Proteopedia - User contributions [en]

User:Stephen Mills

2023-07-21T03:46:31Z

Stephen Mills:

CURRENT POSITION:
Xavier University; Department of Chemistry 
:Associate Professor, August 2013 to present 

PREVIOUS POSITION:
University of San Diego; Department of Chemistry and Biochemistry 
:Assistant Professor, August 2006 to May 2013 
:[[http://www.sandiego.edu/cas/chemistry/faculty/biography.php?ID=71 USD Website]]

EDUCATION:

University of California, Berkeley; Berkeley, CA; Professor Michael A. Marletta, advisor 
:Postdoctoral Fellow, 2001-2005

University of California, Berkeley; Berkeley, CA; Professor Judith P. Klinman, advisor 
:Ph.D. in Chemistry, May 2001 
:“The Role of Copper and its Ligands in an Amine Oxidase from ''Hansenula polymorpha''”

University of California, Berkeley; Berkeley, CA; Professor Paul A. Bartlett, advisor 
:M.S. in Chemistry, Dec. 1994 
:"Synthesis and Evaluation of a Proposed Inactivator of Papain"

University of Illinois at Urbana-Champaign; Champaign, IL 
:B.S. in Chemistry, May 1992, with high distinction
----
*[[User:Stephen Mills/Sandbox]]
*[[User:Stephen Mills/Sandbox 1]]
*[[User:Stephen Mills/Sandbox 2 Peptide tutorial]] moved to Peptide Tutorial 1
*[[User:Stephen Mills/Sandbox 2 Peptide tutorial_2]] moved to Peptide Tutorial 2
*[[User:Stephen Mills/Sandbox 3 Secondary Structure Tutorial 1]]
*[[User:Stephen Mills/Sandbox 4 Secondary Structure: Helices XU]]

*[[User:Stephen Mills/Peptide tutorial 1]]
*[[User:Stephen Mills/Peptide tutorial 2]]
*[[User:Stephen Mills/Secondary Structure: Helices]]
*[[User:Stephen Mills/Secondary Structure: Sheets]]
*[[User:Stephen Mills/Biochemistry Tutorials]]
*[[User:Stephen Mills/XU Peptide Tutorial 1 p1]]
*[[User:Stephen Mills/XU Peptide Tutorial 1 p2]]
*[[User:Stephen Mills/Sandbox_SAM_005]]

Sandbox SAM 005

2023-07-20T19:07:11Z

Stephen Mills:

== Steve's Protein Sandbox for BASIL ==
<StructureSection load='4DIU' size='350' side='right' caption='4DIU Sandbox' scene=''>
This is a sandbox page for '''4DIU'''. Click above on '''edit this page''' to modify. Be careful with the < and > signs.
You may include any references to papers as in: the use of JSmol in Proteopedia <ref>DOI 10.1002/ijch.201300024</ref> or to the article describing Jmol <ref>PMID:21638687</ref> to the rescue.

== Introduction ==
This structure came from the Protein Structure Initiative. This protein does not have an assigned function based on sequence similarity.

== Disease ==

== Protein Purification ==

[[Image:4DIUgel|300px|left|thumb| 4DIU Ni column fractions]]

== Structural highlights ==

This is a sample scene created with SAT to <scene name="/12/3456/Sample/1">color</scene> by Group, and another to make <scene name="/12/3456/Sample/2">a transparent representation</scene> of the protein. You can make your own scenes on SAT starting from scratch or loading and editing one of these sample scenes.

</StructureSection>

This is the <scene name='97/977760/Ligand_shown/1'>ligand for this structure</scene>.

== References ==
<references/>

Sandbox SAM 005

2023-07-20T18:42:46Z

Stephen Mills:

File:4DIUgel.jpeg

2023-07-20T18:37:54Z

Stephen Mills: 4DIU gel from Ni column

4DIU gel from Ni column

File:IMG 1274.jpg

2023-07-20T18:33:46Z

Stephen Mills: 4DIU Gel

4DIU Gel

Sandbox SAM 005

2023-07-20T18:29:12Z

Stephen Mills: New page: == Steve's Protein Sandbox for BASIL == <StructureSection load='4DIU' size='350' side='right' caption='4DIU Sandbox' scene=''> This is a sandbox page for '''4DIU'''. Click above on '''edit...

== Steve's Protein Sandbox for BASIL ==
<StructureSection load='4DIU' size='350' side='right' caption='4DIU Sandbox' scene=''>
This is a sandbox page for '''4DIU'''. Click above on '''edit this page''' to modify. Be careful with the < and > signs.
You may include any references to papers as in: the use of JSmol in Proteopedia <ref>DOI 10.1002/ijch.201300024</ref> or to the article describing Jmol <ref>PMID:21638687</ref> to the rescue.

== Introduction ==
This structure came from the Protein Structure Initiative. This protein does not have an assigned function based on sequence similarity.

== Disease ==

== Relevance ==

== Structural highlights ==

This is a sample scene created with SAT to <scene name="/12/3456/Sample/1">color</scene> by Group, and another to make <scene name="/12/3456/Sample/2">a transparent representation</scene> of the protein. You can make your own scenes on SAT starting from scratch or loading and editing one of these sample scenes.

</StructureSection>
== References ==
<references/>

User:Stephen Mills/Biochemistry Tutorials

2022-01-13T18:26:44Z

Stephen Mills:

Biochemistry Protein Structure Tutorials

These tutorials are meant to give you an introduction to amino acids and peptides, their structures and the structures they adopt. I recommend starting with the first and working your way through in order.

The first tutorial will introduce you to the amino acids, how they are represented and how they are connected (their primary structure). You will practice recognizing them and using their names and one-letter codes. There are two pages to this tutorial.

The second tutorial introduces you to the secondary structures that peptides adopt - specifically α-helices and β-sheets. This tutorial has two pages as well.

