User:Robert Dutnall/Sandbox 1 alpha helix
From Proteopedia
| Line 1: | Line 1: | ||
| - | "?JMOLJAR=http://chemapps.stolaf.edu/jmol/docs/examples-12/JmolAppletSigned0.jar" | ||
== Biochemistry Tutorial #2 - Secondary Structure == | == Biochemistry Tutorial #2 - Secondary Structure == | ||
| Line 6: | Line 5: | ||
''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.'' | ''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 structure by holding down the right mouse button and dragging. | + | You can rotate the structure 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: | Other things you can do: | ||
| Line 19: | Line 18: | ||
<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'/> | <Structure load='Tut_alpha_helix.pdb' size='500' frame='true' align='left' caption='' scene='User:Robert_Dutnall/Sandbox_1_alpha_helix/A_helix_load/1'/> | ||
| - | All the atoms are shown in this initial orientation (C = green; N = blue; O = red; S = yellow; H = white). | + | All the atoms are shown in this initial orientation (C = green; N = blue; O = red; S = yellow; H = white). The helix axis runs vertically, approximately parallel to the plane of the screen. |
| - | <scene name='User:Robert_Dutnall/Sandbox_1_alpha_helix/A_helix_mainchain/3'>Click here </scene>to show only the polypeptide mainchain (NH, Cα, and C=O). | + | <scene name='User:Robert_Dutnall/Sandbox_1_alpha_helix/A_helix_mainchain/3'>Click here</scene> to show only the polypeptide mainchain (NH, Cα, and C=O). |
| - | Identify the N- and C-termini. <scene name='User:Robert_Dutnall/Sandbox_1_alpha_helix/A_helix_mainchain_label/ | + | Identify the N- and C-termini. <scene name='User:Robert_Dutnall/Sandbox_1_alpha_helix/A_helix_mainchain_label/4'>Click here to see if you were correct.</scene> |
| - | <scene name='User:Robert_Dutnall/Sandbox_1_alpha_helix/A_helix_mainchain_label_ribbon/ | + | <scene name='User:Robert_Dutnall/Sandbox_1_alpha_helix/A_helix_mainchain_label_ribbon/3'>Click here to add a ribbon that will help show the path of the mainchain. </scene> You should be able to see that it is helical with a right-handed twist (you rotate to the right as you move along the helix axis). |
| - | Click the "toggle spin" button in the box to stop the structure from rotating. | + | Click the "toggle spin" button in the box to stop the structure from rotating. Now use your mouse to rotate the structure to look down the helix axis. If you have any problems with finding this view, <scene name='User:Robert_Dutnall/Sandbox_1_alpha_helix/A_helix_mainchain_label_axis/3'>click here </scene>to zoom in and look down the helix axis from the N-terminal end. |
| - | + | <scene name='User:Robert_Dutnall/Sandbox_1_alpha_helix/A_helix_mainchain_label/4'>Click here to zoom out again.</scene> Look at the structure carefully and identify the mainchain NH and C=O groups. What is the orientation of these groups with respect to the helix axis? | |
| - | <scene name='User:Robert_Dutnall/Sandbox_1_alpha_helix/A_helix_mainchain_label_hbonds/ | + | <scene name='User:Robert_Dutnall/Sandbox_1_alpha_helix/A_helix_mainchain_label_hbonds/8'>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/ | + | <scene name='User:Robert_Dutnall/Sandbox_1_alpha_helix/A_helix_mainchain_label_hbonds/7'>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'). |
| - | What is the general orientation of the side chains with respect to the helix axis? | + | <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>). | ||
= = | = = | ||
Revision as of 19:48, 25 August 2011
Biochemistry Tutorial #2 - Secondary Structure
Blah, blah, blah
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 structure 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
An α-helix
This is a 19 amino acid chain in α-helical conformation.
|
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.
to show only the polypeptide mainchain (NH, Cα, and C=O).
Identify the N- and C-termini.
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, to zoom in and look down the helix axis from the N-terminal end.
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?
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).
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').
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 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 or ).
