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Issue 48, 2006
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Modeling heme proteins using atomistic simulations

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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.

Graphical abstract: Modeling heme proteins using atomistic simulations

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Publication details

The article was received on 14 Aug 2006, accepted on 28 Sep 2006 and first published on 11 Oct 2006


Article type: Invited Article
DOI: 10.1039/B611741B
Citation: Phys. Chem. Chem. Phys., 2006,8, 5611-5628
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    Modeling heme proteins using atomistic simulations

    D. E. Bikiel, L. Boechi, L. Capece, A. Crespo, P. M. De Biase, S. Di Lella, M. C. González Lebrero, M. A. Martí, A. D. Nadra, L. L. Perissinotti, D. A. Scherlis and D. A. Estrin, Phys. Chem. Chem. Phys., 2006, 8, 5611
    DOI: 10.1039/B611741B

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