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 simulatio...

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Autores principales: Bikiel, D.E., Boechi, L., Capece, L., Crespo, A., De Biase, P.M., Di Lella, S., González Lebrero, M.C., Martí, M.A., Nadra, A.D., Perissinotti, L.L., Scherlis, D.A., Estrin, D.A.
Formato: JOUR
Materias:
hemoprotein
ligand
article
chemical model
chemistry
computer simulation
hydrogen bond
protein conformation
quantum theory
Computer Simulation
Hemeproteins
Hydrogen Bonding
Ligands
Models, Chemical
Protein Conformation
Quantum Theory
Acceso en línea:http://hdl.handle.net/20.500.12110/paper_14639076_v8_n48_p5611_Bikiel
Aporte de:
Biblioteca Digital - Facultad de Ciencias Exactas y Naturales (UBA) de Universidad de Buenos Aires
id todo:paper_14639076_v8_n48_p5611_Bikiel
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spelling todo:paper_14639076_v8_n48_p5611_Bikiel2023-10-03T16:17:03Z Modeling heme proteins using atomistic simulations Bikiel, D.E. Boechi, L. Capece, L. Crespo, A. De Biase, P.M. Di Lella, S. González Lebrero, M.C. Martí, M.A. Nadra, A.D. Perissinotti, L.L. Scherlis, D.A. Estrin, D.A. hemoprotein ligand article chemical model chemistry computer simulation hydrogen bond protein conformation quantum theory Computer Simulation Hemeproteins Hydrogen Bonding Ligands Models, Chemical Protein Conformation Quantum Theory 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. © the Owner Societies. Fil:Bikiel, D.E. Universidad de Buenos Aires. Facultad de Ciencias Exactas y Naturales; Argentina. Fil:Boechi, L. Universidad de Buenos Aires. Facultad de Ciencias Exactas y Naturales; Argentina. Fil:Capece, L. Universidad de Buenos Aires. Facultad de Ciencias Exactas y Naturales; Argentina. Fil:Crespo, A. Universidad de Buenos Aires. Facultad de Ciencias Exactas y Naturales; Argentina. Fil:De Biase, P.M. Universidad de Buenos Aires. Facultad de Ciencias Exactas y Naturales; Argentina. Fil:González Lebrero, M.C. Universidad de Buenos Aires. Facultad de Ciencias Exactas y Naturales; Argentina. Fil:Martí, M.A. Universidad de Buenos Aires. Facultad de Ciencias Exactas y Naturales; Argentina. Fil:Nadra, A.D. Universidad de Buenos Aires. Facultad de Ciencias Exactas y Naturales; Argentina. Fil:Perissinotti, L.L. Universidad de Buenos Aires. Facultad de Ciencias Exactas y Naturales; Argentina. Fil:Estrin, D.A. Universidad de Buenos Aires. Facultad de Ciencias Exactas y Naturales; Argentina. JOUR info:eu-repo/semantics/openAccess http://creativecommons.org/licenses/by/2.5/ar http://hdl.handle.net/20.500.12110/paper_14639076_v8_n48_p5611_Bikiel
institution Universidad de Buenos Aires
institution_str I-28
repository_str R-134
collection Biblioteca Digital - Facultad de Ciencias Exactas y Naturales (UBA)
topic hemoprotein
ligand
article
chemical model
chemistry
computer simulation
hydrogen bond
protein conformation
quantum theory
Computer Simulation
Hemeproteins
Hydrogen Bonding
Ligands
Models, Chemical
Protein Conformation
Quantum Theory
spellingShingle hemoprotein
ligand
article
chemical model
chemistry
computer simulation
hydrogen bond
protein conformation
quantum theory
Computer Simulation
Hemeproteins
Hydrogen Bonding
Ligands
Models, Chemical
Protein Conformation
Quantum Theory
Bikiel, D.E.
Boechi, L.
Capece, L.
Crespo, A.
De Biase, P.M.
Di Lella, S.
González Lebrero, M.C.
Martí, M.A.
Nadra, A.D.
Perissinotti, L.L.
Scherlis, D.A.
Estrin, D.A.
Modeling heme proteins using atomistic simulations
topic_facet hemoprotein
ligand
article
chemical model
chemistry
computer simulation
hydrogen bond
protein conformation
quantum theory
Computer Simulation
Hemeproteins
Hydrogen Bonding
Ligands
Models, Chemical
Protein Conformation
Quantum Theory
description 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. © the Owner Societies.
format JOUR
author Bikiel, D.E.
Boechi, L.
Capece, L.
Crespo, A.
De Biase, P.M.
Di Lella, S.
González Lebrero, M.C.
Martí, M.A.
Nadra, A.D.
Perissinotti, L.L.
Scherlis, D.A.
Estrin, D.A.
author_facet Bikiel, D.E.
Boechi, L.
Capece, L.
Crespo, A.
De Biase, P.M.
Di Lella, S.
González Lebrero, M.C.
Martí, M.A.
Nadra, A.D.
Perissinotti, L.L.
Scherlis, D.A.
Estrin, D.A.
author_sort Bikiel, D.E.
title Modeling heme proteins using atomistic simulations
title_short Modeling heme proteins using atomistic simulations
title_full Modeling heme proteins using atomistic simulations
title_fullStr Modeling heme proteins using atomistic simulations
title_full_unstemmed Modeling heme proteins using atomistic simulations
title_sort modeling heme proteins using atomistic simulations
url http://hdl.handle.net/20.500.12110/paper_14639076_v8_n48_p5611_Bikiel
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