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,...
Guardado en:
Autores principales: | , , , |
---|---|
Publicado: |
2008
|
Materias: | |
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 |
Aporte de: |
id |
paper:paper_00766879_v437_n_p477_Marti |
---|---|
record_format |
dspace |
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 |
_version_ |
1768541838018347008 |