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>. In space filling depiction, you can see how <scene name='77/778341/Space/1'>tightly packed</scene> the main chain is (no space in the middle). | + | 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>. |
| + | <jmol> | ||
| + | <jmolButton> | ||
| + | <script> var a = [0.2, 0.3, 0.5, 0.7, 1.0]; for(var i IN a) {spacefill @i; delay 0.4;} | ||
| + | </script> | ||
| + | <text>increase sphere radii</text> | ||
| + | </jmolButton> | ||
| + | </jmol> | ||
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| + | In space filling depiction, you can see how <scene name='77/778341/Space/1'>tightly packed</scene> the main chain is (no space in the middle). | ||
Apart from the characteristic hydrogen bonding patters, the other identifying feature of alpha helices are the main chain torsion angles phi and psi. If you plot phi against psi for each residue (so-called Ramachandran plot), you find that the phi/psi combination found in alpha helices fall into one of the three "allowed" (i.e. observed) areas for non-glycine residues. For a more detailed explanation, see [[Ramachandran Plot]] or http://www.cryst.bbk.ac.uk/PPS95/course/3_geometry/rama.html. | Apart from the characteristic hydrogen bonding patters, the other identifying feature of alpha helices are the main chain torsion angles phi and psi. If you plot phi against psi for each residue (so-called Ramachandran plot), you find that the phi/psi combination found in alpha helices fall into one of the three "allowed" (i.e. observed) areas for non-glycine residues. For a more detailed explanation, see [[Ramachandran Plot]] or http://www.cryst.bbk.ac.uk/PPS95/course/3_geometry/rama.html. | ||
Revision as of 19:28, 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.
