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J Am Chem Soc. 2005 Nov 2;127(43):14970-1.

A simple method to predict protein flexibility using secondary chemical shifts.

Author information

1
Departments of Computing Science and Biological Sciences, University of Alberta, Edmonton, AB, Canada T6G 2E8.

Abstract

Protein motions play a critical role in many biological processes, such as enzyme catalysis, allosteric regulation, antigen-antibody interactions, and protein-DNA binding. NMR spectroscopy occupies a unique place among methods for investigating protein dynamics due to its ability to provide site-specific information about protein motions over a large range of time scales. However, most NMR methods require a detailed knowledge of the 3D structure and/or the collection of additional experimental data (NOEs, T1, T2, etc.) to accurately measure protein dynamics. Here we present a simple method based on chemical shift data that allows accurate, quantitative, site-specific mapping of protein backbone mobility without the need of a three-dimensional structure or the collection and analysis of NMR relaxation data. Further, we show that this chemical shift method is able to quantitatively predict per-residue RMSD values (from both MD simulations and NMR structural ensembles) as well as model-free backbone order parameters.

PMID:
16248604
DOI:
10.1021/ja054842f
[Indexed for MEDLINE]

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