Journal of Biomolecular NMR

, Volume 40, Issue 1, pp 31–48 | Cite as

Application of the random coil index to studying protein flexibility

Article

Abstract

Protein flexibility lies at the heart of many protein–ligand binding events and enzymatic activities. However, the experimental measurement of protein motions is often difficult, tedious and error-prone. As a result, there is a considerable interest in developing simpler and faster ways of quantifying protein flexibility. Recently, we described a method, called Random Coil Index (RCI), which appears to be able to quantitatively estimate model-free order parameters and flexibility in protein structural ensembles using only backbone chemical shifts. Because of its potential utility, we have undertaken a more detailed investigation of the RCI method in an attempt to ascertain its underlying principles, its general utility, its sensitivity to chemical shift errors, its sensitivity to data completeness, its applicability to other proteins, and its general strengths and weaknesses. Overall, we find that the RCI method is very robust and that it represents a useful addition to traditional methods of studying protein flexibility. We have implemented many of the findings and refinements reported here into a web server that allows facile, automated predictions of model-free order parameters, MD RMSF and NMR RMSD values directly from backbone 1H, 13C and 15N chemical shift assignments. The server is available at http://wishart.biology.ualberta.ca/rci.

Keywords

NMR Chemical shift Protein Flexibility Order parameters 

Supplementary material

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Copyright information

© Springer Science+Business Media B.V. 2007

Authors and Affiliations

  1. 1.Department of Computing ScienceUniversity of AlbertaEdmontonCanada
  2. 2.NRC National Institute for NanotechnologyUniversity of AlbertaEdmontonCanada

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