As you finish each tutorial, you will be asked to write down several pieces of information. Those answers will be submitted to your instructor as they have indicated.

*[[User:Stephen Mills/Peptide tutorial 1|Peptide tutorial 1 part 1]]
*[[User:Stephen Mills/Peptide tutorial 2|Peptide tutorial 1 part 2]]
*[[Introduction_to_molecular_visualization]]
*[[User:Stephen Mills/Secondary Structure: Helices|Secondary Structure tutorial - Helices]]
*[[User:Stephen Mills/Secondary Structure: Sheets|Secondary Structure tutorial - Sheets]]

File:Arginine.pdb

2021-02-01T22:13:24Z

Stephen Mills: uploaded a new version of "Image:Arginine.pdb"

== Summary ==
Arginine drawn in PyMOL
== Licensing ==
{{PD-self}}

File:Arginine.pdb

2021-02-01T21:21:52Z

Stephen Mills: uploaded a new version of "Image:Arginine.pdb": Arginine

== Summary ==
Arginine drawn in PyMOL
== Licensing ==
{{PD-self}}

User:Stephen Mills

2021-02-01T19:45:48Z

Stephen Mills:

User:Stephen Mills/Sandbox 4 Secondary Structure: Helices XU

2015-08-27T18:41:32Z

Stephen Mills:

==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_XU.pdb' size='500' frame='true' align='left' caption='' scene='71/711023/Initial_alpha_helix/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.

User:Stephen Mills/Sandbox 4 Secondary Structure: Helices XU

2015-08-27T18:15:13Z

Stephen Mills:

==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_XU.pdb' size='500' frame='true' align='left' caption='' scene='' />

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.

User:Stephen Mills/Sandbox 4 Secondary Structure: Helices XU

2015-08-27T18:09:05Z

Stephen Mills:

'''Bold text'''==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_XU.pdb' size='500' frame='true' align='left' caption='' scene name='71/711023/Initial_alpha_helix/1'>Initial_alpha_helix</scene>

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.

File:Tut alpha helix XU.pdb

2015-08-27T18:04:28Z

Stephen Mills: Helix for Secondary Structure tutorial

Helix for Secondary Structure tutorial

User:Stephen Mills/Sandbox 4 Secondary Structure: Helices XU

2015-08-27T17:47:41Z

Stephen Mills: New page: '''Bold text'''==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 ~ -...

'''Bold text'''==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' name='initial_alpha_helix'/>

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. 
<Structure load='' size='350' frame='true' align='right' caption='Insert caption here' scene='Insert optional scene name here' />

User:Stephen Mills

2015-08-27T17:43:49Z

Stephen Mills:

CURRENT POSITION:
Xavier University; Department of Chemistry 
:Assistant Professor, August 2013 to present 

PREVIOUS POSITION:
University of San Diego; Department of Chemistry and Biochemistry 
:Assistant Professor, August 2006 to May 2013 
:[[http://www.sandiego.edu/cas/chemistry/faculty/biography.php?ID=71 USD Website]]

EDUCATION:

University of California, Berkeley; Berkeley, CA; Professor Michael A. Marletta, advisor 
:Postdoctoral Fellow, 2001-2005

University of California, Berkeley; Berkeley, CA; Professor Judith P. Klinman, advisor 
:Ph.D. in Chemistry, May 2001 
:“The Role of Copper and its Ligands in an Amine Oxidase from ''Hansenula polymorpha''”

University of California, Berkeley; Berkeley, CA; Professor Paul A. Bartlett, advisor 
:M.S. in Chemistry, Dec. 1994 
:"Synthesis and Evaluation of a Proposed Inactivator of Papain"

University of Illinois at Urbana-Champaign; Champaign, IL 
:B.S. in Chemistry, May 1992, with high distinction
----
*[[User:Stephen Mills/Sandbox]]
*[[User:Stephen Mills/Sandbox 1]]
*[[User:Stephen Mills/Sandbox 2 Peptide tutorial]] moved to Peptide Tutorial 1
*[[User:Stephen Mills/Sandbox 2 Peptide tutorial_2]] moved to Peptide Tutorial 2
*[[User:Stephen Mills/Sandbox 3 Secondary Structure Tutorial 1]]
*[[User:Stephen Mills/Sandbox 4 Secondary Structure: Helices XU]]

*[[User:Stephen Mills/Peptide tutorial 1]]
*[[User:Stephen Mills/Peptide tutorial 2]]
*[[User:Stephen Mills/Secondary Structure: Helices]]
*[[User:Stephen Mills/Secondary Structure: Sheets]]
*[[User:Stephen Mills/Biochemistry Tutorials]]
*[[User:Stephen Mills/XU Peptide Tutorial 1 p1]]
*[[User:Stephen Mills/XU Peptide Tutorial 1 p2]]

File:Tut alpha helix.pdb

2015-08-27T14:55:03Z

Stephen Mills: uploaded a new version of "Image:Tut alpha helix.pdb"

== Licensing ==
{{PD-self}}

File:Tut 3-10 helix.pdb

2015-02-06T21:22:35Z

Stephen Mills: uploaded a new version of "Image:Tut 3-10 helix.pdb"

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

File:Tut 3-10 helix Mills.pdb

2015-02-06T21:18:23Z

Stephen Mills: 3-10 Helix for Helices tutorial

3-10 Helix for Helices tutorial

User:Stephen Mills/Secondary Structure: Sheets

2014-08-26T15:34:02Z

Stephen Mills: /* H-bonds in antiparallel sheets */

== 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' name='beta_sheet'/>

<scene name='User:Robert_Dutnall/Sandbox_1_sheets/Parallel_mainchain/2' target='beta_sheet'>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' target='beta_sheet'>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' target='beta_sheet'>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' target='beta_sheet'>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' target='beta_sheet'>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?
 

