ArticlePhysical review. E, Statistical, nonlinear, and soft matter physics2009
Conformational change path between closed and open forms of C2 domain of coagulation factor V on a two-dimensional free-energy surface.
Article in Physical review. E, Statistical, nonlinear, and soft matter physics, 2009. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 3 papers.
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Who cites it
3 citing papers in PubMed.
- Elucidating the complex membrane binding of a protein with multiple anchoring domains using extHMMM.PLoS computational biology · 2024Article
- Membrane binding and lipid-protein interaction of the C2 domain from coagulation factor V.Current research in structural biology · 2024Article
- Uncovering Membrane-Bound Models of Coagulation Factors by Combined Experimental and Computational Approaches.Thrombosis and haemostasis · 2021Review
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Authors and funding
3 authors.
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Abstract
We test a hypothesis that the closed form of the C2 domain of coagulation factor V is more stable than the open form in an aqueous environment using a two-dimensional free-energy calculation with a simple dielectric solvent model. Our result shows that while the free-energy difference between two forms is small, favoring the closed form, a two-dimensional free-energy surface (FES) reveals that a transition state (1.53 kcal/mol) exists between the two conformations. By mapping the one-dimensional order parameter DeltaQ onto the two-dimensional FES, we search the conformational change path with the highest Boltzmann weighting factor between the closed and open form of the factor V C2 domain. The predicted transition path from the closed to open form is not that of simple side chain movements, but instead concerted movements of several loops. We also present a one-dimensional free-energy profile using a collective order parameter, which in a coarse manner locates the energy barriers found on the two-dimensional FES.
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