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: Martí, Marcelo Adrián, Capece, Luciana, Crespo, Alejandro, Estrin, Dario Ariel
Publicado: 2008
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Acceso en línea:https://bibliotecadigital.exactas.uba.ar/collection/paper/document/paper_00766879_v437_n_p477_Marti
http://hdl.handle.net/20.500.12110/paper_00766879_v437_n_p477_Marti
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spelling paper:paper_00766879_v437_n_p477_Marti2023-06-08T15:07:21Z Nitric Oxide Reactivity with Globins as Investigated Through Computer Simulation Martí, Marcelo Adrián Capece, Luciana Crespo, Alejandro Estrin, Dario Ariel 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. 2008 https://bibliotecadigital.exactas.uba.ar/collection/paper/document/paper_00766879_v437_n_p477_Marti 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
Martí, Marcelo Adrián
Capece, Luciana
Crespo, Alejandro
Estrin, Dario Ariel
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.
author Martí, Marcelo Adrián
Capece, Luciana
Crespo, Alejandro
Estrin, Dario Ariel
author_facet Martí, Marcelo Adrián
Capece, Luciana
Crespo, Alejandro
Estrin, Dario Ariel
author_sort Martí, Marcelo Adrián
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
publishDate 2008
url https://bibliotecadigital.exactas.uba.ar/collection/paper/document/paper_00766879_v437_n_p477_Marti
http://hdl.handle.net/20.500.12110/paper_00766879_v437_n_p477_Marti
work_keys_str_mv AT martimarceloadrian nitricoxidereactivitywithglobinsasinvestigatedthroughcomputersimulation
AT capeceluciana nitricoxidereactivitywithglobinsasinvestigatedthroughcomputersimulation
AT crespoalejandro nitricoxidereactivitywithglobinsasinvestigatedthroughcomputersimulation
AT estrindarioariel nitricoxidereactivitywithglobinsasinvestigatedthroughcomputersimulation
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