Modeling heme proteins using atomistic simulations.
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.
Bikiel
Damián E
DE
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.
Boechi
Leonardo
L
Capece
Luciana
L
Crespo
Alejandro
A
De Biase
Pablo M
PM
Di Lella
Santiago
S
González Lebrero
Mariano C
MC
Martí
Marcelo A
MA
Nadra
Alejandro D
AD
Perissinotti
Laura L
LL
Scherlis
Damián A
DA
Estrin
Darío A
DA
D003198:Computer Simulation; D006420:Hemeproteins / Q000737:chemistry*; D006860:Hydrogen Bonding; D008024:Ligands; D008956:Models, Chemical; D011487:Protein Conformation; D011789:Quantum Theory
D006420:Hemeproteins; D008024:Ligands