==H-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' name='beta_sheet_Hbonds'/>
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' target='beta_sheet_Hbonds'>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' target='beta_sheet_Hbonds'>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' target='beta_sheet_Hbonds'>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' target='beta_sheet_Hbonds'>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' target='beta_sheet_Hbonds'>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' name='anti_sheet'/>

<scene name='User:Robert_Dutnall/Sandbox_1_sheets/Antiparallel_mainchain/3' target='anti_sheet'>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' target='anti_sheet'>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' target='anti_sheet'>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' target='anti_sheet'>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' target='anti_sheet'>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.
 

==H-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' name='anti_Hbonds'/>

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' target='anti_Hbonds'>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' target='anti_Hbonds'>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' target='anti_Hbonds'>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='46/463272/Antipara_mainchain_turn_zoom/1' target='anti_Hbonds'>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)''' Here are a couple of links that might help you figure this out. [http://www.nku.edu/~russellk/tutorial/peptide/peptide.html NKU tutorial] and [http://sbb.uvm.edu/~sje/351/sub2.3.html UVM COMET].

<scene name='User:Robert_Dutnall/Sandbox_1_sheets/Antipara_mainchain_sidechains/1' target='anti_Hbonds'>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' name='mixed_sheet'/>

<scene name='User:Robert_Dutnall/Sandbox_1_sheets/Mixed_sheet_mainchain/2' target='mixed_sheet'>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' target='mixed_sheet'>Pair 1.</scene>

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

<scene name='User:Robert_Dutnall/Sandbox_1_sheets/Mixed_sheet_mainchain_pair3/1' target='mixed_sheet'>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:Stephen Mills/Secondary Structure: Helices|Click here if you want to go back to the first part of this tutorial.]]

[[User:Stephen_Mills/Biochemistry_Tutorials|Click here to go back to the main Tutorial page.]]

User:Stephen Mills/Secondary Structure: Helices

2014-08-23T02:54:51Z

Stephen Mills: /* H-Bonding in α-helices */

== 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' name='initial_alpha_helix'/>

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_load/1' target='initial_alpha_helix'>Click here</scene> to go back to the initial view. 

<scene name='User:Stephen_Mills/Secondary_Structure:_Helices/A_helix_load/1' target='initial_alpha_helix'>Click here</scene> to show the helix in a space-filling representation. This representation shows the atoms with a radius that is approximately correct.

<scene name='User:Robert_Dutnall/Sandbox_1_alpha_helix/A_helix_mainchain/3' target='initial_alpha_helix'>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' target='initial_alpha_helix'>Click here to see if you were correct.</scene>

<scene name='User:Robert_Dutnall/Sandbox_1_alpha_helix/A_helix_mainchain_label_ribbon/3' target='initial_alpha_helix'>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' target='initial_alpha_helix'>click here </scene>to zoom in and look down the helix axis from the N-terminal end.
 
What is in the middle of the helix?
 
Now,
<scene name='User:Stephen_Mills/Secondary_Structure:_Helices/A_helix_main_axis_spacefill/1' target='initial_alpha_helix'>click here</scene> to see the helix in a space-filling representation. 

Now, answer that question again - what is in the middle of the helix?
 

==H-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' name='Hbonds'/>
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' target='Hbonds'>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' target='Hbonds'>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' target='Hbonds'>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' target='Hbonds'>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' target='Hbonds'>click here</scene> or <scene name='User:Robert_Dutnall/Sandbox_1_alpha_helix/A_helix_sidechains_cropped/2' target='Hbonds'>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' name='310_helix'/>

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' target='310_helix'>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' target='310_helix'>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' target='310_helix'>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.
 

==H-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' name='310_hbonds'/>
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' target='310_hbonds'>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' target='310_hbonds'>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' target='310_hbonds'>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' target='310_hbonds'>click here to look from the side</scene> or <scene name='User:Robert_Dutnall/Sandbox_1_alpha_helix/310_helix_sidechains_tricol_ax/1' target='310_hbonds'>click here to view down the helix axis</scene>.

<scene name='User:Robert_Dutnall/Sandbox_1_alpha_helix/310_helix_load/4' target='310_hbonds'>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:Stephen_Mills/Secondary_Structure:_Sheets|Click here to go on to part 2 of this tutorial.]]

[[User:Stephen_Mills/Biochemistry_Tutorials|Click here to go back to the main Tutorial page.]]

User:Stephen Mills/Secondary Structure: Sheets

2014-08-23T02:52:20Z

Stephen Mills: /* A mixed β-sheet */

== 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' name='beta_sheet'/>

<scene name='User:Robert_Dutnall/Sandbox_1_sheets/Parallel_mainchain/2' target='beta_sheet'>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' target='beta_sheet'>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' target='beta_sheet'>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' target='beta_sheet'>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' target='beta_sheet'>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?
 

==H-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' name='beta_sheet_Hbonds'/>
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' target='beta_sheet_Hbonds'>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' target='beta_sheet_Hbonds'>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' target='beta_sheet_Hbonds'>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' target='beta_sheet_Hbonds'>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' target='beta_sheet_Hbonds'>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' name='anti_sheet'/>

<scene name='User:Robert_Dutnall/Sandbox_1_sheets/Antiparallel_mainchain/3' target='anti_sheet'>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' target='anti_sheet'>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' target='anti_sheet'>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' target='anti_sheet'>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' target='anti_sheet'>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.
 

==H-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' name='anti_Hbonds'/>

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' target='anti_Hbonds'>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' target='anti_Hbonds'>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' target='anti_Hbonds'>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='46/463272/Antipara_mainchain_turn_zoom/1' target='anti_Hbonds'>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' target='anti_Hbonds'>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' name='mixed_sheet'/>

<scene name='User:Robert_Dutnall/Sandbox_1_sheets/Mixed_sheet_mainchain/2' target='mixed_sheet'>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' target='mixed_sheet'>Pair 1.</scene>

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

<scene name='User:Robert_Dutnall/Sandbox_1_sheets/Mixed_sheet_mainchain_pair3/1' target='mixed_sheet'>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:Stephen Mills/Secondary Structure: Helices|Click here if you want to go back to the first part of this tutorial.]]

