Slow conformational exchange and overall rocking motion in ubiquitin protein crystals

Vilius Kurauskas, Sergei A. Izmailov, Olga N. Rogacheva, Audrey Hessel, Isabel Ayala, Joyce Woodhouse, Anastasya Shilova, Yi Xue, Tairan Yuwen, Nicolas Coquelle, Jacques-Philippe Colletier, Nikolai R. Skrynnikov () and Paul Schanda ()
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Vilius Kurauskas: Université Grenoble Alpes
Sergei A. Izmailov: St. Petersburg State University
Olga N. Rogacheva: St. Petersburg State University
Audrey Hessel: Université Grenoble Alpes
Isabel Ayala: Université Grenoble Alpes
Joyce Woodhouse: Université Grenoble Alpes
Anastasya Shilova: European Synchrotron Radiation Facility
Yi Xue: Purdue University
Tairan Yuwen: Purdue University
Nicolas Coquelle: Université Grenoble Alpes
Jacques-Philippe Colletier: Université Grenoble Alpes
Nikolai R. Skrynnikov: St. Petersburg State University
Paul Schanda: Université Grenoble Alpes

Nature Communications, 2017, vol. 8, issue 1, 1-12

Abstract: Abstract Proteins perform their functions in solution but their structures are most frequently studied inside crystals. Here we probe how the crystal packing alters microsecond dynamics, using solid-state NMR measurements and multi-microsecond MD simulations of different crystal forms of ubiquitin. In particular, near-rotary-resonance relaxation dispersion (NERRD) experiments probe angular backbone motion, while Bloch–McConnell relaxation dispersion data report on fluctuations of the local electronic environment. These experiments and simulations reveal that the packing of the protein can significantly alter the thermodynamics and kinetics of local conformational exchange. Moreover, we report small-amplitude reorientational motion of protein molecules in the crystal lattice with an ~3–5° amplitude on a tens-of-microseconds time scale in one of the crystals, but not in others. An intriguing possibility arises that overall motion is to some extent coupled to local dynamics. Our study highlights the importance of considering the packing when analyzing dynamics of crystalline proteins.

Date: 2017
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DOI: 10.1038/s41467-017-00165-8

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