Small ligand-globin interactions: Reviewing lessons derived from computer simulation

In this work we review the application of classical and quantum-mechanical atomistic computer simulation tools to the investigation of small ligand interaction with globins. In the first part, studies of ligand migration, with its connection to kinetic association rate constants (kon), are presented...

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Autores principales:	Capece, Luciana, Boechi, Leonardo, Perissinotti, Laura L., Arroyo Mañez, Pau, Bikiel, Damian Ezequiel, Martí, Marcelo Adrián, Estrin, Dario Ariel
Publicado:	2013
Materias:	Computer simulation Globin Heme protein Molecular dynamics QM/MM amino acid cytochrome c globin heme hemoglobin ligand nitrite oxygen hemoprotein amino acid composition article binding site computer simulation conformation controlled study crystal structure denitrifying bacterium dissociation equilibrium constant Escherichia coli experimental study hydrogen bond ligand binding molecular dynamics molecular mechanics nonhuman Paracoccus pantotrophus Paramecium caudatum point mutation priority journal protein protein interaction proton transport Pseudomonas aeruginosa quantum mechanics Raman spectrometry reduction kinetics site directed mutagenesis Wolinella succinogenes animal chemistry human metabolism quantum theory review Animals Computer Simulation Globins Humans Ligands Quantum Theory
Acceso en línea:	https://bibliotecadigital.exactas.uba.ar/collection/paper/document/paper_15709639_v1834_n9_p1722_Capece http://hdl.handle.net/20.500.12110/paper_15709639_v1834_n9_p1722_Capece
Aporte de:	Biblioteca Digital - Facultad de Ciencias Exactas y Naturales (UBA) de Universidad de Buenos Aires