[[User:Stephen_Mills/Biochemistry_Tutorials|Click here to go back to the main Tutorial page.]]

User:Stephen Mills/Secondary Structure: Sheets

2014-08-23T02:50:39Z

Stephen Mills: /* H-bonds in antiparallel sheets */

== 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' name='beta_sheet'/>

<scene name='User:Robert_Dutnall/Sandbox_1_sheets/Parallel_mainchain/2' target='beta_sheet'>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' target='beta_sheet'>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' target='beta_sheet'>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' target='beta_sheet'>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' target='beta_sheet'>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?
 

==H-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' name='beta_sheet_Hbonds'/>
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' target='beta_sheet_Hbonds'>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' target='beta_sheet_Hbonds'>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' target='beta_sheet_Hbonds'>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' target='beta_sheet_Hbonds'>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' target='beta_sheet_Hbonds'>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' name='anti_sheet'/>

<scene name='User:Robert_Dutnall/Sandbox_1_sheets/Antiparallel_mainchain/3' target='anti_sheet'>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' target='anti_sheet'>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' target='anti_sheet'>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' target='anti_sheet'>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' target='anti_sheet'>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.
 

==H-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' name='anti_Hbonds'/>

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' target='anti_Hbonds'>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' target='anti_Hbonds'>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' target='anti_Hbonds'>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='46/463272/Antipara_mainchain_turn_zoom/1' target='anti_Hbonds'>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' target='anti_Hbonds'>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:Stephen Mills/Secondary Structure: Helices|Click here if you want to go back to the first part of this tutorial.]]

[[User:Stephen_Mills/Biochemistry_Tutorials|Click here to go back to the main Tutorial page.]]

User:Stephen Mills/Secondary Structure: Sheets

2014-08-23T02:44:18Z

Stephen Mills: /* Anti-Parallel β-sheet */

== 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' name='beta_sheet'/>

<scene name='User:Robert_Dutnall/Sandbox_1_sheets/Parallel_mainchain/2' target='beta_sheet'>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' target='beta_sheet'>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' target='beta_sheet'>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' target='beta_sheet'>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' target='beta_sheet'>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?
 

==H-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' name='beta_sheet_Hbonds'/>
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' target='beta_sheet_Hbonds'>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' target='beta_sheet_Hbonds'>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' target='beta_sheet_Hbonds'>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' target='beta_sheet_Hbonds'>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' target='beta_sheet_Hbonds'>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' name='anti_sheet'/>

<scene name='User:Robert_Dutnall/Sandbox_1_sheets/Antiparallel_mainchain/3' target='anti_sheet'>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' target='anti_sheet'>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' target='anti_sheet'>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' target='anti_sheet'>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' target='anti_sheet'>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.
 

==H-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:Stephen Mills/Secondary Structure: Helices|Click here if you want to go back to the first part of this tutorial.]]

[[User:Stephen_Mills/Biochemistry_Tutorials|Click here to go back to the main Tutorial page.]]

User:Stephen Mills/Secondary Structure: Sheets

2014-08-23T02:42:01Z

Stephen Mills: /* H-bonds in Parallel Sheets */

== 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' name='beta_sheet'/>

<scene name='User:Robert_Dutnall/Sandbox_1_sheets/Parallel_mainchain/2' target='beta_sheet'>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' target='beta_sheet'>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' target='beta_sheet'>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' target='beta_sheet'>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' target='beta_sheet'>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?
 

==H-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' name='beta_sheet_Hbonds'/>
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' target='beta_sheet_Hbonds'>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' target='beta_sheet_Hbonds'>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' target='beta_sheet_Hbonds'>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' target='beta_sheet_Hbonds'>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' target='beta_sheet_Hbonds'>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.
 

==H-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:Stephen Mills/Secondary Structure: Helices|Click here if you want to go back to the first part of this tutorial.]]

[[User:Stephen_Mills/Biochemistry_Tutorials|Click here to go back to the main Tutorial page.]]

User:Stephen Mills/Secondary Structure: Sheets

2014-08-23T02:37:37Z

Stephen Mills: /* Parallel β-sheet */

== 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' name='beta_sheet'/>

<scene name='User:Robert_Dutnall/Sandbox_1_sheets/Parallel_mainchain/2' target='beta_sheet'>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' target='beta_sheet'>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' target='beta_sheet'>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' target='beta_sheet'>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' target='beta_sheet'>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?
 

==H-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.

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.
 

==H-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:Stephen Mills/Secondary Structure: Helices|Click here if you want to go back to the first part of this tutorial.]]

[[User:Stephen_Mills/Biochemistry_Tutorials|Click here to go back to the main Tutorial page.]]

User:Stephen Mills/Secondary Structure: Helices

2014-08-23T02:29:38Z

Stephen Mills: /* H-Bonding in α-helices */

== 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' name='initial_alpha_helix'/>

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_load/1' target='initial_alpha_helix'>Click here</scene> to go back to the initial view. 

<scene name='User:Stephen_Mills/Secondary_Structure:_Helices/A_helix_load/1' target='initial_alpha_helix'>Click here</scene> to show the helix in a space-filling representation. This representation shows the atoms with a radius that is approximately correct.

<scene name='User:Robert_Dutnall/Sandbox_1_alpha_helix/A_helix_mainchain/3' target='initial_alpha_helix'>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' target='initial_alpha_helix'>Click here to see if you were correct.</scene>

<scene name='User:Robert_Dutnall/Sandbox_1_alpha_helix/A_helix_mainchain_label_ribbon/3' target='initial_alpha_helix'>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' target='initial_alpha_helix'>click here </scene>to zoom in and look down the helix axis from the N-terminal end.
 
