Dioxygen affinity in heme proteins investigated by computer simulation

We present an investigation of the molecular basis of the modulation of oxygen affinity in heme proteins using computer simulation. QM-MM calculations are applied to explore distal and proximal effects on O2 binding to the heme, while classical molecular dynamics simulations are employed to investig...

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Autores principales:	Marti, M.A., Crespo, A., Capece, L., Boechi, L., Bikiel, D.E., Scherlis, D.A., Estrin, D.A.
Formato:	JOUR
Materias:	DFT Heme protein Molecular dynamics Oxygen binding QM-MM cytochrome c hemoglobin hemoprotein myoglobin nitrogen oxygen polypeptide Achromobacter xylosoxidans Ascaris lumbricoides binding affinity calculation computer simulation energy kinetics legume methodology migration molecular dynamics Mycobacterium tuberculosis nematode nervous tissue nonhuman oxygen transport plant root quantum mechanics review Animals Binding Sites Computer Simulation Hemeproteins Hemoglobins Humans Kinetics Ligands Models, Molecular Myoglobin Oxygen Quantum Theory Alcaligenes Cerebratulus lacteus Fabaceae Mammalia
Acceso en línea:	http://hdl.handle.net/20.500.12110/paper_01620134_v100_n4_p761_Marti
Aporte de:	Biblioteca Digital - Facultad de Ciencias Exactas y Naturales (UBA) de Universidad de Buenos Aires

