Ab initio quantum chemical and mixed quantum mechanics/molecular mechanics (QM/MM) methods for studying enzymatic catalysis.
We describe large scale ab initio quantum chemical and mixed quantum mechanics/molecular mechanics (QM/MM) methods for studying enzymatic reactions. First, technical aspects of the methodology are reviewed, including the hybrid density functional theory (DFT) methods that are typically employed for the QM aspect of the calculations, and various approaches to defining the interface between the QM and MM regions in QM/MM approaches. The modeling of the enzymatic catalytic cycle for three examples--methane monooxygenase, cytochrome P450, and triose phosphate isomerase--are discussed in some depth, followed by a brief summary of other systems that have been investigated by ab initio methods over the past several years. Finally, a discussion of the qualitative and quantitative conclusions concerning enzymatic catalysis that are available from modern ab initio approaches is presented, followed by a conclusion briefly summarizing future prospects.
Friesner
Richard A
RA
Department of Chemistry, Columbia University, New York, New York 10027, USA. rich@chem.columbia.edu
Guallar
Victor
V
D000906:Antibodies; D001665:Binding Sites; D002384:Catalysis; D003577:Cytochrome P-450 Enzyme System / Q000737:chemistry* / Q000378:metabolism; D004789:Enzyme Activation; D010105:Oxygenases / Q000737:chemistry* / Q000378:metabolism; D011789:Quantum Theory; D012997:Solvents / Q000737:chemistry; D014305:Triose-Phosphate Isomerase / Q000737:chemistry* / Q000378:metabolism
D000906:Antibodies; D012997:Solvents; D003577:Cytochrome P-450 Enzyme System; D010105:Oxygenases; C021555:methane monooxygenase; D014305:Triose-Phosphate Isomerase