Flexibility of β-Sheets: Principal Component Analysis of Database Protein Structures

Eldon G. Emberly, Ranjan Mukhopadhyay, Chao Tang, Ned S. Wingreen

Research output: Contribution to journalArticlepeer-review

33 Scopus citations

Abstract

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.

Original languageEnglish (US)
Pages (from-to)91-98
Number of pages8
JournalProteins: Structure, Function and Genetics
Volume55
Issue number1
DOIs
StatePublished - Apr 1 2004

All Science Journal Classification (ASJC) codes

  • Structural Biology
  • Biochemistry
  • Molecular Biology

Keywords

  • Flexibility
  • Principal component analysis
  • Secondary structure
  • β-sheet

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