Paper Citing NAMD - Abstract
Potoyan, Davit A.; Zhuravlev, Pavel I.; Papoian, Garegin A.
Computing Free Energy of a Large-Scale Allosteric Transition in Adenylate Kinase Using All Atom Explicit Solvent Simulations
JOURNAL OF PHYSICAL CHEMISTRY B, 116:1709-1715, FEB 9 2012
During allosteric motions proteins navigate rugged energy landscapes. Hence, mapping of these multidimensional landscapes into lower dimensional manifolds is important for gaining deeper insights into allosteric dynamics. Using a recently developed computational technique, we calculated the free energy difference between the open and closed states of adenylate kinase, an allosteric protein which was extensively studied previously using both experimental and theoretical approaches. Two independent simulations indicate reasonable convergence of the computed free energy profiles. The numerical value of the open/closed free energy difference is only 1-2 k(B)T, much smaller than some of the prior estimates. We also found that the conformations structurally close to the open form still retain many LID-NMP contacts, suggesting that the conformational basin of the dosed form is larger than expected. The latter suggestion may explain the discrepancy in relative populations of open and closed forms of unligated adenylate kinase, observed in NMR and FRET experiments.
