Mapping of protein structural ensembles by chemical shifts

Applying the chemical shift prediction programs SHIFTX and SHIFTS to a data base of protein structures with known chemical shifts we show that the averaged chemical shifts predicted from the structural ensembles explain better the experimental data than the lowest energy structures. This is in agree...

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Bibliographic Details
Published in:Journal of biomolecular NMR 2010-10, Vol.48 (2), p.71-83
Main Authors: Baskaran, Kumaran, Brunner, Konrad, Munte, Claudia E, Kalbitzer, Hans Robert
Format: Article
Language:English
Subjects:
Algorithms
Biochemistry
Biological and Medical Physics
Biophysics
Carbon - chemistry
Chemical shift
Hydrogen - chemistry
Molecular Dynamics Simulation
Nuclear Magnetic Resonance, Biomolecular - methods
Physics
Physics and Astronomy
Protein Conformation
Proteins - chemistry
Proteins - metabolism
Reproducibility of Results
Solution structure
Spectroscopy/Spectrometry
Structural ensemble
Temperature
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Summary:Applying the chemical shift prediction programs SHIFTX and SHIFTS to a data base of protein structures with known chemical shifts we show that the averaged chemical shifts predicted from the structural ensembles explain better the experimental data than the lowest energy structures. This is in agreement with the fact that proteins in solution occur in multiple conformational states in fast exchange on the chemical shift time scale. However, in contrast to the real conditions in solution at ambient temperatures, the standard NMR structural calculation methods as well chemical shift prediction methods are optimized to predict the lowest energy ground state structure that is only weakly populated at physiological temperatures. An analysis of the data shows that a chemical shift prediction can be used as measure to define the minimum size of the structural bundle required for a faithful description of the structural ensemble.
ISSN:0925-2738
1573-5001
DOI:10.1007/s10858-010-9438-4