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Mapping of protein structural ensembles by chemical shifts

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Abstract

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.

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Acknowledgments

This work was supported by the Bundesministerium für Bildung und Forschung (BMBF), the Deutsche Forschungsgemeinschaft (DFG), the priority program 760 “Medical Chemistry: molecular ligand–receptor interaction” and the European Union (Extend-NMR, SPINE2).

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Authors and Affiliations

  1. Department of Biophysics and Physical Biochemistry, University of Regensburg, 93040, Regensburg, Federal Republic of Germany

    Kumaran Baskaran, Konrad Brunner, Claudia E. Munte & Hans Robert Kalbitzer

  2. Institut für Biophysik und Physikalische Biochemie, Lehrstuhl Biophysik, Universität Regensburg, Postfach, 93040, Regensburg, Federal Republic of Germany

    Hans Robert Kalbitzer

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  1. Kumaran Baskaran
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  2. Konrad Brunner
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  3. Claudia E. Munte
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  4. Hans Robert Kalbitzer
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Correspondence to Hans Robert Kalbitzer.

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Baskaran, K., Brunner, K., Munte, C.E. et al. Mapping of protein structural ensembles by chemical shifts. J Biomol NMR 48, 71–83 (2010). https://doi.org/10.1007/s10858-010-9438-4

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  • DOI: https://doi.org/10.1007/s10858-010-9438-4

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