User:Stephen Mills/Secondary Structure: Helices: Difference between revisions

<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'/>

<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>).

<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'/>

<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.

<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.  

<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 120^o 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>