HIV-1 protease cleavage mechanism: A theoretical investigation based on classical MD simulation and reaction path calculations using a hybrid QM/MM potential

被引:47
作者
Chatfield, DC
Eurenius, KP
Brooks, BR
机构
[1] Florida Int Univ, Dept Chem, Miami, FL 33199 USA
[2] NIH, Div Comp Res & Technol, Struct Biol Lab, Bethesda, MD 20892 USA
来源
THEOCHEM-JOURNAL OF MOLECULAR STRUCTURE | 1998年 / 423卷 / 1-2期
基金
美国国家卫生研究院;
关键词
computer simulation; enzyme catalysis; HIV-protease; molecular dynamics; QM/MM potential;
D O I
10.1016/S0166-1280(96)04875-0
中图分类号
O64 [物理化学(理论化学)、化学物理学];
学科分类号
070304 ; 081704 ;
摘要
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.
引用
收藏
页码:79 / 92
页数:14
相关论文
共 82 条
[1]  
ANTONOV VK, 1981, EUR J BIOCHEM, V117, P195
[2]   MECHANISM OF PEPSIN CATALYSIS - GENERAL BASE CATALYSIS BY ACTIVE-SITE CARBOXYLATE ION [J].
ANTONOV, VK ;
GINODMAN, LM ;
KAPITANNIKOV, YV ;
BARSHEVSKAYA, TN ;
GUROVA, AG ;
RUMSH, LD .
FEBS LETTERS, 1978, 88 (01) :87-90
[3]   SIMULATION OF ENZYME-REACTIONS USING VALENCE-BOND FORCE-FIELDS AND OTHER HYBRID QUANTUM-CLASSICAL APPROACHES [J].
AQVIST, J ;
WARSHEL, A .
CHEMICAL REVIEWS, 1993, 93 (07) :2523-2544
[4]   COMPUTER-SIMULATION AND ANALYSIS OF THE REACTION PATHWAY OF TRIOSEPHOSPHATE ISOMERASE [J].
BASH, PA ;
FIELD, MJ ;
DAVENPORT, RC ;
PETSKO, GA ;
RINGE, D ;
KARPLUS, M .
BIOCHEMISTRY, 1991, 30 (24) :5826-5832
[5]   A QUANTUM-MECHANICAL STUDY OF THE ACTIVE-SITE OF ASPARTIC PROTEINASES [J].
BEVERIDGE, AJ ;
HEYWOOD, GC .
BIOCHEMISTRY, 1993, 32 (13) :3325-3333
[6]  
BEVERIDGE AJ, 1994, THEOCHEM, V306, P235
[7]   3-DIMENSIONAL STRUCTURE OF THE COMPLEX OF THE RHIZOPUS-CHINENSIS CARBOXYL PROTEINASE AND PEPSTATIN AT 2.5-A RESOLUTION [J].
BOTT, R ;
SUBRAMANIAN, E ;
DAVIES, DR .
BIOCHEMISTRY, 1982, 21 (26) :6956-6962
[8]  
BOTT R, 1985, BIOCHEMISTRY-US, V24, P3701
[9]   CHARMM - A PROGRAM FOR MACROMOLECULAR ENERGY, MINIMIZATION, AND DYNAMICS CALCULATIONS [J].
BROOKS, BR ;
BRUCCOLERI, RE ;
OLAFSON, BD ;
STATES, DJ ;
SWAMINATHAN, S ;
KARPLUS, M .
JOURNAL OF COMPUTATIONAL CHEMISTRY, 1983, 4 (02) :187-217
[10]   HIV-1 PROTEASE CLEAVAGE MECHANISM ELUCIDATED WITH MOLECULAR-DYNAMICS SIMULATION [J].
CHATFIELD, DC ;
BROOKS, BR .
JOURNAL OF THE AMERICAN CHEMICAL SOCIETY, 1995, 117 (20) :5561-5572