View source for User:Stephen Mills/Secondary Structure: 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 ≠ 180<sup>o</sup>) 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 ~ -120<sup>o</sup>, φ ~ +105<sup>o</sup>. 

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?
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==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.
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==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 ~ -150<sup>o</sup>, φ ~ +135<sup>o</sup>. 

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

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