TitleFlexibility of alpha-helices: results of a statistical analysis of database protein structures.
Publication TypeJournal Article
Year of Publication2003
AuthorsEmberly, EG, Mukhopadhyay, R, Wingreen, NS, Tang, C
JournalJ Mol Biol
Volume327
Issue1
Pagination229-37
Date Published2003 Mar 14
KeywordsDatabases, Protein, Models, Chemical, Models, Molecular, Pliability, Protein Folding, Protein Structure, Secondary, Proteins
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.

Alternate JournalJ. Mol. Biol.