Modeling heme proteins using atomistic simulations

DAMIAN E. BIKIEL; LEONARDO BOECHI; LUCIANA CAPECE; ALEJANDRO CRESPO; PABLO M. DE BIASE; SANTIAGO DI LELLA; MARIANO C. GONZALEZ LEBRERO; MARCELO A. MARTI; ALEJANDRO D. NADRA; LAURA L. PERISSINOTTI; DAMIÁN A. SCHERLIS; DARIO A. ESTRIN

PHYSICAL CHEMISTRY CHEMICAL PHYSICS

ROYAL SOC CHEMISTRY

Año: 2006 vol. 8 p. 5611 - 5628

1463-9076

Heme proteins, the family of proteins containing an iron-porphyrin complex as a prosthetic group, are found in all living organisms, and perform a wide variety of tasks ranging from electron transport, oxidation of organic molecules and the sensing and transport of small molecules. In this work we will review the application of classical and quantum-mechanically based simulation tools to the investigation of several relevant issues in heme proteins chemistry: conformational studies, ligand migration and solvation effects studied by means of classical molecular dynamics simulations, electronic structure and spin state energetics of the heme active site studies using quantum-mechanically (QM) based techniques, interaction of heme proteins with small ligands studied by QM and hybrid quantum-classical (QM-MM) simulations, and finally chemical reactivity and catalysis in heme proteins, investigated by QM and QM-MM calculations.