title: QM and QM/MM Methods Compared: Case Studies on Reaction Mechanisms of Metalloenzymes.
abstract: The review focus is a comparison of QM and QM/MM modeling techniques applied to study of metalloenzymes. The chapter aim is to highlight many of the advantages and potential pitfalls of the exciting and revolutionary QM/MM techniques using both large QM/MM systems and QM-only modeling as references. The review is illustrated by case studies for isopenicillin N synthase, ethylbenzene dehydrogenase, cytochrome P450 enzyme, AlkB DNA repair enzyme as well as 4-hydroxyphenylpyruvate dioxygenase. We find many advantages in various QM/MM techniques, over the more traditional QM cluster approaches, while at the same time offering some advice about how to avoid potential complications arising from some of these approaches' most notable drawbacks. We conclude that while there will always be an important role for QM cluster models, in computational studies, the revolutionary developments in QM/MM techniques open a bright and exciting future of new research.
authors.affiliation: Jerzy Haber Institute of Catalysis and Surface Chemistry, Polish Academy of Sciences, Kraków, Poland.
authors.forename: Tomasz
authors.initials: T
authors.lastname: Borowski
authors.affiliation: Jerzy Haber Institute of Catalysis and Surface Chemistry, Polish Academy of Sciences, Kraków, Poland; Manchester Institute of Biotechnology and Faculty of Life Sciences, The University of Manchester, Manchester, United Kingdom.
authors.forename: Matthew
authors.initials: M
authors.lastname: Quesne
authors.affiliation: Jerzy Haber Institute of Catalysis and Surface Chemistry, Polish Academy of Sciences, Kraków, Poland. Electronic address: ncszalen@cyfronet.pl.
authors.forename: Maciej
authors.initials: M
authors.lastname: Szaleniec
mesh_terms: D015111:4-Hydroxyphenylpyruvate Dioxygenase / Q000737:chemistry*; D000071501:AlkB Homolog 4, Lysine Demethylase; D001419:Bacteria / Q000737:chemistry / Q000201:enzymology; D001426:Bacterial Proteins / Q000737:chemistry*; D055162:Biocatalysis; D003577:Cytochrome P-450 Enzyme System / Q000737:chemistry*; D049308:Dioxygenases / Q000737:chemistry*; D006801:Humans; D006900:Hydroxylation; D007700:Kinetics; D056004:Molecular Dynamics Simulation; D010088:Oxidoreductases / Q000737:chemistry*; D011789:Quantum Theory; D013237:Stereoisomerism; D013379:Substrate Specificity; D013816:Thermodynamics
chemical_list: D001426:Bacterial Proteins; D003577:Cytochrome P-450 Enzyme System; D010088:Oxidoreductases; D049308:Dioxygenases; D015111:4-Hydroxyphenylpyruvate Dioxygenase; C557720:ALKBH4 protein, human; D000071501:AlkB Homolog 4, Lysine Demethylase; C038370:isopenicillin N synthetase; C121602:ethylbenzene dehydrogenase
keywords: 4-Hydroxyphenylpyruvate dioxygenase; AlkB DNA repair enzyme; Cytochrome P450 enzyme; Ethylbenzene dehydrogenase; Metalloenzymes; QM/MM