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spelling	todo:paper_01620134_v100_n4_p761_Marti2023-10-03T15:01:25Z Dioxygen affinity in heme proteins investigated by computer simulation Marti, M.A. Crespo, A. Capece, L. Boechi, L. Bikiel, D.E. Scherlis, D.A. Estrin, D.A. DFT Heme protein Molecular dynamics Oxygen binding QM-MM cytochrome c hemoglobin hemoprotein myoglobin nitrogen oxygen polypeptide Achromobacter xylosoxidans Ascaris lumbricoides binding affinity calculation computer simulation energy kinetics legume methodology migration molecular dynamics Mycobacterium tuberculosis nematode nervous tissue nonhuman oxygen transport plant root quantum mechanics review Animals Binding Sites Computer Simulation Hemeproteins Hemoglobins Humans Kinetics Ligands Models, Molecular Myoglobin Oxygen Quantum Theory Achromobacter xylosoxidans Alcaligenes Ascaris lumbricoides Cerebratulus lacteus Fabaceae Mammalia Mycobacterium tuberculosis We present an investigation of the molecular basis of the modulation of oxygen affinity in heme proteins using computer simulation. QM-MM calculations are applied to explore distal and proximal effects on O2 binding to the heme, while classical molecular dynamics simulations are employed to investigate ligand migration across the polypeptide to the active site. Trends in binding energies and in the kinetic constants are illustrated through a number of selected examples highlighting the virtues and the limitations of the applied methodologies. These examples cover a wide range of O2-affinities, and include: the truncated-N and truncated-O hemoglobins from Mycobacterium tuberculosis, the mammalian muscular O2 storage protein: myoglobin, the hemoglobin from the parasitic nematode Ascaris lumbricoides, the oxygen transporter in the root of leguminous plants: leghemoglobin, the Cerebratulus lacteus nerve tissue hemoglobin, and the Alcaligenes xyloxidans cytochrome c′. © 2005 Elsevier Inc. All rights reserved. Fil:Marti, M.A. 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:Capece, L. 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:Bikiel, D.E. 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_01620134_v100_n4_p761_Marti
institution	Universidad de Buenos Aires
institution_str	I-28
repository_str	R-134
collection	Biblioteca Digital - Facultad de Ciencias Exactas y Naturales (UBA)
topic	DFT Heme protein Molecular dynamics Oxygen binding QM-MM cytochrome c hemoglobin hemoprotein myoglobin nitrogen oxygen polypeptide Achromobacter xylosoxidans Ascaris lumbricoides binding affinity calculation computer simulation energy kinetics legume methodology migration molecular dynamics Mycobacterium tuberculosis nematode nervous tissue nonhuman oxygen transport plant root quantum mechanics review Animals Binding Sites Computer Simulation Hemeproteins Hemoglobins Humans Kinetics Ligands Models, Molecular Myoglobin Oxygen Quantum Theory Achromobacter xylosoxidans Alcaligenes Ascaris lumbricoides Cerebratulus lacteus Fabaceae Mammalia Mycobacterium tuberculosis
spellingShingle	DFT Heme protein Molecular dynamics Oxygen binding QM-MM cytochrome c hemoglobin hemoprotein myoglobin nitrogen oxygen polypeptide Achromobacter xylosoxidans Ascaris lumbricoides binding affinity calculation computer simulation energy kinetics legume methodology migration molecular dynamics Mycobacterium tuberculosis nematode nervous tissue nonhuman oxygen transport plant root quantum mechanics review Animals Binding Sites Computer Simulation Hemeproteins Hemoglobins Humans Kinetics Ligands Models, Molecular Myoglobin Oxygen Quantum Theory Achromobacter xylosoxidans Alcaligenes Ascaris lumbricoides Cerebratulus lacteus Fabaceae Mammalia Mycobacterium tuberculosis Marti, M.A. Crespo, A. Capece, L. Boechi, L. Bikiel, D.E. Scherlis, D.A. Estrin, D.A. Dioxygen affinity in heme proteins investigated by computer simulation
topic_facet	DFT Heme protein Molecular dynamics Oxygen binding QM-MM cytochrome c hemoglobin hemoprotein myoglobin nitrogen oxygen polypeptide Achromobacter xylosoxidans Ascaris lumbricoides binding affinity calculation computer simulation energy kinetics legume methodology migration molecular dynamics Mycobacterium tuberculosis nematode nervous tissue nonhuman oxygen transport plant root quantum mechanics review Animals Binding Sites Computer Simulation Hemeproteins Hemoglobins Humans Kinetics Ligands Models, Molecular Myoglobin Oxygen Quantum Theory Achromobacter xylosoxidans Alcaligenes Ascaris lumbricoides Cerebratulus lacteus Fabaceae Mammalia Mycobacterium tuberculosis
description	We present an investigation of the molecular basis of the modulation of oxygen affinity in heme proteins using computer simulation. QM-MM calculations are applied to explore distal and proximal effects on O2 binding to the heme, while classical molecular dynamics simulations are employed to investigate ligand migration across the polypeptide to the active site. Trends in binding energies and in the kinetic constants are illustrated through a number of selected examples highlighting the virtues and the limitations of the applied methodologies. These examples cover a wide range of O2-affinities, and include: the truncated-N and truncated-O hemoglobins from Mycobacterium tuberculosis, the mammalian muscular O2 storage protein: myoglobin, the hemoglobin from the parasitic nematode Ascaris lumbricoides, the oxygen transporter in the root of leguminous plants: leghemoglobin, the Cerebratulus lacteus nerve tissue hemoglobin, and the Alcaligenes xyloxidans cytochrome c′. © 2005 Elsevier Inc. All rights reserved.
format	JOUR
author	Marti, M.A. Crespo, A. Capece, L. Boechi, L. Bikiel, D.E. Scherlis, D.A. Estrin, D.A.
author_facet	Marti, M.A. Crespo, A. Capece, L. Boechi, L. Bikiel, D.E. Scherlis, D.A. Estrin, D.A.
author_sort	Marti, M.A.
title	Dioxygen affinity in heme proteins investigated by computer simulation
title_short	Dioxygen affinity in heme proteins investigated by computer simulation
title_full	Dioxygen affinity in heme proteins investigated by computer simulation
title_fullStr	Dioxygen affinity in heme proteins investigated by computer simulation
title_full_unstemmed	Dioxygen affinity in heme proteins investigated by computer simulation
title_sort	dioxygen affinity in heme proteins investigated by computer simulation
url	http://hdl.handle.net/20.500.12110/paper_01620134_v100_n4_p761_Marti
work_keys_str_mv	AT martima dioxygenaffinityinhemeproteinsinvestigatedbycomputersimulation AT crespoa dioxygenaffinityinhemeproteinsinvestigatedbycomputersimulation AT capecel dioxygenaffinityinhemeproteinsinvestigatedbycomputersimulation AT boechil dioxygenaffinityinhemeproteinsinvestigatedbycomputersimulation AT bikielde dioxygenaffinityinhemeproteinsinvestigatedbycomputersimulation AT scherlisda dioxygenaffinityinhemeproteinsinvestigatedbycomputersimulation AT estrinda dioxygenaffinityinhemeproteinsinvestigatedbycomputersimulation
_version_	1807317128700755968

Dioxygen affinity in heme proteins investigated by computer simulation

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