Enzyme mechanisms with hybrid quantum and molecular mechanical potentials. I. Theoretical considerations

✍ Scribed by Kirsten P. Eurenius; David C. Chatfield; Bernard R. Brooks; Milan Hodoscek

• Book ID: 102654473
• Publisher: John Wiley and Sons
• Year: 1996
• Tongue: English
• Weight: 884 KB
• Volume: 60
• Category: Article
• ISSN: 0020-7608
• DOI: 10.1002/(sici)1097-461x(1996)60:6<1189::aid-qua7>3.0.co;2-w

✦ Synopsis

The application of hybrid quantum mechanical and molecular mechanical (QM/MM) potentials to the study of chemical reactions in enzymes is outlined. The discussion is general and addresses the difficulties encountered in an enzyme QM/MM study. First, general criteria for determining whether a particular enzyme is an appropriate candidate for a QM/MM approach are outlined. Methods for obtaining starting structures are detailed. The importance of choosing appropriate levels of ab initio or semiempirical theory is emphasized. Approaches for interfacing the QM and MM regions are briefly discussed, with greater detail given to describing our CHARMM-GAMESS interface. Techniques for partitioning the system into QM and MM regions are explored. Link atom placement, as distant from reacting atoms as possible within the confines of computational efficiency, is examined in some detail. Methods for determining reaction paths are also discussed.