

Robert Dutnall:

== Biochemistry Tutorial #2 - Secondary Structure ==

The secondary structure of a protein is defined by the local conformation of its backbone (polypeptide mainchain). There are two major types of regular secondary structures in proteins: helices and sheets. There are also regular turn structures. Turns often connect one element of secondary structure to another in the overall fold of the protein. Other parts of the protein mainchain may adopt more irregularly defined loops. This tutorial will focus mainly on

''Note: in these tutorials, the images are 3D interactive images. You can manipulate them as you wish to get a better view of the molecules.''

You can rotate the structures by holding down the right mouse button and dragging. At any time you can click the 'toggle spin' button in box to stop/start the structure spinning.

Other things you can do:
::To rotate: left drag
::To Zoom: scroll button or shift + left drag
::To Translate: ctrl + right drag
::Right click to bring up an options menu

=Helices=

==An α-helix==

α-helices are the most common type of regular helix found in proteins. They are characterized by the following helix parameters:
::Dihedral angles: Φ ~ -60o, φ ~ -45o
::Repeat (number of residues per turn) = 3.6
::Rise (translation along axis per amino acid residue) = 1.5 Angstroms (0.15 nm)
::Twist (rotation around axis per amino acid residue) = 100o (= 360o/repeat)
::Pitch (translation along axis per turn) = 5.4 Angstroms (= Repeat x Rise)

The helix shown below is a 19 amino acid chain in α-helical conformation.
<Structure load='Tut_alpha_helix.pdb' size='500' frame='true' align='left' caption='' scene='User:Robert_Dutnall/Sandbox_1_alpha_helix/A_helix_load/1'/>

All the atoms are shown in this initial orientation (C = green; N = blue; O = red; S = yellow; H = white). The helix axis runs vertically, approximately parallel to the plane of the screen.

<scene name='User:Robert_Dutnall/Sandbox_1_alpha_helix/A_helix_mainchain/3'>Click here</scene> to show only the polypeptide mainchain (NH, Cα, and C=O).

Identify the N- and C-termini. <scene name='User:Robert_Dutnall/Sandbox_1_alpha_helix/A_helix_mainchain_label/4'>Click here to see if you were correct.</scene>

<scene name='User:Robert_Dutnall/Sandbox_1_alpha_helix/A_helix_mainchain_label_ribbon/3'>Click here to add a ribbon that will help show the path of the mainchain. </scene> You should be able to see that it is helical with a right-handed twist (you rotate to the right as you move along the helix axis).

Click the "toggle spin" button in the box to stop the structure from rotating. Now use your mouse to rotate the structure to look down the helix axis. If you have any problems with finding this view, <scene name='User:Robert_Dutnall/Sandbox_1_alpha_helix/A_helix_mainchain_label_axis/3'>click here </scene>to zoom in and look down the helix axis from the N-terminal end.

<scene name='User:Robert_Dutnall/Sandbox_1_alpha_helix/A_helix_mainchain_label/4'>Click here to zoom out again.</scene> Look at the structure carefully and identify the mainchain NH and C=O groups. What is the orientation of these groups with respect to the helix axis?

<scene name='User:Robert_Dutnall/Sandbox_1_alpha_helix/A_helix_mainchain_label_hbonds/10'>Click here to zoom in a little and add hydrogen bonds for the mainchain (dashed lines).</scene> The hydrogen bonds connect backbone NH groups and C=O groups. The N-H group is the hydrogen bond donor, the oxygen in the C=O group is the acceptor (N-H--->O=C). Each hydrogen bond is approximately 3.0 Angstroms (0.3 nm) in length (measured between the N and the O). These hydrogen bonds connect amino acids that are spaced 4 residues apart in the primary sequence. The NH group is from amino acid X and the O is from amino acid X-4 (where X is the number of the amino acid in the sequence).

<scene name='User:Robert_Dutnall/Sandbox_1_alpha_helix/A_helix_mainchain_label_hbonds/9'>Click here to zoom out again.</scene> You should be able to see that all of the mainchain NH and C=O groups are involved in hydrogen bonds. This is possible because 1) all the mainchain NH groups and C=O groups are parallel to the helix axis, 2) all the NH groups point toward the N-terminus of the helix, and 3) all the C=O groups point toward the C-terminus. Only the NH groups in the first (N-terminal) turn, and the C=O groups in the last (C-terminal) turn of the helix do not have hydrogen bonding partners. However, if this helix were part of a larger protein, these groups would participate in hydrogen bonds with other parts of the protein. This is called 'helix capping' and the other groups involved are typically from amino acid side chains (that are called 'helix capping residues').

