@article{90681,
  keywords = {Models, Molecular, Proteins, Pliability, Protein Folding, Protein Structure, Secondary, Databases, Protein, Models, Chemical},
  author = {Eldon Emberly and Ranjan Mukhopadhyay and Ned Wingreen and Chao Tang},
  title = {Flexibility of alpha-helices: results of a statistical analysis of database protein structures.},
  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. },
  year = {2003},
  journal = {J Mol Biol},
  volume = {327},
  pages = {229-37},
  month = {03/2003},
  issn = {0022-2836},
  language = {eng},
}