Gallery of Biomolecular Simulations

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HIV-1 Protease is one of the enzymes encoded by human immunodeficiency virus, and it is crucial for HIV replication. A mechanism of the reaction has been studied through quantum-classical molecular dynamics simulations. The potential energy surface for the atoms participating in the reaction was calculated with the approximate valence bond (AVB) method, as parameterized for this enzyme [1]. The rest of the protein and explicit solvent and ions were treated with a classical force field. This figure shows the steered MD/AVB dynamics of the nucleophilic attack in the reaction involving the lytic water molecule [2]. This process was preceded by dissociation of the water molecule and transfer of one of its protons onto an oxygen of one of the aspartic acids in the active site. The animation is based on the MD/AVB trajectory, and was prepared by Krzysztof Nowinski (ICM University of Warsaw) under AVS.

[1] Parameterization of the Approximate Valence Bond (AVB) Method to Describe Potential Energy Surface in the Reaction Catalyzed by HIV-1 Protease Int. J. Quant. Chem., 82, p. 86-103, (2001) Joanna Trylska, Pawel Grochowski, Maciej Geller

[2] Molecular Dynamics Simulations of the First Steps of the Reaction Catalyzed by HIV-1 Protease Biophys. J., 83, p. 794-807, (2002) Joanna Trylska, Piotr Bala, Maciej Geller, Pawel Grochowski

For more information on the HIV-1 protease work described here, please contact Joanna Trylska.

McCammon Group, UCSD (http://mccammon.ucsd.edu/)
Created by Cameron Mura on Sat Jun 7 17:55:13 PDT 2003.
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