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Structure and hydrogen bonding
| 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 with the side chains (green) pointing away from the helical axis. The alpha helix is stabilized by from amino acid n to n+4. There are . In space filling depiction, you can see how the main chain is (no space in the middle).
Which amino acids are found in alpha helices?
Proline is a helix breaker because its main chain nitrogen is not available for hydrogen bonding. Amino acid side chains whose movement is largely restricted in an alpha helix (branched at beta carbon like threonine or valine) are disfavored, as is glycine. Here is an example of a at the position of a .
Alpha helices in soluble (globular) proteins
Example: myoglobin
Example: DNA binding
Alpha helices in transmembrane proteins
opioid receptors: http://pdb101.rcsb.org/motm/217
Alpha helices in filamentous proteins
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Experimental evidence
a) CD spectroscopy
b) NMR chemical shifts
c) Fiber diffraction
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.
References
