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J Struct Biol. 2007 Mar;157(3):606-15. Epub 2006 Aug 23.

Flap opening dynamics in HIV-1 protease explored with a coarse-grained model.

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NEST-INFM-CNR Scuola Normale Superiore, Piazza dei Cavalieri, 7 I-56126 Pisa, Italy.


We present a one-bead coarse-grained model that enables dynamical simulations of proteins on the time scale of tens of microseconds. The parameterization of the force field includes accurate conformational terms that allow for fast and reliable exploration of the configurational space. The model is applied to the dynamics of flap opening in HIV-1 protease. The experimental structure of the recently crystallized semi-open conformation of HIV-1 protease is well reproduced in the simulation, which supports the accuracy of our model. Thanks to very long simulations and extensive sampling of opening and closing events, we also investigate the thermodynamics and kinetics of the opening process. We have shown that the effect of the solvent slows down the dynamics to the experimentally observed time scales. The model is found to be reliable for application to substrate docking simulations, which are currently in progress.

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