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

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

Research output: Contribution to journalArticlepeer-review

43 Scopus citations

Abstract

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

Original languageEnglish (US)
Pages (from-to)229-237
Number of pages9
JournalJournal of Molecular Biology
Volume327
Issue number1
DOIs
StatePublished - Mar 14 2003

All Science Journal Classification (ASJC) codes

  • Structural Biology
  • Molecular Biology

Keywords

  • Database protein structures
  • Protein folds
  • α-helices

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