Nitric Oxide Reactivity with Globins as Investigated Through Computer Simulation

This chapter reviews the application of classical and quantum-mechanical atomistic simulation tools used in the investigation of several relevant issues in nitric oxide reactivity with globins and presents different simulation strategies based on classical force fields: standard molecular dynamics,...

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Autores principales:	Marti, M.A., Capece, L., Bidon-Chanal, A., Crespo, A., Guallar, V., Luque, F.J., Estrin, D.A.
Formato:	SER
Materias:	globin heme hemoglobin ligand nitric oxide oxygen protein myoglobin truncated hemoglobin chemical reaction computer simulation energy molecular dynamics molecular mechanics mutant Mycobacterium tuberculosis nonhuman oxygen affinity parameter priority journal quantum mechanics review sampling wild type biomechanics chemical structure chemistry comparative study drug detoxification energy metabolism enzyme specificity kinetics metabolism protein binding protein folding quantum theory signal transduction theoretical model Biomechanics Computer Simulation Energy Metabolism Globins Heme Kinetics Metabolic Detoxication, Drug Models, Molecular Models, Theoretical Myoglobin Nitric Oxide Oxygen Protein Binding Protein Folding Quantum Theory Signal Transduction Substrate Specificity Truncated Hemoglobins
Acceso en línea:	http://hdl.handle.net/20.500.12110/paper_00766879_v437_n_p477_Marti
Aporte de:	Biblioteca Digital - Facultad de Ciencias Exactas y Naturales (UBA) de Universidad de Buenos Aires

