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

• Published in: Biophysical chemistry Vol. 203-204; pp. 28 - 32
• Main Authors: Wu, Sangwook, Shim, Joong-Youn, Lee, Chang Jun, Pedersen, Lee G.
• Format: Journal Article
• Language: English
• Published: Netherlands Elsevier B.V 01-08-2015
• Subjects: Coagulation cascade; Crystallography, X-Ray; Factor Va; Models, Molecular; Prethrombin-2; Protein Conformation; Prothrombin - chemistry; Prothrombin activation; Solutions; Thrombin; Prothrombin activation; Thrombin; Coagulation cascade; Prethrombin-2; Factor Va
• ISSN: 0301-4622; 1873-4200
• DOI: 10.1016/j.bpc.2015.05.005

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 200ns, 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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•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.