<scene name='User:Robert_Dutnall/Sandbox_1_alpha_helix/A_helix_sidechains/3'>Click here to show the side chains again.</scene> The atoms of each amino side chain have been colored light blue to show them more clearly. <scene name='User:Robert_Dutnall/Sandbox_1_alpha_helix/A_helix_sidechains_axis/1'>Click here to change the view to look down the helix axis.</scene>

What is the general orientation of the side chains with respect to the helix axis? You should observe that each side chain points away from the helix axis, but points down toward the N-terminus of the helix (this is clearer if you only show the first bond of each side chain: <scene name='User:Robert_Dutnall/Sandbox_1_alpha_helix/A_helix_sidechains_cropped/1'>click here</scene> or <scene name='User:Robert_Dutnall/Sandbox_1_alpha_helix/A_helix_sidechains_cropped/2'>click here</scene>).

==An 310-helix==

310-helices are less common than α-helices. They are characterized by the following helix parameters:
::Dihedral angles: Φ ~ -49o, φ ~ -26o
::Repeat (number of residues per turn) = 3.0
::Rise (translation along axis per amino acid residue) = 2.0 Angstroms (0.15 nm)
::Twist (rotation around axis per amino acid residue) = 120o (= 360o/repeat)
::Pitch (translation along axis per turn) = 6.0 Angstroms (= Repeat x Rise)

The helix shown below is a 19 amino acid chain in α-helical conformation.
<Structure load='Tut_310_helix.pdb' size='500' frame='true' align='left' caption='' scene='User:Robert_Dutnall/Sandbox_1_alpha_helix/310_helix_load/1'/>

All the atoms are shown in this initial orientation (C = green; N = blue; O = red; S = yellow; H = white). The helix axis runs vertically, approximately parallel to the plane of the screen.

<scene name='User:Robert_Dutnall/Sandbox_1_alpha_helix/A_helix_mainchain/3'>Click here</scene> to show only the polypeptide mainchain (NH, Cα, and C=O).

Identify the N- and C-termini. <scene name='User:Robert_Dutnall/Sandbox_1_alpha_helix/A_helix_mainchain_label/4'>Click here to see if you were correct.</scene>

<scene name='User:Robert_Dutnall/Sandbox_1_alpha_helix/A_helix_mainchain_label_ribbon/3'>Click here to add a ribbon that will help show the path of the mainchain. </scene> You should be able to see that it is helical with a right-handed twist (you rotate to the right as you move along the helix axis).

Click the "toggle spin" button in the box to stop the structure from rotating. Now use your mouse to rotate the structure to look down the helix axis. If you have any problems with finding this view, <scene name='User:Robert_Dutnall/Sandbox_1_alpha_helix/A_helix_mainchain_label_axis/3'>click here </scene>to zoom in and look down the helix axis from the N-terminal end.

<scene name='User:Robert_Dutnall/Sandbox_1_alpha_helix/A_helix_mainchain_label/4'>Click here to zoom out again.</scene> Look at the structure carefully and identify the mainchain NH and C=O groups. What is the orientation of these groups with respect to the helix axis?

<scene name='User:Robert_Dutnall/Sandbox_1_alpha_helix/A_helix_mainchain_label_hbonds/10'>Click here to zoom in a little and add hydrogen bonds for the mainchain (dashed lines).</scene> The hydrogen bonds connect backbone NH groups and C=O groups. The N-H group is the hydrogen bond donor, the oxygen in the C=O group is the acceptor (N-H--->O=C). Each hydrogen bond is approximately 3.0 Angstroms (0.3 nm) in length (measured between the N and the O). These hydrogen bonds connect amino acids that are spaced 4 residues apart in the primary sequence. The NH group is from amino acid X and the O is from amino acid X-4 (where X is the number of the amino acid in the sequence).

<scene name='User:Robert_Dutnall/Sandbox_1_alpha_helix/A_helix_mainchain_label_hbonds/9'>Click here to zoom out again.</scene> You should be able to see that all of the mainchain NH and C=O groups are involved in hydrogen bonds. This is possible because 1) all the mainchain NH groups and C=O groups are parallel to the helix axis, 2) all the NH groups point toward the N-terminus of the helix, and 3) all the C=O groups point toward the C-terminus. Only the NH groups in the first (N-terminal) turn, and the C=O groups in the last (C-terminal) turn of the helix do not have hydrogen bonding partners. However, if this helix were part of a larger protein, these groups would participate in hydrogen bonds with other parts of the protein. This is called 'helix capping' and the other groups involved are typically from amino acid side chains (that are called 'helix capping residues').

<scene name='User:Robert_Dutnall/Sandbox_1_alpha_helix/A_helix_sidechains/3'>Click here to show the side chains again.</scene> The atoms of each amino side chain have been colored light blue to show them more clearly. <scene name='User:Robert_Dutnall/Sandbox_1_alpha_helix/A_helix_sidechains_axis/1'>Click here to change the view to look down the helix axis.</scene>

What is the general orientation of the side chains with respect to the helix axis? You should observe that each side chain points away from the helix axis, but points down toward the N-terminus of the helix (this is clearer if you only show the first bond of each side chain: <scene name='User:Robert_Dutnall/Sandbox_1_alpha_helix/A_helix_sidechains_cropped/1'>click here</scene> or <scene name='User:Robert_Dutnall/Sandbox_1_alpha_helix/A_helix_sidechains_cropped/2'>click here</scene>).

= =