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spelling	todo:paper_00766879_v437_n_p477_Marti2023-10-03T14:54:11Z Nitric Oxide Reactivity with Globins as Investigated Through Computer Simulation Marti, M.A. Capece, L. Bidon-Chanal, A. Crespo, A. Guallar, V. Luque, F.J. Estrin, D.A. globin heme hemoglobin ligand nitric oxide oxygen protein myoglobin nitric oxide oxygen truncated hemoglobin chemical reaction computer simulation energy molecular dynamics molecular mechanics mutant Mycobacterium tuberculosis nonhuman oxygen affinity parameter priority journal quantum mechanics review sampling wild type biomechanics chemical structure chemistry comparative study drug detoxification energy metabolism enzyme specificity kinetics metabolism protein binding protein folding quantum theory signal transduction theoretical model Mycobacterium tuberculosis Biomechanics Computer Simulation Energy Metabolism Globins Heme Kinetics Metabolic Detoxication, Drug Models, Molecular Models, Theoretical Mycobacterium tuberculosis Myoglobin Nitric Oxide Oxygen Protein Binding Protein Folding Quantum Theory Signal Transduction Substrate Specificity Truncated Hemoglobins This chapter reviews the application of classical and quantum-mechanical atomistic simulation tools used in the investigation of several relevant issues in nitric oxide reactivity with globins and presents different simulation strategies based on classical force fields: standard molecular dynamics, essential dynamics, umbrella sampling, multiple steering molecular dynamics, and a novel technique for exploring the protein energy landscape. It also presents hybrid quantum-classical schemes as a tool to obtain relevant information regarding binding energies and chemical reactivity of globins. As illustrative examples, investigations of the structural flexibility, ligand migration profiles, oxygen affinity, and reactivity toward nitric oxide of truncated hemoglobin N of Mycobacterium tuberculosis are presented. © 2008 Elsevier Inc. All rights reserved. Fil:Marti, M.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:Crespo, 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. SER info:eu-repo/semantics/openAccess http://creativecommons.org/licenses/by/2.5/ar http://hdl.handle.net/20.500.12110/paper_00766879_v437_n_p477_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	globin heme hemoglobin ligand nitric oxide oxygen protein myoglobin nitric oxide oxygen truncated hemoglobin chemical reaction computer simulation energy molecular dynamics molecular mechanics mutant Mycobacterium tuberculosis nonhuman oxygen affinity parameter priority journal quantum mechanics review sampling wild type biomechanics chemical structure chemistry comparative study drug detoxification energy metabolism enzyme specificity kinetics metabolism protein binding protein folding quantum theory signal transduction theoretical model Mycobacterium tuberculosis Biomechanics Computer Simulation Energy Metabolism Globins Heme Kinetics Metabolic Detoxication, Drug Models, Molecular Models, Theoretical Mycobacterium tuberculosis Myoglobin Nitric Oxide Oxygen Protein Binding Protein Folding Quantum Theory Signal Transduction Substrate Specificity Truncated Hemoglobins
spellingShingle	globin heme hemoglobin ligand nitric oxide oxygen protein myoglobin nitric oxide oxygen truncated hemoglobin chemical reaction computer simulation energy molecular dynamics molecular mechanics mutant Mycobacterium tuberculosis nonhuman oxygen affinity parameter priority journal quantum mechanics review sampling wild type biomechanics chemical structure chemistry comparative study drug detoxification energy metabolism enzyme specificity kinetics metabolism protein binding protein folding quantum theory signal transduction theoretical model Mycobacterium tuberculosis Biomechanics Computer Simulation Energy Metabolism Globins Heme Kinetics Metabolic Detoxication, Drug Models, Molecular Models, Theoretical Mycobacterium tuberculosis Myoglobin Nitric Oxide Oxygen Protein Binding Protein Folding Quantum Theory Signal Transduction Substrate Specificity Truncated Hemoglobins Marti, M.A. Capece, L. Bidon-Chanal, A. Crespo, A. Guallar, V. Luque, F.J. Estrin, D.A. Nitric Oxide Reactivity with Globins as Investigated Through Computer Simulation
topic_facet	globin heme hemoglobin ligand nitric oxide oxygen protein myoglobin nitric oxide oxygen truncated hemoglobin chemical reaction computer simulation energy molecular dynamics molecular mechanics mutant Mycobacterium tuberculosis nonhuman oxygen affinity parameter priority journal quantum mechanics review sampling wild type biomechanics chemical structure chemistry comparative study drug detoxification energy metabolism enzyme specificity kinetics metabolism protein binding protein folding quantum theory signal transduction theoretical model Mycobacterium tuberculosis Biomechanics Computer Simulation Energy Metabolism Globins Heme Kinetics Metabolic Detoxication, Drug Models, Molecular Models, Theoretical Mycobacterium tuberculosis Myoglobin Nitric Oxide Oxygen Protein Binding Protein Folding Quantum Theory Signal Transduction Substrate Specificity Truncated Hemoglobins
description	This chapter reviews the application of classical and quantum-mechanical atomistic simulation tools used in the investigation of several relevant issues in nitric oxide reactivity with globins and presents different simulation strategies based on classical force fields: standard molecular dynamics, essential dynamics, umbrella sampling, multiple steering molecular dynamics, and a novel technique for exploring the protein energy landscape. It also presents hybrid quantum-classical schemes as a tool to obtain relevant information regarding binding energies and chemical reactivity of globins. As illustrative examples, investigations of the structural flexibility, ligand migration profiles, oxygen affinity, and reactivity toward nitric oxide of truncated hemoglobin N of Mycobacterium tuberculosis are presented. © 2008 Elsevier Inc. All rights reserved.
format	SER
author	Marti, M.A. Capece, L. Bidon-Chanal, A. Crespo, A. Guallar, V. Luque, F.J. Estrin, D.A.
author_facet	Marti, M.A. Capece, L. Bidon-Chanal, A. Crespo, A. Guallar, V. Luque, F.J. Estrin, D.A.
author_sort	Marti, M.A.
title	Nitric Oxide Reactivity with Globins as Investigated Through Computer Simulation
title_short	Nitric Oxide Reactivity with Globins as Investigated Through Computer Simulation
title_full	Nitric Oxide Reactivity with Globins as Investigated Through Computer Simulation
title_fullStr	Nitric Oxide Reactivity with Globins as Investigated Through Computer Simulation
title_full_unstemmed	Nitric Oxide Reactivity with Globins as Investigated Through Computer Simulation
title_sort	nitric oxide reactivity with globins as investigated through computer simulation
url	http://hdl.handle.net/20.500.12110/paper_00766879_v437_n_p477_Marti
work_keys_str_mv	AT martima nitricoxidereactivitywithglobinsasinvestigatedthroughcomputersimulation AT capecel nitricoxidereactivitywithglobinsasinvestigatedthroughcomputersimulation AT bidonchanala nitricoxidereactivitywithglobinsasinvestigatedthroughcomputersimulation AT crespoa nitricoxidereactivitywithglobinsasinvestigatedthroughcomputersimulation AT guallarv nitricoxidereactivitywithglobinsasinvestigatedthroughcomputersimulation AT luquefj nitricoxidereactivitywithglobinsasinvestigatedthroughcomputersimulation AT estrinda nitricoxidereactivitywithglobinsasinvestigatedthroughcomputersimulation
_version_	1782030654855184384

Nitric Oxide Reactivity with Globins as Investigated Through Computer Simulation

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