What is in the middle of the helix?
 
Now,
<scene name='User:Stephen_Mills/Secondary_Structure:_Helices/A_helix_main_axis_spacefill/1' target='initial_alpha_helix'>click here</scene> to see the helix in a space-filling representation. 

Now, answer that question again - what is in the middle of the helix?
 

==H-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' name='h-bonds'/>
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? Click <scene name='User:Robert_Dutnall/Sandbox_1_alpha_helix/A_helix_mainchain_label/4' target='h-bonds'>here</scene> if the image doesn't load properly.

<scene name='User:Robert_Dutnall/Sandbox_1_alpha_helix/A_helix_mainchain_label_hbonds/10' target='h-bonds'>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' target='h-bonds'>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' target='h-bonds'>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' target='h-bonds'>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' target='h-bonds'>click here</scene> or <scene name='User:Robert_Dutnall/Sandbox_1_alpha_helix/A_helix_sidechains_cropped/2' target='h-bonds'>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' name='310_helix'/>

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' target='310_helix'>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' target='310_helix'>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' target='310_helix'>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.
 

==H-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' name='310_hbonds'/>
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' target='310_hbonds'>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' target='310_hbonds'>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' target='310_hbonds'>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' target='310_hbonds'>click here to look from the side</scene> or <scene name='User:Robert_Dutnall/Sandbox_1_alpha_helix/310_helix_sidechains_tricol_ax/1' target='310_hbonds'>click here to view down the helix axis</scene>.

<scene name='User:Robert_Dutnall/Sandbox_1_alpha_helix/310_helix_load/4' target='310_hbonds'>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:Stephen_Mills/Secondary_Structure:_Sheets|Click here to go on to part 2 of this tutorial.]]

[[User:Stephen_Mills/Biochemistry_Tutorials|Click here to go back to the main Tutorial page.]]

User:Stephen Mills/Secondary Structure: Helices

2014-08-23T02:18:29Z

Stephen Mills: /* H-Bonding in 3-10 Helices */

== 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' name='initial_alpha_helix'/>

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_load/1' target='initial_alpha_helix'>Click here</scene> to go back to the initial view. 

<scene name='User:Stephen_Mills/Secondary_Structure:_Helices/A_helix_load/1' target='initial_alpha_helix'>Click here</scene> to show the helix in a space-filling representation. This representation shows the atoms with a radius that is approximately correct.

<scene name='User:Robert_Dutnall/Sandbox_1_alpha_helix/A_helix_mainchain/3' target='initial_alpha_helix'>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' target='initial_alpha_helix'>Click here to see if you were correct.</scene>

<scene name='User:Robert_Dutnall/Sandbox_1_alpha_helix/A_helix_mainchain_label_ribbon/3' target='initial_alpha_helix'>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' target='initial_alpha_helix'>click here </scene>to zoom in and look down the helix axis from the N-terminal end.
 
What is in the middle of the helix?
 
Now,
<scene name='User:Stephen_Mills/Secondary_Structure:_Helices/A_helix_main_axis_spacefill/1' target='initial_alpha_helix'>click here</scene> to see the helix in a space-filling representation. 

Now, answer that question again - what is in the middle of the helix?
 

==H-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' name='h-bonds'/>
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' target='h-bonds'>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' target='h-bonds'>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' target='h-bonds'>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' target='h-bonds'>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' target='h-bonds'>click here</scene> or <scene name='User:Robert_Dutnall/Sandbox_1_alpha_helix/A_helix_sidechains_cropped/2' target='h-bonds'>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' name='310_helix'/>

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' target='310_helix'>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' target='310_helix'>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' target='310_helix'>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.
 

==H-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' name='310_hbonds'/>
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' target='310_hbonds'>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' target='310_hbonds'>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' target='310_hbonds'>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' target='310_hbonds'>click here to look from the side</scene> or <scene name='User:Robert_Dutnall/Sandbox_1_alpha_helix/310_helix_sidechains_tricol_ax/1' target='310_hbonds'>click here to view down the helix axis</scene>.

<scene name='User:Robert_Dutnall/Sandbox_1_alpha_helix/310_helix_load/4' target='310_hbonds'>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:Stephen_Mills/Secondary_Structure:_Sheets|Click here to go on to part 2 of this tutorial.]]

[[User:Stephen_Mills/Biochemistry_Tutorials|Click here to go back to the main Tutorial page.]]

User:Stephen Mills/Secondary Structure: Helices

2014-08-23T02:15:23Z

Stephen Mills: /* The 310-helix */

== 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' name='initial_alpha_helix'/>

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_load/1' target='initial_alpha_helix'>Click here</scene> to go back to the initial view. 

<scene name='User:Stephen_Mills/Secondary_Structure:_Helices/A_helix_load/1' target='initial_alpha_helix'>Click here</scene> to show the helix in a space-filling representation. This representation shows the atoms with a radius that is approximately correct.

<scene name='User:Robert_Dutnall/Sandbox_1_alpha_helix/A_helix_mainchain/3' target='initial_alpha_helix'>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' target='initial_alpha_helix'>Click here to see if you were correct.</scene>

<scene name='User:Robert_Dutnall/Sandbox_1_alpha_helix/A_helix_mainchain_label_ribbon/3' target='initial_alpha_helix'>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' target='initial_alpha_helix'>click here </scene>to zoom in and look down the helix axis from the N-terminal end.
 
What is in the middle of the helix?
 
Now,
<scene name='User:Stephen_Mills/Secondary_Structure:_Helices/A_helix_main_axis_spacefill/1' target='initial_alpha_helix'>click here</scene> to see the helix in a space-filling representation. 

Now, answer that question again - what is in the middle of the helix?
 

