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User:Tilman Schirmer/Sandbox 100

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== Secondary structure of proteins ==
 
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====Repetitive torsion angles ====
 
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<applet load='180-180.pdb' size='400' frame='true' align='right' scene='User:Tilman_Schirmer/Sandbox_100/Extended/2'/>
 
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A polypeptide chain with a repetition of identical phi-psi torsion angles yields a helical structure.
 
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----
----
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phi-psi = (180<sup>o</sup>, 180<sup>o</sup>), fully extended chain:
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see also preceding chapter [[User:Tilman_Schirmer/Sandbox_99|peptide bond]]
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<scene name='User:Tilman_Schirmer/Sandbox_100/Extended/2'>model</scene>,
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<scene name='User:Tilman_Schirmer/Sandbox_100/Extended/3'> Calpha-trace</scene><br>
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----
----
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phi-psi = (-140<sup>o</sup>, 130<sup>o</sup>), extended chain:
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== Secondary structure of proteins ==
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<scene name='User:Tilman_Schirmer/Sandbox_100/Beta/1'>model</scene>,
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<scene name='User:Tilman_Schirmer/Sandbox_100/Beta/2'>Calpha-trace</scene>; this is the '''β-strand''' conformation found in beta-sheets <br>
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Note: <br>
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outline:
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polypeptide forms a <scene name='User:Tilman_Schirmer/Sandbox_100/Beta/4'>zig-zag</scene> with side-chains protruding towards alternating (up, down) directions<br>
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[[User:Tilman Schirmer/Sandbox 110|Repetitive torsion angles]]
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the polypeptide main-chain is <scene name='User:Tilman_Schirmer/Sandbox_100/Beta/3'>left-twisted</scene> as can been seen when looking along the chain <br>
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[[User:Tilman Schirmer/Sandbox 111|α-Helix]]
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the <scene name='User:Tilman_Schirmer/Sandbox_100/Beta/5'>side-chains</scene> point towards alternate directions<br>
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[[User:Tilman Schirmer/Sandbox 112|parallel β-sheet]]
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----
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phi-psi = (70<sup>o</sup>, 180<sup>o</sup>):
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[[User:Tilman Schirmer/Sandbox 113|antiparallel β-sheet]]
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<scene name='User:Tilman_Schirmer/Sandbox_100/Elongated_helix/1'>model</scene>,
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<scene name='User:Tilman_Schirmer/Sandbox_100/Elongated_helix/2'>Calpha-trace</scene>; note that there are clashes (where?)<br>
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----
 
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phi-psi = (-60<sup>o</sup>, -40<sup>o</sup>), '''α-helix''':
 
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<scene name='User:Tilman_Schirmer/Sandbox_100/Helix/1'>model</scene>,
 
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<scene name='User:Tilman_Schirmer/Sandbox_100/Helix/2'>Calpha-trace</scene><br>
 
----
----
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phi-psi = (-50<sup>o</sup>, -26<sup>o</sup>), '''3<sub>10</sub> helix''':
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== Next Topic ==
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<scene name='User:Tilman_Schirmer/Sandbox_100/310helix/1'>model</scene>,
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<scene name='User:Tilman_Schirmer/Sandbox_100/310helix/2'>Calpha-trace</scene>
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----
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==== α-Helix ====
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<applet load='180-180.pdb' size='400' frame='true' align='right' scene='User:Tilman_Schirmer/Sandbox_100/Helix/1'/>
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An α-Helix is stabilized by main-chain <scene name='User:Tilman_Schirmer/Sandbox_100/Helix/3'>hydogen bonds</scene> between O<sub>i</sub> and N<sub>i+4</sub>. With <scene name='User:Tilman_Schirmer/Sandbox_100/Helix/4'>side-chains</scene>.
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<br><br><br><br><br><br><br><br><br><br><br><br><br><br><br><br><br><br><br><br><br>
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==== parallel β-sheet ====
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<applet load='1tmy.pdb' size='400' frame='true' align='right' scene='User:Tilman_Schirmer/Sandbox_100/Parallel_sheet/4'/>
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With <scene name='User:Tilman_Schirmer/Sandbox_100/Parallel_sheet/5'>side-chains</scene>.
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<br><br><br><br><br><br><br><br><br><br><br><br><br><br><br><br><br><br><br><br><br><br><br>
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==== antiparallel β-sheet ====
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<applet load='1ema.pdb' size='400' frame='true' align='right' scene='User:Tilman_Schirmer/Sandbox_100/Antiparallel_beta-sheet/1'/>
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With <scene name='User:Tilman_Schirmer/Sandbox_100/Antiparallel_beta-sheet/2'>side-chains</scene>.
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<br><br><br><br><br><br><br><br><br><br><br><br><br><br><br><br><br><br><br><br>
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== Anatomy of a protein ==
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<applet load='1tmy.pdb' size='400' frame='true' align='right' scene='User:Tilman_Schirmer/Sandbox_100/Cartoon/1'/>
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<scene name='User:Tilman_Schirmer/Sandbox_100/Cartoon/2'>Cartoon</scene>
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<scene name='User:Tilman_Schirmer/Sandbox_100/Backbone/2'>C-alpha trace</scene>
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<scene name='User:Tilman_Schirmer/Sandbox_100/Backbone/3'>Backbone</scene>
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<scene name='User:Tilman_Schirmer/Sandbox_100/Ball-and-stick/1'>Ball and stick</scene>
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-----
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<scene name='User:Tilman_Schirmer/Sandbox_100/Beta_sheets/2'>Beta sheets</scene>
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<scene name='User:Tilman_Schirmer/Sandbox_100/Beta_sheets_backbone/2'>Beta sheets backbone</scene>
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<scene name='User:Tilman_Schirmer/Sandbox_100/Beta_sheets_calpha/2'>Beta sheets and C-Alpha atoms</scene>
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-----
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<scene name='User:Tilman_Schirmer/Sandbox_100/Alpha_helix/1'>Alpha helix</scene>
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<scene name='User:Tilman_Schirmer/Sandbox_100/Alpha_helix_backbone/2'>Alpha helix backbone</scene>
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<scene name='User:Tilman_Schirmer/Sandbox_100/Alpha_helix_calpha/2'>Alpha helix and C-alpha atoms</scene>
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-----
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<scene name='User:Tilman_Schirmer/Sandbox_100/Turn/2'>Turn</scene>
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<scene name='User:Tilman_Schirmer/Sandbox_100/Turn_backbone/1'>Turn backbone</scene>
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<br><br><br><br><br><br><br><br><br><br><br><br><br><br><br><br><br><br><br><br><br><br><br>
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[[User:Tilman_Schirmer/Sandbox_120|anatomy of a protein]]
== Notes ==
== Notes ==
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see also http://proteopedia.org/wiki/index.php/User:James_D_Watson/Structural_Templates
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see also http://proteopedia.org/wiki/index.php/User:James_D_Watson/Structural_Templates, [[Secondary_structure]]

Current revision

see also preceding chapter peptide bond

Secondary structure of proteins

outline:

Repetitive torsion angles

α-Helix

parallel β-sheet

antiparallel β-sheet


Next Topic

anatomy of a protein

Notes

see also http://proteopedia.org/wiki/index.php/User:James_D_Watson/Structural_Templates, Secondary_structure

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Tilman Schirmer

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