Protein dynamics and ligand migration interplay as studied by computer simulation

Since proteins are dynamic systems in living organisms, the employment of methodologies contemplating this crucial characteristic results fundamental to allow revealing several aspects of their function. In this work, we present results obtained using classical mechanical atomistic simulation tools...

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Autores principales:	Arroyo Mañez, Pau, Bikiel, Damian Ezequiel, Boechi, Leonardo, Capece, Luciana, Estrin, Dario Ariel, Martí, Marcelo Adrián, Nadra, Alejandro Daniel, Petruk, Ariel Alcides
Publicado:	2011
Materias:	Ligand migration Molecular dynamics Protein dynamics amine oxidase (copper containing) catalase cytochrome P450 dehalogenase hemoglobin hemoprotein hydrogenase hydrolase ligand myoglobin neuroglobin nitric oxide nitrophorin unclassified drug accelerated molecular dynamics activated molecular dynamics computer simulation conformational transition human implicit ligand sampling ligand binding ligand migration locally enhanced sampling mathematical analysis metadynamics methodology molecular dynamics multiple steered molecular dynamic nonhuman Pichia angusta priority journal protein dynamics protein energy landscape exploration protein function random activated molecular dynamics review thermodynamics Binding Sites Computer Simulation Ligands Models, Molecular Molecular Dynamics Simulation Proteins
Acceso en línea:	https://bibliotecadigital.exactas.uba.ar/collection/paper/document/paper_15709639_v1814_n8_p1054_ArroyoManez http://hdl.handle.net/20.500.12110/paper_15709639_v1814_n8_p1054_ArroyoManez
Aporte de:	Biblioteca Digital - Facultad de Ciencias Exactas y Naturales (UBA) de Universidad de Buenos Aires