==H-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' name='h-bonds'/>
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' target='h-bonds'>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' target='h-bonds'>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' target='h-bonds'>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' target='h-bonds'>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' target='h-bonds'>click here</scene> or <scene name='User:Robert_Dutnall/Sandbox_1_alpha_helix/A_helix_sidechains_cropped/2' target='h-bonds'>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' name='310_helix'/>

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' target='310_helix'>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' target='310_helix'>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' target='310_helix'>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.
 

==H-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:Stephen_Mills/Secondary_Structure:_Sheets|Click here to go on to part 2 of this tutorial.]]

[[User:Stephen_Mills/Biochemistry_Tutorials|Click here to go back to the main Tutorial page.]]

User:Stephen Mills/Secondary Structure: Helices

2014-08-23T01:53:56Z

Stephen Mills: /* H-Bonding in α-helices */

== 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' name='initial_alpha_helix'/>

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_load/1' target='initial_alpha_helix'>Click here</scene> to go back to the initial view. 

<scene name='User:Stephen_Mills/Secondary_Structure:_Helices/A_helix_load/1' target='initial_alpha_helix'>Click here</scene> to show the helix in a space-filling representation. This representation shows the atoms with a radius that is approximately correct.

<scene name='User:Robert_Dutnall/Sandbox_1_alpha_helix/A_helix_mainchain/3' target='initial_alpha_helix'>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' target='initial_alpha_helix'>Click here to see if you were correct.</scene>

<scene name='User:Robert_Dutnall/Sandbox_1_alpha_helix/A_helix_mainchain_label_ribbon/3' target='initial_alpha_helix'>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' target='initial_alpha_helix'>click here </scene>to zoom in and look down the helix axis from the N-terminal end.
 
What is in the middle of the helix?
 
Now,
<scene name='User:Stephen_Mills/Secondary_Structure:_Helices/A_helix_main_axis_spacefill/1' target='initial_alpha_helix'>click here</scene> to see the helix in a space-filling representation. 

Now, answer that question again - what is in the middle of the helix?
 

==H-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' name='h-bonds'/>
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' target='h-bonds'>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' target='h-bonds'>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' target='h-bonds'>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' target='h-bonds'>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' target='h-bonds'>click here</scene> or <scene name='User:Robert_Dutnall/Sandbox_1_alpha_helix/A_helix_sidechains_cropped/2' target='h-bonds'>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.
 

==H-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:Stephen_Mills/Secondary_Structure:_Sheets|Click here to go on to part 2 of this tutorial.]]

[[User:Stephen_Mills/Biochemistry_Tutorials|Click here to go back to the main Tutorial page.]]

User:Stephen Mills/Secondary Structure: Helices

2014-08-23T01:48:07Z

Stephen Mills: /* The α-helix */

== 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' name='initial_alpha_helix'/>

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_load/1' target='initial_alpha_helix'>Click here</scene> to go back to the initial view. 

<scene name='User:Stephen_Mills/Secondary_Structure:_Helices/A_helix_load/1' target='initial_alpha_helix'>Click here</scene> to show the helix in a space-filling representation. This representation shows the atoms with a radius that is approximately correct.

<scene name='User:Robert_Dutnall/Sandbox_1_alpha_helix/A_helix_mainchain/3' target='initial_alpha_helix'>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' target='initial_alpha_helix'>Click here to see if you were correct.</scene>

<scene name='User:Robert_Dutnall/Sandbox_1_alpha_helix/A_helix_mainchain_label_ribbon/3' target='initial_alpha_helix'>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' target='initial_alpha_helix'>click here </scene>to zoom in and look down the helix axis from the N-terminal end.
 
What is in the middle of the helix?
 
Now,
<scene name='User:Stephen_Mills/Secondary_Structure:_Helices/A_helix_main_axis_spacefill/1' target='initial_alpha_helix'>click here</scene> to see the helix in a space-filling representation. 

Now, answer that question again - what is in the middle of the helix?
 

==H-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.
 

==H-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:Stephen_Mills/Secondary_Structure:_Sheets|Click here to go on to part 2 of this tutorial.]]

[[User:Stephen_Mills/Biochemistry_Tutorials|Click here to go back to the main Tutorial page.]]

User:Stephen Mills

2014-08-21T04:36:53Z

Stephen Mills:

CURRENT POSITION:
Xavier University; Department of Chemistry 
:Assistant Professor, August 2013 to present 

PREVIOUS POSITION:
University of San Diego; Department of Chemistry and Biochemistry 
:Assistant Professor, August 2006 to May 2013 
:[[http://www.sandiego.edu/cas/chemistry/faculty/biography.php?ID=71 USD Website]]

EDUCATION:

University of California, Berkeley; Berkeley, CA; Professor Michael A. Marletta, advisor 
:Postdoctoral Fellow, 2001-2005

University of California, Berkeley; Berkeley, CA; Professor Judith P. Klinman, advisor 
:Ph.D. in Chemistry, May 2001 
:“The Role of Copper and its Ligands in an Amine Oxidase from ''Hansenula polymorpha''”

University of California, Berkeley; Berkeley, CA; Professor Paul A. Bartlett, advisor 
:M.S. in Chemistry, Dec. 1994 
:"Synthesis and Evaluation of a Proposed Inactivator of Papain"

University of Illinois at Urbana-Champaign; Champaign, IL 
:B.S. in Chemistry, May 1992, with high distinction
----
*[[User:Stephen Mills/Sandbox]]
*[[User:Stephen Mills/Sandbox 1]]
*[[User:Stephen Mills/Sandbox 2 Peptide tutorial]] moved to Peptide Tutorial 1
*[[User:Stephen Mills/Sandbox 2 Peptide tutorial_2]] moved to Peptide Tutorial 2
*[[User:Stephen Mills/Sandbox 3 Secondary Structure Tutorial 1]]
*[[User:Stephen Mills/Peptide tutorial 1]]
*[[User:Stephen Mills/Peptide tutorial 2]]
*[[User:Stephen Mills/Secondary Structure: Helices]]
*[[User:Stephen Mills/Secondary Structure: Sheets]]
*[[User:Stephen Mills/Biochemistry Tutorials]]
*[[User:Stephen Mills/XU Peptide Tutorial 1 p1]]
*[[User:Stephen Mills/XU Peptide Tutorial 1 p2]]

User:Stephen Mills/Biochemistry Tutorials

2014-08-21T04:36:29Z

Stephen Mills:

Biochemistry Protein Structure Tutorials

These tutorials are meant to give you an introduction to amino acids and peptides, their structures and the structures they adopt. I recommend starting with the first and working your way through in order.

