Alpha helix
From Proteopedia
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==Structure and hydrogen bonding== | ==Structure and hydrogen bonding== | ||
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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> | 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> | ||
<jmolLink> | <jmolLink> | ||
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<text>increase the sphere radii</text> | <text>increase the sphere radii</text> | ||
Revision as of 21:09, 17 January 2018
Contents |
Structure and hydrogen bonding
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Types of proteins and folds that contain alpha helices
Alpha helices in soluble (globular) proteins
Example: myoglobin Example: helical DNA binding domains
Alpha helices in transmembrane proteins
A common fold found in transmembrane proteins are alpha-helical bundles running from one side to the other side of the membrane. An alpha helix of 19 amino acids (with a length of about 30 angstroms) has the right size to cross the double-layer of a typical membrane. If the helix runs at an angle instead of perfectly perpendicular to the membrane, it has to be a bit longer. There is a write-up on opioid receptiors that illustrates this fold in the Molecule of the Month series by David Goodsell (http://pdb101.rcsb.org/motm/217).
Alpha helices in coiled coils
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 contiguous 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. (search for Christmas tree in http://www-structmed.cimr.cam.ac.uk/Course/Fitting/fittingtalk.html)
