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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2006
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Acceso en línea: | https://bibliotecadigital.exactas.uba.ar/collection/paper/document/paper_01620134_v100_n4_p761_Marti http://hdl.handle.net/20.500.12110/paper_01620134_v100_n4_p761_Marti |
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paper:paper_01620134_v100_n4_p761_Marti2023-06-08T15:13:33Z Dioxygen affinity in heme proteins investigated by computer simulation Martí, Marcelo Adrián Crespo, Alejandro Capece, Luciana Boechi, Leonardo Bikiel, Damian Ezequiel Estrin, Dario Ariel 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. 2006 https://bibliotecadigital.exactas.uba.ar/collection/paper/document/paper_01620134_v100_n4_p761_Marti 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 Martí, Marcelo Adrián Crespo, Alejandro Capece, Luciana Boechi, Leonardo Bikiel, Damian Ezequiel Estrin, Dario Ariel 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. |
author |
Martí, Marcelo Adrián Crespo, Alejandro Capece, Luciana Boechi, Leonardo Bikiel, Damian Ezequiel Estrin, Dario Ariel |
author_facet |
Martí, Marcelo Adrián Crespo, Alejandro Capece, Luciana Boechi, Leonardo Bikiel, Damian Ezequiel Estrin, Dario Ariel |
author_sort |
Martí, Marcelo Adrián |
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 |
publishDate |
2006 |
url |
https://bibliotecadigital.exactas.uba.ar/collection/paper/document/paper_01620134_v100_n4_p761_Marti http://hdl.handle.net/20.500.12110/paper_01620134_v100_n4_p761_Marti |
work_keys_str_mv |
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