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, Damian Ezequiel, Boechi, Leonardo, Capece, Luciana, Crespo, Alejandro, De Biase, Pablo Martín, González Lebrero, Mariano Camilo, Martí, Marcelo Adrián, Nadra, Alejandro Daniel, Perissinotti, Laura L., Estrin, Dario Ariel
Publicado: 2006
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:https://bibliotecadigital.exactas.uba.ar/collection/paper/document/paper_14639076_v8_n48_p5611_Bikiel
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 paper:paper_14639076_v8_n48_p5611_Bikiel
record_format dspace
spelling paper:paper_14639076_v8_n48_p5611_Bikiel2023-06-08T16:16:38Z Modeling heme proteins using atomistic simulations Bikiel, Damian Ezequiel Boechi, Leonardo Capece, Luciana Crespo, Alejandro De Biase, Pablo Martín González Lebrero, Mariano Camilo Martí, Marcelo Adrián Nadra, Alejandro Daniel Perissinotti, Laura L. Estrin, Dario Ariel 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. 2006 https://bibliotecadigital.exactas.uba.ar/collection/paper/document/paper_14639076_v8_n48_p5611_Bikiel 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, Damian Ezequiel
Boechi, Leonardo
Capece, Luciana
Crespo, Alejandro
De Biase, Pablo Martín
González Lebrero, Mariano Camilo
Martí, Marcelo Adrián
Nadra, Alejandro Daniel
Perissinotti, Laura L.
Estrin, Dario Ariel
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.
author Bikiel, Damian Ezequiel
Boechi, Leonardo
Capece, Luciana
Crespo, Alejandro
De Biase, Pablo Martín
González Lebrero, Mariano Camilo
Martí, Marcelo Adrián
Nadra, Alejandro Daniel
Perissinotti, Laura L.
Estrin, Dario Ariel
author_facet Bikiel, Damian Ezequiel
Boechi, Leonardo
Capece, Luciana
Crespo, Alejandro
De Biase, Pablo Martín
González Lebrero, Mariano Camilo
Martí, Marcelo Adrián
Nadra, Alejandro Daniel
Perissinotti, Laura L.
Estrin, Dario Ariel
author_sort Bikiel, Damian Ezequiel
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
publishDate 2006
url https://bibliotecadigital.exactas.uba.ar/collection/paper/document/paper_14639076_v8_n48_p5611_Bikiel
http://hdl.handle.net/20.500.12110/paper_14639076_v8_n48_p5611_Bikiel
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