id	paper:paper_15709639_v1814_n8_p1054_ArroyoManez
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spelling	paper:paper_15709639_v1814_n8_p1054_ArroyoManez2023-06-08T16:24:16Z Protein dynamics and ligand migration interplay as studied by computer simulation Arroyo Mañez, Pau Bikiel, Damian Ezequiel Boechi, Leonardo Capece, Luciana Estrin, Dario Ariel Martí, Marcelo Adrián Nadra, Alejandro Daniel Petruk, Ariel Alcides Ligand migration Molecular dynamics Protein dynamics amine oxidase (copper containing) catalase cytochrome P450 dehalogenase hemoglobin hemoprotein hydrogenase hydrolase ligand myoglobin neuroglobin nitric oxide nitrophorin unclassified drug accelerated molecular dynamics activated molecular dynamics computer simulation conformational transition human implicit ligand sampling ligand binding ligand migration locally enhanced sampling mathematical analysis metadynamics methodology molecular dynamics multiple steered molecular dynamic nonhuman Pichia angusta priority journal protein dynamics protein energy landscape exploration protein function random activated molecular dynamics review thermodynamics Binding Sites Computer Simulation Ligands Models, Molecular Molecular Dynamics Simulation Proteins Since proteins are dynamic systems in living organisms, the employment of methodologies contemplating this crucial characteristic results fundamental to allow revealing several aspects of their function. In this work, we present results obtained using classical mechanical atomistic simulation tools applied to understand the connection between protein dynamics and ligand migration. Firstly, we will present a review of the different sampling schemes used in the last years to obtain both ligand migration pathways and the thermodynamic information associated with the process. Secondly, we will focus on representative examples in which the schemes previously presented are employed, concerning the following: i) ligand migration, tunnels, and cavities in myoglobin and neuroglobin; ii) ligand migration in truncated hemoglobin members; iii) NO escape and conformational changes in nitrophorins; iv) ligand selectivity in catalase and hydrogenase; and v) larger ligand migration: the P450 and haloalkane dehalogenase cases. This article is part of a Special Issue entitled: Protein Dynamics: Experimental and Computational Approaches. © 2010 Elsevier B.V. All rights reserved. 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:Boechi, L. 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:Estrin, D.A. Universidad de Buenos Aires. Facultad de Ciencias Exactas y Naturales; Argentina. Fil:Martí, M.A. Universidad de Buenos Aires. Facultad de Ciencias Exactas y Naturales; Argentina. Fil:Nadra, A.D. Universidad de Buenos Aires. Facultad de Ciencias Exactas y Naturales; Argentina. Fil:Petruk, A.A. Universidad de Buenos Aires. Facultad de Ciencias Exactas y Naturales; Argentina. 2011 https://bibliotecadigital.exactas.uba.ar/collection/paper/document/paper_15709639_v1814_n8_p1054_ArroyoManez http://hdl.handle.net/20.500.12110/paper_15709639_v1814_n8_p1054_ArroyoManez
institution	Universidad de Buenos Aires
institution_str	I-28
repository_str	R-134
collection	Biblioteca Digital - Facultad de Ciencias Exactas y Naturales (UBA)
topic	Ligand migration Molecular dynamics Protein dynamics amine oxidase (copper containing) catalase cytochrome P450 dehalogenase hemoglobin hemoprotein hydrogenase hydrolase ligand myoglobin neuroglobin nitric oxide nitrophorin unclassified drug accelerated molecular dynamics activated molecular dynamics computer simulation conformational transition human implicit ligand sampling ligand binding ligand migration locally enhanced sampling mathematical analysis metadynamics methodology molecular dynamics multiple steered molecular dynamic nonhuman Pichia angusta priority journal protein dynamics protein energy landscape exploration protein function random activated molecular dynamics review thermodynamics Binding Sites Computer Simulation Ligands Models, Molecular Molecular Dynamics Simulation Proteins
spellingShingle	Ligand migration Molecular dynamics Protein dynamics amine oxidase (copper containing) catalase cytochrome P450 dehalogenase hemoglobin hemoprotein hydrogenase hydrolase ligand myoglobin neuroglobin nitric oxide nitrophorin unclassified drug accelerated molecular dynamics activated molecular dynamics computer simulation conformational transition human implicit ligand sampling ligand binding ligand migration locally enhanced sampling mathematical analysis metadynamics methodology molecular dynamics multiple steered molecular dynamic nonhuman Pichia angusta priority journal protein dynamics protein energy landscape exploration protein function random activated molecular dynamics review thermodynamics Binding Sites Computer Simulation Ligands Models, Molecular Molecular Dynamics Simulation Proteins Arroyo Mañez, Pau Bikiel, Damian Ezequiel Boechi, Leonardo Capece, Luciana Estrin, Dario Ariel Martí, Marcelo Adrián Nadra, Alejandro Daniel Petruk, Ariel Alcides Protein dynamics and ligand migration interplay as studied by computer simulation
topic_facet	Ligand migration Molecular dynamics Protein dynamics amine oxidase (copper containing) catalase cytochrome P450 dehalogenase hemoglobin hemoprotein hydrogenase hydrolase ligand myoglobin neuroglobin nitric oxide nitrophorin unclassified drug accelerated molecular dynamics activated molecular dynamics computer simulation conformational transition human implicit ligand sampling ligand binding ligand migration locally enhanced sampling mathematical analysis metadynamics methodology molecular dynamics multiple steered molecular dynamic nonhuman Pichia angusta priority journal protein dynamics protein energy landscape exploration protein function random activated molecular dynamics review thermodynamics Binding Sites Computer Simulation Ligands Models, Molecular Molecular Dynamics Simulation Proteins
description	Since proteins are dynamic systems in living organisms, the employment of methodologies contemplating this crucial characteristic results fundamental to allow revealing several aspects of their function. In this work, we present results obtained using classical mechanical atomistic simulation tools applied to understand the connection between protein dynamics and ligand migration. Firstly, we will present a review of the different sampling schemes used in the last years to obtain both ligand migration pathways and the thermodynamic information associated with the process. Secondly, we will focus on representative examples in which the schemes previously presented are employed, concerning the following: i) ligand migration, tunnels, and cavities in myoglobin and neuroglobin; ii) ligand migration in truncated hemoglobin members; iii) NO escape and conformational changes in nitrophorins; iv) ligand selectivity in catalase and hydrogenase; and v) larger ligand migration: the P450 and haloalkane dehalogenase cases. This article is part of a Special Issue entitled: Protein Dynamics: Experimental and Computational Approaches. © 2010 Elsevier B.V. All rights reserved.
author	Arroyo Mañez, Pau Bikiel, Damian Ezequiel Boechi, Leonardo Capece, Luciana Estrin, Dario Ariel Martí, Marcelo Adrián Nadra, Alejandro Daniel Petruk, Ariel Alcides
author_facet	Arroyo Mañez, Pau Bikiel, Damian Ezequiel Boechi, Leonardo Capece, Luciana Estrin, Dario Ariel Martí, Marcelo Adrián Nadra, Alejandro Daniel Petruk, Ariel Alcides
author_sort	Arroyo Mañez, Pau
title	Protein dynamics and ligand migration interplay as studied by computer simulation
title_short	Protein dynamics and ligand migration interplay as studied by computer simulation
title_full	Protein dynamics and ligand migration interplay as studied by computer simulation
title_fullStr	Protein dynamics and ligand migration interplay as studied by computer simulation
title_full_unstemmed	Protein dynamics and ligand migration interplay as studied by computer simulation
title_sort	protein dynamics and ligand migration interplay as studied by computer simulation
publishDate	2011
url	https://bibliotecadigital.exactas.uba.ar/collection/paper/document/paper_15709639_v1814_n8_p1054_ArroyoManez http://hdl.handle.net/20.500.12110/paper_15709639_v1814_n8_p1054_ArroyoManez
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_version_	1768544383802540032

Protein dynamics and ligand migration interplay as studied by computer simulation

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