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Posts tagged ‘Ubiquitin’

Dynamics in Protein Crystals

Posted: 01.06.2016

We have investigated dynamics in two crystal forms of ubiquitin (PDB entries 3ONS and 3N30) 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 solid state NMR techniques and showed similar or identical characteristic times (tens of microseconds) in 3N30 crystals. This raise a question: is this merely a coincidence or, otherwise, are these two motional modes coupled? To answer this question we performed MD simulations of 3ONS and 3N30 crystals. To quantify the effect of rocking motion we have used temporal correlation functions.


Crystal MD simulations provide useful insight into rocking motion. We demonstrated that 3N30 crystal is prone to rocking and observed a weak coupling between rocking motion and βI↔βII exchange. Our data are also supported by X-Ray and ssNMR evidence and appear to be quite accurate in explaining the population balance between different conformations.

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