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J Mol Biol. 2003 Mar 14;327(1):229-37.

Flexibility of alpha-helices: results of a statistical analysis of database protein structures.

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1
NEC Research Institute, 4 Independence Way, Princeton, NJ 08540, USA.

Abstract

Alpha-helices stand out as common and relatively invariant secondary structural elements of proteins. However, alpha-helices are not rigid bodies and their deformations can be significant in protein function (e.g. coiled coils). To quantify the flexibility of alpha-helices we have performed a structural principal-component analysis of helices of different lengths from a representative set of protein folds in the Protein Data Bank. We find three dominant modes of flexibility: two degenerate bend modes and one twist mode. The data are consistent with independent Gaussian distributions for each mode. The mode eigenvalues, which measure flexibility, follow simple scaling forms as a function of helix length. The dominant bend and twist modes and their harmonics are reproduced by a simple spring model, which incorporates hydrogen-bonding and excluded volume. As an application, we examine the amount of bend and twist in helices making up all coiled-coil proteins in SCOP. Incorporation of alpha-helix flexibility into structure refinement and design is discussed.

PMID:
12614621
DOI:
10.1016/s0022-2836(03)00097-4
[Indexed for MEDLINE]

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