Wu, Sangwook; Shim, Joong-Youn; Lee, Chang Jun; Pedersen, Lee G.
Do the crystallographic forms of prethrombin-2 revert to a single form in solution?
BIOPHYSICAL CHEMISTRY, 203:28-32, AUG-SEP 2015

It has been earlier established (Pozzi et al. Biochemistry 50 (2011) 10195-10202) that prethrombin-2 crystallizes into two similar but distinct forms: a collapsed form and an alternative form. We employed long molecular dynamics (MD) simulations for these two forms to obtain solvent-equilibrated forms. We find that, at 200 ns, the simulated solution collapsed form is quite similar to the X-ray crystal collapsed form, while the simulated solution alternative form deviates from the X-ray crystal alternative form as well as from the solution collapsed form. A detailed structural analysis suggests that the fluctuation of the 140s-loop, in cross-talk with the 220s-loop, may alter the conformation of the W215-E217 segment near the nascent thrombin active site. A rationale is provided for the manner in which interactions of prethrombin-2 with FVa may affect the equilibrium between the two forms of prethrombin-2. (C) 2015 Elsevier B.V. All rights reserved.

DOI:10.1016/j.bpc.2015.05.005

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