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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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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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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DOI: https://doi.org/10.1038/nature03199