Protocol abstract


Nature Protocols 1, 683 - 688 (2006)
Published online: 6 July 2006 | doi:10.1038/nprot.2006.108

Subject Category: Spectroscopy and structural analysis

NMR: prediction of protein flexibility

Mark Berjanskii1 & David S Wishart1,2


We present a protocol for predicting protein flexibility from NMR chemical shifts. The protocol consists of (i) ensuring that the chemical shift assignments are correctly referenced or, if not, performing a reference correction using information derived from the chemical shift index, (ii) calculating the random coil index (RCI), and (iii) predicting the expected root mean square fluctuations (RMSFs) and order parameters (S2) of the protein from the RCI. The key advantages of this protocol over existing methods for studying protein dynamics are that (i) it does not require prior knowledge of a protein's tertiary structure, (ii) it is not sensitive to the protein's overall tumbling and (iii) it does not require additional NMR measurements beyond the standard experiments for backbone assignments. When chemical shift assignments are available, protein flexibility parameters, such as S2 and RMSF, can be calculated within 1–2 h using a spreadsheet program.

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  1. Department of Computing Science, 2-21 Athabasca Hall, University of Alberta, Edmonton, Alberta T6G 2E8, Canada.
  2. NRC National Institute for Nanotechnology, Edmonton, Alberta, Canada.

Correspondence to: David S Wishart1,2 e-mail: david.wishart@ualberta.ca

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