title: Computational enzymatic catalysis--clarifying enzymatic mechanisms with the help of computers.
abstract: Enzymes play a biologically essential role in performing and controlling an important share of the chemical processes occurring in life. However, despite their critical role in nature, attaining a clear understanding of the way an enzyme acts, i.e. its catalytic mechanism, is a cumbersome task that requires the cooperative efforts of a large number of different scientific techniques. Computational methods offer a particularly insightful way to study such mechanisms, always beautifully complementing the information arising from experimental techniques and working as an excellent alternative for assessing the viability of different mechanistic proposals. This review highlights two important computational strategies to study enzymatic catalysis - the cluster modeling approach and the hybrid quantum mechanical/molecular mechanical (QM/MM) method - complemented with a selection of hand-picked examples of our own work.
authors.affiliation: REQUIMTE, Departamento de Química e Bioquímica, Faculdade de Ciências da Universidade do Porto, Rua do Campo Alegre, s/n, 4169-007 Porto, Portugal.
authors.forename: Sérgio Filipe
authors.initials: SF
authors.lastname: Sousa
authors.forename: Pedro Alexandrino
authors.initials: PA
authors.lastname: Fernandes
authors.forename: Maria João
authors.initials: MJ
authors.lastname: Ramos
mesh_terms: D055162:Biocatalysis; D051231:Farnesyltranstransferase / Q000737:chemistry* / Q000378:metabolism; D006801:Humans; D008958:Models, Molecular; D056004:Molecular Dynamics Simulation; D011789:Quantum Theory; D001616:beta-Galactosidase / Q000737:chemistry* / Q000378:metabolism; D001619:beta-N-Acetylhexosaminidases / Q000737:chemistry* / Q000378:metabolism
chemical_list: D051231:Farnesyltranstransferase; D001616:beta-Galactosidase; D001619:beta-N-Acetylhexosaminidases