Modeling enzyme reactivity in organic solvents and water through computer simulations

被引:22
作者
Colombo, G [1 ]
Carrea, G [1 ]
机构
[1] CNR, Ist Chim Riconoscimento Mol, I-20131 Milan, Italy
关键词
molecular modeling; structure; reactivity of enzymes; organic solvents; QM/MM methods;
D O I
10.1016/S0168-1656(02)00034-2
中图分类号
Q81 [生物工程学(生物技术)]; Q93 [微生物学];
学科分类号
071005 ; 0836 ; 090102 ; 100705 ;
摘要
In this article, we review how molecular modeling techniques can be used to shed light on how water and organic solvents influence the reactivity of enzymes. The application of thermodynamics-based models allowed the first qualitative predictions on the selectivity of many reaction types. However, it was with the application of quantum mechanical/molecular mechanical (QM/MM) methods that quantitative models of actual reactivity patterns could be realistically formulated. (C) 2002 Elsevier Science B.V. All rights reserved.
引用
收藏
页码:23 / 33
页数:11
相关论文
共 36 条
[1]   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
[2]   Hybrid ab initio quantum mechanics molecular mechanics calculations of free energy surfaces for enzymatic reactions:: The nucleophilic attack in subtilisin [J].
Bentzien, J ;
Muller, RP ;
Florián, J ;
Warshel, A .
JOURNAL OF PHYSICAL CHEMISTRY B, 1998, 102 (12) :2293-2301
[3]  
Brooks C. L., 1988, PROTEINS THEORETICAL
[4]   ROLE OF SOLVENTS IN THE CONTROL OF ENZYME SELECTIVITY IN ORGANIC MEDIA [J].
CARREA, G ;
OTTOLINA, G ;
RIVA, S .
TRENDS IN BIOTECHNOLOGY, 1995, 13 (02) :63-70
[5]   Application of structure-based thermodynamic calculations to the rationalization of the enantioselectivity of subtilisin in organic solvents [J].
Colombo, G ;
Ottolina, G ;
Carrea, G ;
Bernardi, A ;
Scolastico, C .
TETRAHEDRON-ASYMMETRY, 1998, 9 (07) :1205-1214
[6]   Rationalization of the enantioselectivity of subtilisin in DMF [J].
Colombo, G ;
Toba, S ;
Merz, KM .
JOURNAL OF THE AMERICAN CHEMICAL SOCIETY, 1999, 121 (14) :3486-3493
[7]   Modelling the enantioselectivity of subtilisin in water and organic solvents: insights from molecular dynamics and quantum mechanical/molecular mechanical studies [J].
Colombo, G ;
Ottolina, G ;
Carrea, G ;
Merz, KM .
CHEMICAL COMMUNICATIONS, 2000, (07) :559-560
[8]   A 2ND GENERATION FORCE-FIELD FOR THE SIMULATION OF PROTEINS, NUCLEIC-ACIDS, AND ORGANIC-MOLECULES [J].
CORNELL, WD ;
CIEPLAK, P ;
BAYLY, CI ;
GOULD, IR ;
MERZ, KM ;
FERGUSON, DM ;
SPELLMEYER, DC ;
FOX, T ;
CALDWELL, JW ;
KOLLMAN, PA .
JOURNAL OF THE AMERICAN CHEMICAL SOCIETY, 1995, 117 (19) :5179-5197
[9]   CATALYTIC PATHWAY OF SERINE PROTEASES - CLASSICAL AND QUANTUM-MECHANICAL CALCULATIONS [J].
DAGGETT, V ;
SCHRODER, S ;
KOLLMAN, P .
JOURNAL OF THE AMERICAN CHEMICAL SOCIETY, 1991, 113 (23) :8926-8935
[10]   Semiempirical molecular orbital calculations with linear system size scaling [J].
Dixon, SL ;
Merz, KM .
JOURNAL OF CHEMICAL PHYSICS, 1996, 104 (17) :6643-6649