NMR: prediction of protein flexibility
- 6 July 2006
- journal article
- Published by Springer Science and Business Media LLC in Nature Protocols
- Vol. 1 (2), 683-688
- https://doi.org/10.1038/nprot.2006.108
Abstract
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.This publication has 24 references indexed in Scilit:
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