Flexibility of α-helices:: Results of a statistical analysis of database protein structures

JOURNAL OF MOLECULAR BIOLOGY

卷:327

Article

Emberly, EG ; Mukhopadhyay, R ; Wingreen, NS ; Tang, C

关键词: alpha-helices;    database protein structures;    protein folds;   

DOI  :  10.1016/S0022-2836(03)00097-4

来源: Elsevier

【 摘 要 】

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 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 alpha-helix flexibility into structure refinement and design is discussed. (C) 2003 Elsevier Science Ltd. All rights reserved.

【 授权许可】

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