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Dynamics in protein crystals: insights from MD simulations complement new solid-state NMR and X-ray data

Posted: 03.09.2016

O. N. Rogacheva , S. A. Izmailov , V. Kurauskas , A. Shilova , P. Ma, Y. Xue, N. Coquelle, J. D. Haller, T. Yuwen, I. Ayala, A. Hessel, J. Woodhouse, O. Mikhailovskii, D. Willbold, J. Colletier, N. R. Skrynnikov, P. Schanda “Dynamics in protein crystals: insights from MD simulations complement new solid-state NMR and X-ray data” The FEBS Journal 283 (Suppl. 1), 237 (2016).

DOI: 10.1111/febs.13808

We have investigated dynamics in three different crystal forms of ubiquitin, as well as ubiquitin in solution, with particular emphasis on (i) conformational exchange between β turn type I and II in the region 51-54 and (ii) rocking dynamics where protein molecules as a whole undergo subtle reorientational motion within the confines of the crystal lattice. Experimentally, both motional processes have been probed using relaxation dispersion techniques, including recently developed nearrotary-resonance dipolar relaxation dispersion experiments. Thereby it has been determined that rocking motion in one of the crystal forms (PDB ID 3N30) occurs on the time scale of tens of microseconds, whereas the conformational exchange has characteristic time constant of ca. 100 μs. Using Molecular Dynamics simulations, we have shown that the similarity of motional time scales is not accidental: βI↔βII exchange and rocking motion appear to be coupled. We have investigated the mechanisms of this coupling and predicted a number of point mutations that are expected to abrogate (or enhance) rocking. The crystals of ubiquitin containing these mutations have been modeled in silico. We have also investigated the interactions (in particular, crystal contacts) that control the balance between βI and βII conformations in different crystal forms. Finally, we have used MD simulations as a basis for chemical shift calculations and illustrated how relaxation dispersion effects can emerge as a function of βI↔βII exchange in conjunction with the rocking motion. The MD simulation study was supported by RSF grant 15-14-20038.

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