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J Mol Biol. 2004 Apr 9;337(5):1195-205.

Amino acid propensities are position-dependent throughout the length of alpha-helices.

Author information

1
Department of Physics, University of Pennsylvania, Philadelphia, PA 19104, USA.

Abstract

The 20 commonly occurring amino acids have been shown to have distinct position-dependent, helix-forming propensities near the ends of alpha-helices. Here, we show that the amino acids also have very strong position-dependent propensities throughout the length of a helix. Most helices are amphiphilic, and they have a strong tendency to both begin and end on the solvent-inaccessible face of the helix. These position-specific propensities should provide valuable parameters to guide de novo protein design, and should allow more precise prediction of helical topology in natural proteins.

PMID:
15046987
DOI:
10.1016/j.jmb.2004.02.004
[Indexed for MEDLINE]

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