The first tutorial will introduce you to the amino acids, how they are represented and how they are connected (their primary structure). You will practice recognizing them and using their names and one-letter codes. There are two pages to this tutorial.

The second tutorial introduces you to the secondary structures that peptides adopt - specifically α-helices and β-sheets. This tutorial has two pages as well.

As you finish each tutorial, you will be asked to write down several pieces of information. Those answers will be submitted to your instructor as they have indicated.

*[[User:Stephen Mills/Peptide tutorial 1|Peptide tutorial 1 part 1]]
*[[User:Stephen Mills/Peptide tutorial 2|Peptide tutorial 1 part 2]]
*[[User:Stephen Mills/Secondary Structure: Helices|Secondary Structure tutorial - Helices]]
*[[User:Stephen Mills/Secondary Structure: Sheets|Secondary Structure tutorial - Sheets]]

User:Stephen Mills/Peptide tutorial 2

2014-08-21T04:35:25Z

Stephen Mills: /* Oligopeptides */

==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' name='CysAsp'/>

What is the short-hand notation for this dipeptide?

<scene name='User:Stephen_Mills/Sandbox_2_Peptide_tutorial_2/Cysasplabels/2' target='CysAsp'>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' target='CysAsp'>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' target='CysAsp'>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' target='CysAsp'>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' target='CysAsp'>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' name='penta'/>

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' target='penta'>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' target='penta'>
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 down the sequence in the 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:Stephen_Mills/Biochemistry_Tutorials|Click here to go back to the main Tutorial page.]]

User:Stephen Mills/Peptide tutorial 2

2014-08-21T04:34:16Z

Stephen Mills: /* Let's look at another dipeptide. */

==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' name='CysAsp'/>

What is the short-hand notation for this dipeptide?

<scene name='User:Stephen_Mills/Sandbox_2_Peptide_tutorial_2/Cysasplabels/2' target='CysAsp'>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' target='CysAsp'>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' target='CysAsp'>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' target='CysAsp'>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' target='CysAsp'>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 down the sequence in the 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:Stephen_Mills/Biochemistry_Tutorials|Click here to go back to the main Tutorial page.]]

User:Stephen Mills/Peptide tutorial 1

2014-08-21T04:31:01Z

Stephen Mills: /* Backbone Atoms */

== 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' name='Arg_labels'/>

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' target='Arg_labels'>Click here to see the N and C groups labelled.</scene>

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

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/Peptide_tutorial_1/Tyrosinelabels/1' target='Tyr_labels'>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' name='Arg_alpha'/>

<scene name='User:Stephen_Mills/Sandbox_2_Peptide_tutorial/Argininealpha/2' target='Arg_alpha'>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' name='Tyr_alpha'/>

<scene name='User:Stephen_Mills/Sandbox_2_Peptide_tutorial/Tyrosinealpha/2' target='Tyr_alpha'>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' name='ArgTyr'/>

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

<scene name='User:Stephen_Mills/Peptide_tutorial_1/Argtyraalabels/2' target='ArgTyr'>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' name='ArgTyrAmide'/>

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' target='ArgTyrAmide'>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' target='ArgTyrAmide'>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' name='ArgTyrBackbone'/>

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' target='ArgTyrBackbone'>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:Stephen_Mills/Biochemistry_Tutorials|Click here to go back to the main Tutorial page.]]

User:Stephen Mills/Peptide tutorial 1

2014-08-21T04:29:41Z

Stephen Mills: /* Dipeptides */

== 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' name='Arg_labels'/>

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' target='Arg_labels'>Click here to see the N and C groups labelled.</scene>

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

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/Peptide_tutorial_1/Tyrosinelabels/1' target='Tyr_labels'>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' name='Arg_alpha'/>

<scene name='User:Stephen_Mills/Sandbox_2_Peptide_tutorial/Argininealpha/2' target='Arg_alpha'>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' name='Tyr_alpha'/>

<scene name='User:Stephen_Mills/Sandbox_2_Peptide_tutorial/Tyrosinealpha/2' target='Tyr_alpha'>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' name='ArgTyr'/>

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

<scene name='User:Stephen_Mills/Peptide_tutorial_1/Argtyraalabels/2' target='ArgTyr'>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' name='ArgTyrAmide'/>

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' target='ArgTyrAmide'>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' target='ArgTyrAmide'>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:Stephen_Mills/Biochemistry_Tutorials|Click here to go back to the main Tutorial page.]]

User:Stephen Mills/Peptide tutorial 1

2014-08-21T04:25:00Z

Stephen Mills: /* Alpha Carbons */

== 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' name='Arg_labels'/>

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' target='Arg_labels'>Click here to see the N and C groups labelled.</scene>

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

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/Peptide_tutorial_1/Tyrosinelabels/1' target='Tyr_labels'>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' name='Arg_alpha'/>

<scene name='User:Stephen_Mills/Sandbox_2_Peptide_tutorial/Argininealpha/2' target='Arg_alpha'>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' name='Tyr_alpha'/>

<scene name='User:Stephen_Mills/Sandbox_2_Peptide_tutorial/Tyrosinealpha/2' target='Tyr_alpha'>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:Stephen_Mills/Biochemistry_Tutorials|Click here to go back to the main Tutorial page.]]

