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Flexibility of a-Helices: Results of a Statistical Analysis of Database Protein Structures


, : Flexibility of a-Helices: Results of a Statistical Analysis of Database Protein Structures. Journal of Molecular Biology 327(1): 9-37

a-Helices stand out as common and relatively invariant secondary structural elements of proteins. However, a-helices are not rigid bodies and their deformations can be significant in protein function (e.g. coiled coils). To quantify the flexibility of a-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 a-helix flexibility into structure refinement and design is discussed. Reprinted by permission of the publisher.

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