Alpha helix
From Proteopedia
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==Structure and hydrogen bonding== | ==Structure and hydrogen bonding== | ||
<StructureSection load='3nir' size='340' side='right' caption='Caption for this structure' scene=''> | <StructureSection load='3nir' size='340' side='right' caption='Caption for this structure' scene=''> | ||
| - | The following 4 scenes are inspired by a nice set of figures in Stryer's biochemistry textbook (https://www.ncbi.nlm.nih.gov/books/NBK22580/figure/A322/?report=objectonly). In an alpha helix, the main chain arranges in a <scene name='77/778341/Ribbon/1'>right-handed helix</scene> with the side chains (green) pointing away from the helical axis. The alpha helix is stabilized by <scene name='77/778341/Hbonds/2'>hydrogen bonds</scene> from amino acid n to n+4. There are <scene name='77/778341/Wheel/1'>3.6 residues per turn</scene>. If you | + | The following 4 scenes are inspired by a nice set of figures in Stryer's biochemistry textbook (https://www.ncbi.nlm.nih.gov/books/NBK22580/figure/A322/?report=objectonly). In an alpha helix, the main chain arranges in a <scene name='77/778341/Ribbon/1'>right-handed helix</scene> with the side chains (green) pointing away from the helical axis. The alpha helix is stabilized by <scene name='77/778341/Hbonds/2'>hydrogen bonds</scene> from amino acid n to n+4. There are <scene name='77/778341/Wheel/1'>3.6 residues per turn</scene>. If you <jmol> |
| - | <jmol> | + | |
<jmolLink> | <jmolLink> | ||
<script> select visible; var a = [0.5, 0.7, 1.0, 1.5, 1.8]; for(var i IN a) {spacefill @i; delay 0.4;} | <script> select visible; var a = [0.5, 0.7, 1.0, 1.5, 1.8]; for(var i IN a) {spacefill @i; delay 0.4;} | ||
Revision as of 19:38, 16 January 2018
Contents |
Structure and hydrogen bonding
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Experimental evidence
a) CD spectroscopy http://www.cryst.bbk.ac.uk/PPS2/course/section8/ss-960531_21.html
b) NMR chemical shifts
Role of alpha helices in the history of structural biology
a) Pauling predicts it http://onlinelibrary.wiley.com/doi/10.1111/febs.12796/full
b) Determination of hand: There are several methods in X-ray crystallography where crystallographers obtain an electron density, but don't know whether it or its mirror image is correct. Historically, finding electron density that fits a helix was used to break this ambiguity. If the helix was right-handed, the electron density was used as is, but if the helix was left-handed, the mirror image was used.
c) Tracing the chain: When building a model into electron density, the first step was to place continguous C-alpha atoms into the density (with proper spacing). To see in which direction an alpha helix goes, you look at the side chain density. If it points up, the N-terminus is on top, otherwise on the bottom.