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spelling	paper:paper_15709639_v1834_n9_p1722_Capece2023-06-08T16:24:17Z Small ligand-globin interactions: Reviewing lessons derived from computer simulation Capece, Luciana Boechi, Leonardo Perissinotti, Laura L. Arroyo Mañez, Pau Bikiel, Damian Ezequiel Martí, Marcelo Adrián Estrin, Dario Ariel Computer simulation Globin Heme protein Molecular dynamics QM/MM amino acid cytochrome c globin heme hemoglobin ligand nitrite oxygen hemoprotein ligand amino acid composition article binding site computer simulation conformation controlled study crystal structure denitrifying bacterium dissociation equilibrium constant Escherichia coli experimental study hydrogen bond ligand binding molecular dynamics molecular mechanics nonhuman Paracoccus pantotrophus Paramecium caudatum point mutation priority journal protein protein interaction proton transport Pseudomonas aeruginosa quantum mechanics Raman spectrometry reduction kinetics site directed mutagenesis Wolinella succinogenes animal chemistry human metabolism QM/MM quantum theory review Computer simulation Globin Heme protein Molecular dynamics QM/MM Animals Computer Simulation Globins Humans Ligands Quantum Theory In this work we review the application of classical and quantum-mechanical atomistic computer simulation tools to the investigation of small ligand interaction with globins. In the first part, studies of ligand migration, with its connection to kinetic association rate constants (kon), are presented. In the second part, we review studies for a variety of ligands such as O2, NO, CO, HS-, F-, and NO2 - showing how the heme structure, proximal effects, and the interactions with the distal amino acids can modulate protein-ligand binding. The review presents mainly results derived from our previous works on the subject, in the context of other theoretical and experimental studies performed by others. The variety and extent of the presented data yield a clear example of how computer simulation tools have, in the last decade, contributed to our deeper understanding of small ligand interactions with globins. This article is part of a Special Issue entitled: Oxygen Binding and Sensing Proteins. © 2013 Elsevier B.V. All rights reserved. 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:Perissinotti, L.L. Universidad de Buenos Aires. Facultad de Ciencias Exactas y Naturales; Argentina. Fil:Arroyo-Mañez, P. 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:Marti, M.A. 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. 2013 https://bibliotecadigital.exactas.uba.ar/collection/paper/document/paper_15709639_v1834_n9_p1722_Capece http://hdl.handle.net/20.500.12110/paper_15709639_v1834_n9_p1722_Capece
institution	Universidad de Buenos Aires
institution_str	I-28
repository_str	R-134
collection	Biblioteca Digital - Facultad de Ciencias Exactas y Naturales (UBA)
topic	Computer simulation Globin Heme protein Molecular dynamics QM/MM amino acid cytochrome c globin heme hemoglobin ligand nitrite oxygen hemoprotein ligand amino acid composition article binding site computer simulation conformation controlled study crystal structure denitrifying bacterium dissociation equilibrium constant Escherichia coli experimental study hydrogen bond ligand binding molecular dynamics molecular mechanics nonhuman Paracoccus pantotrophus Paramecium caudatum point mutation priority journal protein protein interaction proton transport Pseudomonas aeruginosa quantum mechanics Raman spectrometry reduction kinetics site directed mutagenesis Wolinella succinogenes animal chemistry human metabolism QM/MM quantum theory review Computer simulation Globin Heme protein Molecular dynamics QM/MM Animals Computer Simulation Globins Humans Ligands Quantum Theory
spellingShingle	Computer simulation Globin Heme protein Molecular dynamics QM/MM amino acid cytochrome c globin heme hemoglobin ligand nitrite oxygen hemoprotein ligand amino acid composition article binding site computer simulation conformation controlled study crystal structure denitrifying bacterium dissociation equilibrium constant Escherichia coli experimental study hydrogen bond ligand binding molecular dynamics molecular mechanics nonhuman Paracoccus pantotrophus Paramecium caudatum point mutation priority journal protein protein interaction proton transport Pseudomonas aeruginosa quantum mechanics Raman spectrometry reduction kinetics site directed mutagenesis Wolinella succinogenes animal chemistry human metabolism QM/MM quantum theory review Computer simulation Globin Heme protein Molecular dynamics QM/MM Animals Computer Simulation Globins Humans Ligands Quantum Theory Capece, Luciana Boechi, Leonardo Perissinotti, Laura L. Arroyo Mañez, Pau Bikiel, Damian Ezequiel Martí, Marcelo Adrián Estrin, Dario Ariel Small ligand-globin interactions: Reviewing lessons derived from computer simulation
topic_facet	Computer simulation Globin Heme protein Molecular dynamics QM/MM amino acid cytochrome c globin heme hemoglobin ligand nitrite oxygen hemoprotein ligand amino acid composition article binding site computer simulation conformation controlled study crystal structure denitrifying bacterium dissociation equilibrium constant Escherichia coli experimental study hydrogen bond ligand binding molecular dynamics molecular mechanics nonhuman Paracoccus pantotrophus Paramecium caudatum point mutation priority journal protein protein interaction proton transport Pseudomonas aeruginosa quantum mechanics Raman spectrometry reduction kinetics site directed mutagenesis Wolinella succinogenes animal chemistry human metabolism QM/MM quantum theory review Computer simulation Globin Heme protein Molecular dynamics QM/MM Animals Computer Simulation Globins Humans Ligands Quantum Theory
description	In this work we review the application of classical and quantum-mechanical atomistic computer simulation tools to the investigation of small ligand interaction with globins. In the first part, studies of ligand migration, with its connection to kinetic association rate constants (kon), are presented. In the second part, we review studies for a variety of ligands such as O2, NO, CO, HS-, F-, and NO2 - showing how the heme structure, proximal effects, and the interactions with the distal amino acids can modulate protein-ligand binding. The review presents mainly results derived from our previous works on the subject, in the context of other theoretical and experimental studies performed by others. The variety and extent of the presented data yield a clear example of how computer simulation tools have, in the last decade, contributed to our deeper understanding of small ligand interactions with globins. This article is part of a Special Issue entitled: Oxygen Binding and Sensing Proteins. © 2013 Elsevier B.V. All rights reserved.
author	Capece, Luciana Boechi, Leonardo Perissinotti, Laura L. Arroyo Mañez, Pau Bikiel, Damian Ezequiel Martí, Marcelo Adrián Estrin, Dario Ariel
author_facet	Capece, Luciana Boechi, Leonardo Perissinotti, Laura L. Arroyo Mañez, Pau Bikiel, Damian Ezequiel Martí, Marcelo Adrián Estrin, Dario Ariel
author_sort	Capece, Luciana
title	Small ligand-globin interactions: Reviewing lessons derived from computer simulation
title_short	Small ligand-globin interactions: Reviewing lessons derived from computer simulation
title_full	Small ligand-globin interactions: Reviewing lessons derived from computer simulation
title_fullStr	Small ligand-globin interactions: Reviewing lessons derived from computer simulation
title_full_unstemmed	Small ligand-globin interactions: Reviewing lessons derived from computer simulation
title_sort	small ligand-globin interactions: reviewing lessons derived from computer simulation
publishDate	2013
url	https://bibliotecadigital.exactas.uba.ar/collection/paper/document/paper_15709639_v1834_n9_p1722_Capece http://hdl.handle.net/20.500.12110/paper_15709639_v1834_n9_p1722_Capece
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_version_	1768546134602547200

Small ligand-globin interactions: Reviewing lessons derived from computer simulation

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