%0 Journal Article %1 hlwoodcock:C.1998a %A Chatfield, D. C. %A Eurenius, K. P. %A Brooks, B. R. %D 1998 %J Theochem-Journal of Molecular Structure %K potential bernie free-energies mechanism inhibitor catalysis enzyme virus-1 hiv-protease phospholipase-a2 state-analog computer dynamics human active-site qmmm aqueous-solution quantum combined simulation proteinases immunodeficiency aspartic chemical molecular-dynamics molecular binding %N 1-2 %P 79--92 %T Hiv-1 protease cleavage mechanism: a theoretical investigation based on classical md simulation and reaction path calculations using a hybrid qm/mm potential %V 423 %X The cleavage mechanism of HIV-1 protease (HIV-PR) is investigated with classical molecular dynamics (MD) simulation and with methods incorporating a hybrid quantum mechanical and molecular mechanical (QM/MM) potential function. An Xray structure of an HIV-PR/inhibitor complex was used to generate model HIV-PR/substrate and HIV-PR/intermediate complexes. Analysis of the feasibility of reaction is based on three hypothetical reaction mechanisms and a variety of possible starting conditions. The classical MD simulations were analyzed for conformations consistent with reaction initiation, as reported previously. It was concluded that Asp125 is the general acid in the first reaction step and transfers a proton to the carbonyl oxygen. Simulations suggest that water 301 stabilizes productive reactant and intermediate conformations but does not participate directly in the reaction. A lytic water, when present, is held very tightly in a position propitious for nucleophilic attack at the scissile carbon. For mechanisms consistent with the classical simulations, reaction barriers were calculated using a QM/MM potential. The QM/MM potential and a restrained energy minimization method for calculating reaction paths and barriers are described. Preliminary results identify reasonable barrier heights and transition state conformations and predict that the first reaction step follows a predominantly stepwise rather than concerted pathway. (C) 1998 Elsevier Science B.V.

@article{hlwoodcock:C.1998a, abstract = {The cleavage mechanism of HIV-1 protease (HIV-PR) is investigated with classical molecular dynamics (MD) simulation and with methods incorporating a hybrid quantum mechanical and molecular mechanical (QM/MM) potential function. An Xray structure of an HIV-PR/inhibitor complex was used to generate model HIV-PR/substrate and HIV-PR/intermediate complexes. Analysis of the feasibility of reaction is based on three hypothetical reaction mechanisms and a variety of possible starting conditions. The classical MD simulations were analyzed for conformations consistent with reaction initiation, as reported previously. It was concluded that Asp125 is the general acid in the first reaction step and transfers a proton to the carbonyl oxygen. Simulations suggest that water 301 stabilizes productive reactant and intermediate conformations but does not participate directly in the reaction. A lytic water, when present, is held very tightly in a position propitious for nucleophilic attack at the scissile carbon. For mechanisms consistent with the classical simulations, reaction barriers were calculated using a QM/MM potential. The QM/MM potential and a restrained energy minimization method for calculating reaction paths and barriers are described. Preliminary results identify reasonable barrier heights and transition state conformations and predict that the first reaction step follows a predominantly stepwise rather than concerted pathway. (C) 1998 Elsevier Science B.V.}, added-at = {2006-06-16T05:03:46.000+0200}, author = {Chatfield, D. C. and Eurenius, K. P. and Brooks, B. R.}, biburl = {https://www.bibsonomy.org/bibtex/233befd117c2a2b10b0e597304931729f/hlwoodcock}, citeulike-article-id = {569344}, comment = {YX314 THEOCHEM-J MOL STRUCT}, interhash = {2c9c599e4e24765d0bfbccc3faff06f6}, intrahash = {33befd117c2a2b10b0e597304931729f}, journal = {Theochem-Journal of Molecular Structure}, keywords = {potential bernie free-energies mechanism inhibitor catalysis enzyme virus-1 hiv-protease phospholipase-a2 state-analog computer dynamics human active-site qmmm aqueous-solution quantum combined simulation proteinases immunodeficiency aspartic chemical molecular-dynamics molecular binding}, number = {1-2}, pages = {79--92}, priority = {2}, timestamp = {2006-06-16T05:03:46.000+0200}, title = {Hiv-1 protease cleavage mechanism: a theoretical investigation based on classical md simulation and reaction path calculations using a hybrid qm/mm potential}, volume = 423, year = 1998 }