title: Modeling heme proteins using atomistic simulations.
abstract: Heme proteins are found in all living organisms, and perform a wide variety of tasks ranging from electron transport, to the oxidation of organic compounds, to the sensing and transport of small molecules. In this work we review the application of classical and quantum-mechanical atomistic simulation tools to the investigation of several relevant issues in heme proteins chemistry: (i) conformational analysis, ligand migration, and solvation effects studied using classical molecular dynamics simulations; (ii) electronic structure and spin state energetics of the active sites explored using quantum-mechanics (QM) methods; (iii) the interaction of heme proteins with small ligands studied through hybrid quantum mechanics-molecular mechanics (QM-MM) techniques; (iv) and finally chemical reactivity and catalysis tackled by a combination of quantum and classical tools.
authors.affiliation: Departamento de Química Inorgánica, Analítica y Química Física/INQUIMAE-CONICET, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Ciudad Universitaria, Pabellón II, Buenos Aires, Argentina.
authors.forename: Damián E
authors.initials: DE
authors.lastname: Bikiel
authors.forename: Leonardo
authors.initials: L
authors.lastname: Boechi
authors.forename: Luciana
authors.initials: L
authors.lastname: Capece
authors.forename: Alejandro
authors.initials: A
authors.lastname: Crespo
authors.forename: Pablo M
authors.initials: PM
authors.lastname: De Biase
authors.forename: Santiago
authors.initials: S
authors.lastname: Di Lella
authors.forename: Mariano C
authors.initials: MC
authors.lastname: González Lebrero
authors.forename: Marcelo A
authors.initials: MA
authors.lastname: Martí
authors.forename: Alejandro D
authors.initials: AD
authors.lastname: Nadra
authors.forename: Laura L
authors.initials: LL
authors.lastname: Perissinotti
authors.forename: Damián A
authors.initials: DA
authors.lastname: Scherlis
authors.forename: Darío A
authors.initials: DA
authors.lastname: Estrin
mesh_terms: D003198:Computer Simulation; D006420:Hemeproteins / Q000737:chemistry*; D006860:Hydrogen Bonding; D008024:Ligands; D008956:Models, Chemical; D011487:Protein Conformation; D011789:Quantum Theory
chemical_list: D006420:Hemeproteins; D008024:Ligands