Conformational change path between closed and open forms of C2 domain of coagulation factor V on a two-dimensional free-energy surface
Wu, S (Wu, Sangwook); Lee, CJ (Lee, Chang Jun); Pedersen, LG (Pedersen, Lee G.)
PHYSICAL REVIEW E, 79 (4): Art. No. 041909 Part 1 APR 2009
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 Delta Q 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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