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Simultaneous determination of protein structure and dynamics

Nature volume 433, pages 128–132 (2005)Cite this article

Abstract

We present a protocol for the experimental determination of ensembles of protein conformations that represent simultaneously the native structure and its associated dynamics. The procedure combines the strengths of nuclear magnetic resonance spectroscopy—for obtaining experimental information at the atomic level about the structural and dynamical features of proteins—with the ability of molecular dynamics simulations to explore a wide range of protein conformations. We illustrate the method for human ubiquitin in solution and find that there is considerable conformational heterogeneity throughout the protein structure. The interior atoms of the protein are tightly packed in each individual conformation that contributes to the ensemble but their overall behaviour can be described as having a significant degree of liquid-like character. The protocol is completely general and should lead to significant advances in our ability to understand and utilize the structures of native proteins.

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Figure 1: Cross-validation of ubiquitin structures by comparison with independently determined NMR data.
Figure 2: Variability in structural ensembles of ubiquitin.
Figure 3: Examples of the liquid-like mobility of side chains in the DER ensemble.
Figure 4: Quantifying backbone and side-chain variability in ubiquitin ensembles by comparison of experimental and back-calculated order parameters.

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Acknowledgements

We are very grateful to P. I. de Bakker and T. L. Blundell for assistance in determining the X-ray rapper ensemble of ubiquitin. We thank S. E. Jackson for sharing the experimental data on ubiquitin stability changes before publication. K.L.L. is supported by the Danish Research Agency. M.A.D. was funded by the Marshall Aid Commemoration Commission, US National Science Foundation, and Cambridge Overseas Trust. M.V. is a Royal Society University Research Fellow. The research of M.V. and C.M.D. is supported in part by Programme Grants from the Wellcome and Leverhulme Trusts.

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Author notes

  1. Kresten Lindorff-Larsen

    Present address: Department of Protein Chemistry, Institute of Molecular Biology, University of Copenhagen, Øster Farimagsgade 2A, 4, DK-1353, Copenhagen K, Denmark

  2. Robert B. Best

    Present address: Laboratory of Chemical Physics, NIDDK, National Institutes of Health, Bethesda, Maryland, 20892-0520, USA

  3. Mark A. DePristo

    Present address: Department of Organismic and Evolutionary Biology, Harvard University, 16 Divinity Avenue, Cambridge, Massachusetts, 02138, USA

  4. Kresten Lindorff-Larsen and Robert B. Best: These authors contributed equally to this work

Authors and Affiliations

  1. Department of Chemistry, University of Cambridge, Cambridge, Lensfield Road, CB2 1EW, UK

    Kresten Lindorff-Larsen, Robert B. Best, Christopher M. Dobson & Michele Vendruscolo

  2. Department of Biochemistry, University of Cambridge, Cambridge, 80 Tennis Court Road, CB2 1GA, UK

    Mark A. DePristo

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  1. Kresten Lindorff-Larsen
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Correspondence to Christopher M. Dobson or Michele Vendruscolo.

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Supplementary Methods

Details on all methods for structure determination and analysis. (PDF 62 kb)

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Lindorff-Larsen, K., Best, R., DePristo, M. et al. Simultaneous determination of protein structure and dynamics. Nature 433, 128–132 (2005). https://doi.org/10.1038/nature03199

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