Do the crystallographic forms of prethrombin-2 revert to a single form in solution?

• The two X-ray crystal forms of prethrombin-2 appear to relax into two different forms in solution via MD simulations.
• The two solution forms are characterized by the position of the W215–E217 segment relative to the active site.
• The torsion angle for the disulfide C191–C220 relaxes to unique values for each of the two solution forms.
• The 180s-loop is greatly stabilized in the open solution form derived from the X-ray crystal alternative form.

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.

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