A quantitative model for oxygen uptake and release in a family of hemeproteins

Motivation: Hemeproteins have many diverse functions that largely depend on the rate at which they uptake or release small ligands, like oxygen. These proteins have been extensively studied using either simulations or experiments, albeit only qualitatively and one or two proteins at a time. Results:...

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Autores principales: Bustamante, Juan Pablo, Sued, Mariela, Martí, Marcelo Adrián, Estrin, Dario Ariel, Boechi, Leonardo
Publicado: 2016
Materias:
hemoprotein
ligand
oxygen
truncated hemoglobin
kinetics
metabolism
Hemeproteins
Kinetics
Ligands
Oxygen
Truncated Hemoglobins
Acceso en línea:https://bibliotecadigital.exactas.uba.ar/collection/paper/document/paper_13674803_v32_n12_p1805_Bustamante
http://hdl.handle.net/20.500.12110/paper_13674803_v32_n12_p1805_Bustamante
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Biblioteca Digital - Facultad de Ciencias Exactas y Naturales (UBA) de Universidad de Buenos Aires
id paper:paper_13674803_v32_n12_p1805_Bustamante
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spelling paper:paper_13674803_v32_n12_p1805_Bustamante2023-06-08T16:12:11Z A quantitative model for oxygen uptake and release in a family of hemeproteins Bustamante, Juan Pablo Sued, Mariela Martí, Marcelo Adrián Estrin, Dario Ariel Boechi, Leonardo hemoprotein ligand oxygen truncated hemoglobin kinetics metabolism Hemeproteins Kinetics Ligands Oxygen Truncated Hemoglobins Motivation: Hemeproteins have many diverse functions that largely depend on the rate at which they uptake or release small ligands, like oxygen. These proteins have been extensively studied using either simulations or experiments, albeit only qualitatively and one or two proteins at a time. Results: We present a physical-chemical model, which uses data obtained exclusively from computer simulations, to describe the uptake and release of oxygen in a family of hemeproteins, called truncated hemoglobins (trHbs). Through a rigorous statistical analysis we demonstrate that our model successfully recaptures all the reported experimental oxygen association and dissociation kinetic rate constants, thus allowing us to establish the key factors that determine the rates at which these hemeproteins uptake and release oxygen. We found that internal tunnels as well as the distal site water molecules control ligand uptake, whereas oxygen stabilization by distal site residues controls ligand release. Because these rates largely determine the functions of these hemeproteins, these approaches will also be important tools in characterizing the trHbs members with unknown functions. © 2016 The Author 2016. Fil:Bustamante, J.P. Universidad de Buenos Aires. Facultad de Ciencias Exactas y Naturales; Argentina. Fil:Sued, M. 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:Estrin, D.A. 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. 2016 https://bibliotecadigital.exactas.uba.ar/collection/paper/document/paper_13674803_v32_n12_p1805_Bustamante http://hdl.handle.net/20.500.12110/paper_13674803_v32_n12_p1805_Bustamante
institution Universidad de Buenos Aires
institution_str I-28
repository_str R-134
collection Biblioteca Digital - Facultad de Ciencias Exactas y Naturales (UBA)
topic hemoprotein
ligand
oxygen
truncated hemoglobin
kinetics
metabolism
Hemeproteins
Kinetics
Ligands
Oxygen
Truncated Hemoglobins
spellingShingle hemoprotein
ligand
oxygen
truncated hemoglobin
kinetics
metabolism
Hemeproteins
Kinetics
Ligands
Oxygen
Truncated Hemoglobins
Bustamante, Juan Pablo
Sued, Mariela
Martí, Marcelo Adrián
Estrin, Dario Ariel
Boechi, Leonardo
A quantitative model for oxygen uptake and release in a family of hemeproteins
topic_facet hemoprotein
ligand
oxygen
truncated hemoglobin
kinetics
metabolism
Hemeproteins
Kinetics
Ligands
Oxygen
Truncated Hemoglobins
description Motivation: Hemeproteins have many diverse functions that largely depend on the rate at which they uptake or release small ligands, like oxygen. These proteins have been extensively studied using either simulations or experiments, albeit only qualitatively and one or two proteins at a time. Results: We present a physical-chemical model, which uses data obtained exclusively from computer simulations, to describe the uptake and release of oxygen in a family of hemeproteins, called truncated hemoglobins (trHbs). Through a rigorous statistical analysis we demonstrate that our model successfully recaptures all the reported experimental oxygen association and dissociation kinetic rate constants, thus allowing us to establish the key factors that determine the rates at which these hemeproteins uptake and release oxygen. We found that internal tunnels as well as the distal site water molecules control ligand uptake, whereas oxygen stabilization by distal site residues controls ligand release. Because these rates largely determine the functions of these hemeproteins, these approaches will also be important tools in characterizing the trHbs members with unknown functions. © 2016 The Author 2016.
author Bustamante, Juan Pablo
Sued, Mariela
Martí, Marcelo Adrián
Estrin, Dario Ariel
Boechi, Leonardo
author_facet Bustamante, Juan Pablo
Sued, Mariela
Martí, Marcelo Adrián
Estrin, Dario Ariel
Boechi, Leonardo
author_sort Bustamante, Juan Pablo
title A quantitative model for oxygen uptake and release in a family of hemeproteins
title_short A quantitative model for oxygen uptake and release in a family of hemeproteins
title_full A quantitative model for oxygen uptake and release in a family of hemeproteins
title_fullStr A quantitative model for oxygen uptake and release in a family of hemeproteins
title_full_unstemmed A quantitative model for oxygen uptake and release in a family of hemeproteins
title_sort quantitative model for oxygen uptake and release in a family of hemeproteins
publishDate 2016
url https://bibliotecadigital.exactas.uba.ar/collection/paper/document/paper_13674803_v32_n12_p1805_Bustamante
http://hdl.handle.net/20.500.12110/paper_13674803_v32_n12_p1805_Bustamante
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