Observing the overall rocking motion of a protein in a crystal

Peixiang Ma, Yi Xue, Nicolas Coquelle, Jens D. Haller, Tairan Yuwen, Isabel Ayala, Oleg Mikhailovskii, Dieter Willbold, Jacques-Philippe Colletier (), Nikolai R. Skrynnikov () and Paul Schanda ()
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Peixiang Ma: Université Grenoble Alpes, IBS
Yi Xue: Purdue University
Nicolas Coquelle: Université Grenoble Alpes, IBS
Jens D. Haller: Université Grenoble Alpes, IBS
Tairan Yuwen: Purdue University
Isabel Ayala: Université Grenoble Alpes, IBS
Oleg Mikhailovskii: Purdue University
Dieter Willbold: CEA, Institut de Biologie Structurale
Jacques-Philippe Colletier: Université Grenoble Alpes, IBS
Nikolai R. Skrynnikov: Purdue University
Paul Schanda: Université Grenoble Alpes, IBS

Nature Communications, 2015, vol. 6, issue 1, 1-10

Abstract: Abstract The large majority of three-dimensional structures of biological macromolecules have been determined by X-ray diffraction of crystalline samples. High-resolution structure determination crucially depends on the homogeneity of the protein crystal. Overall ‘rocking’ motion of molecules in the crystal is expected to influence diffraction quality, and such motion may therefore affect the process of solving crystal structures. Yet, so far overall molecular motion has not directly been observed in protein crystals, and the timescale of such dynamics remains unclear. Here we use solid-state NMR, X-ray diffraction methods and μs-long molecular dynamics simulations to directly characterize the rigid-body motion of a protein in different crystal forms. For ubiquitin crystals investigated in this study we determine the range of possible correlation times of rocking motion, 0.1–100 μs. The amplitude of rocking varies from one crystal form to another and is correlated with the resolution obtainable in X-ray diffraction experiments.

Date: 2015
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DOI: 10.1038/ncomms9361

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