User:Stephen Mills/Peptide tutorial 1

2014-08-21T04:22:32Z

Stephen Mills:

== 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' name='Arg_labels'/>

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' target='Arg_labels'>Click here to see the N and C groups labelled.</scene>

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

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/Peptide_tutorial_1/Tyrosinelabels/1' target='Tyr_labels'>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:Stephen_Mills/Biochemistry_Tutorials|Click here to go back to the main Tutorial page.]]

User:Stephen Mills/XU Peptide Tutorial 1 p2

2014-08-21T04:05:39Z

Stephen Mills: New page: = = <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) an...

= =
<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>

User:Stephen Mills

2014-08-21T04:03:28Z

Stephen Mills:

CURRENT POSITION:
Xavier University; Department of Chemistry 
:Assistant Professor, August 2013 to present 

PREVIOUS POSITION:
University of San Diego; Department of Chemistry and Biochemistry 
:Assistant Professor, August 2006 to May 2013 
:[[http://www.sandiego.edu/cas/chemistry/faculty/biography.php?ID=71 USD Website]]

EDUCATION:

University of California, Berkeley; Berkeley, CA; Professor Michael A. Marletta, advisor 
:Postdoctoral Fellow, 2001-2005

University of California, Berkeley; Berkeley, CA; Professor Judith P. Klinman, advisor 
:Ph.D. in Chemistry, May 2001 
:“The Role of Copper and its Ligands in an Amine Oxidase from ''Hansenula polymorpha''”

University of California, Berkeley; Berkeley, CA; Professor Paul A. Bartlett, advisor 
:M.S. in Chemistry, Dec. 1994 
:"Synthesis and Evaluation of a Proposed Inactivator of Papain"

University of Illinois at Urbana-Champaign; Champaign, IL 
:B.S. in Chemistry, May 1992, with high distinction
----
*[[User:Stephen Mills/Sandbox]]
*[[User:Stephen Mills/Sandbox 1]]
*[[User:Stephen Mills/Sandbox 2 Peptide tutorial]] moved to Peptide Tutorial 1
*[[User:Stephen Mills/Sandbox 2 Peptide tutorial_2]] moved to Peptide Tutorial 2
*[[User:Stephen Mills/Sandbox 3 Secondary Structure Tutorial 1]]
*[[User:Stephen Mills/Peptide tutorial 1]]
*[[User:Stephen Mills/Peptide tutorial 2]]
*[[User:Stephen Mills/Secondary Structure: Helices]]
*[[User:Stephen Mills/Secondary Structure: Sheets]]
*[[User:Stephen Mills/Biochemistry Tutorials]]
*[[User:Stephen Mills/XU Peptide Tutorial 1 p1]]

User:Stephen Mills/XU Peptide Tutorial 1 p1

2014-08-21T04:02:20Z

Stephen Mills: 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...

User:Stephen Mills/Peptide tutorial 1

2014-08-21T03:54:35Z

Stephen Mills: Undo revision 1974084 by Stephen Mills (Talk)

== 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:Stephen_Mills/Biochemistry_Tutorials|Click here to go back to the main Tutorial page.]]

User:Stephen Mills/Peptide tutorial 1

2014-08-21T03:54:06Z

Stephen Mills: Undo revision 1974085 by Stephen Mills (Talk)

== 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/Peptide_tutorial_1/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:Stephen_Mills/Biochemistry_Tutorials|Click here to go back to the main Tutorial page.]]

User:Stephen Mills/Peptide tutorial 1

2014-08-21T03:53:47Z

Stephen Mills: Undo revision 1974086 by Stephen Mills (Talk)

== 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/Peptide_tutorial_1/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/Peptide_tutorial_1/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:Stephen_Mills/Biochemistry_Tutorials|Click here to go back to the main Tutorial page.]]

User:Stephen Mills/Peptide tutorial 1

2014-08-21T03:53:18Z

Stephen Mills: Undo revision 1974087 by Stephen Mills (Talk)

== 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/Peptide_tutorial_1/Arginine/3' />

<scene name='45/458451/Argininelabel/1'>Click here when you think you know what it is.</scene>

''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/Peptide_tutorial_1/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:Stephen_Mills/Biochemistry_Tutorials|Click here to go back to the main Tutorial page.]]

User:Stephen Mills/Peptide tutorial 1

2014-08-21T03:49:09Z

Stephen Mills:

== 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/Peptide_tutorial_1/Arginine/3' />

<scene name='45/458451/Argininelabel/1'>Click here when you think you know what it is.</scene>

''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='45/458451/Argininelabel/1' />

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/Peptide_tutorial_1/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:Stephen_Mills/Biochemistry_Tutorials|Click here to go back to the main Tutorial page.]]

User:Stephen Mills/Peptide tutorial 1

2014-08-21T03:43:56Z

Stephen Mills:

== 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/Peptide_tutorial_1/Arginine/3' />

<scene name='45/458451/Argininelabel/1'>Click here when you think you know what it is.</scene>

''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/Peptide_tutorial_1/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:Stephen_Mills/Biochemistry_Tutorials|Click here to go back to the main Tutorial page.]]

User:Stephen Mills/Peptide tutorial 1

2014-08-21T03:38:50Z

Stephen Mills:

== 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/Peptide_tutorial_1/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/Peptide_tutorial_1/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:Stephen_Mills/Biochemistry_Tutorials|Click here to go back to the main Tutorial page.]]

User:Stephen Mills/Peptide tutorial 1

2014-08-21T02:36:34Z

Stephen Mills: /* */

== 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/Peptide_tutorial_1/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:Stephen_Mills/Biochemistry_Tutorials|Click here to go back to the main Tutorial page.]]