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Proteins. 2014 Sep;82(9):1960-70. doi: 10.1002/prot.24550. Epub 2014 Apr 16.

Helix kinks are equally prevalent in soluble and membrane proteins.

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  • 1Department of Statistics, University of Oxford, 1 South Parks Road, Oxford, OX1 3TG, United Kingdom.

Abstract

Helix kinks are a common feature of α-helical membrane proteins, but are thought to be rare in soluble proteins. In this study we find that kinks are a feature of long α-helices in both soluble and membrane proteins, rather than just transmembrane α-helices. The apparent rarity of kinks in soluble proteins is due to the relative infrequency of long helices (≥20 residues) in these proteins. We compare length-matched sets of soluble and membrane helices, and find that the frequency of kinks, the role of Proline, the patterns of other amino acid around kinks (allowing for the expected differences in amino acid distributions between the two types of protein), and the effects of hydrogen bonds are the same for the two types of helices. In both types of protein, helices that contain Proline in the second and subsequent turns are very frequently kinked. However, there are a sizeable proportion of kinked helices that do not contain a Proline in either their sequence or sequence homolog. Moreover, we observe that in soluble proteins, kinked helices have a structural preference in that they typically point into the solvent.

KEYWORDS:

helix bend; helix distortion; helix kink; membrane protein; protein helix; protein structure; soluble protein

PMID:
24638929
PMCID:
PMC4285789
DOI:
10.1002/prot.24550
[PubMed - indexed for MEDLINE]
Free PMC Article
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