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Flexibility of β‐sheets: Principal component analysis of database protein structures
Author(s) -
Emberly Eldon G.,
Mukhopadhyay Ranjan,
Tang Chao,
Wingreen Ned S.
Publication year - 2004
Publication title -
proteins: structure, function, and bioinformatics
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 1.699
H-Index - 191
eISSN - 1097-0134
pISSN - 0887-3585
DOI - 10.1002/prot.10618
Subject(s) - antiparallel (mathematics) , principal component analysis , flexibility (engineering) , eigenvalues and eigenvectors , twist , gaussian , beta sheet , scaling , crystallography , geometry , physics , protein structure , computer science , mathematics , chemistry , artificial intelligence , statistics , nuclear magnetic resonance , quantum mechanics , magnetic field
Protein folds are built primarily from the packing together of two types of structures: α‐helices and β‐sheets. Neither structure is rigid, and the flexibility of helices and sheets is often important in determining the final fold (e.g., coiled coils and β‐barrels). Recent work has quantified the flexibility of α‐helices using a principal component analysis (PCA) of database helical structures (J. Mol. Bio. 2003, 327, pp. 229–237). Here, we extend the analysis to β‐sheet flexibility using PCA on a database of β‐sheet structures. For sheets of varying dimension and geometry, we find two dominant modes of flexibility: twist and bend. The distributions of amplitudes for these modes are found to be Gaussian and independent, suggesting that the PCA twist and bend modes can be identified as the soft elastic normal modes of sheets. We consider the scaling of mode eigenvalues with sheet size and find that parallel β‐sheets are more rigid than antiparallel sheets over the entire range studied. Finally, we discuss the application of our PCA results to modeling and design of β‐sheet proteins. Proteins 2004. © 2004 Wiley‐Liss, Inc.