Quaternary structure effects on the hexacoordination equilibrium in rice hemoglobin rHb1: Insights from molecular dynamics simulations

Nonsymbiotic hemoglobins (nsHbs) form a widely distributed class of plant proteins, which function remains unknown. Despite the fact that class 1 plant nonsymbiotic hemoglobins are hexacoordinate (6c) heme proteins (hxHbs), their hexacoordination equilibrium constants are much lower than in hxHbs fr...

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Autores principales:	Morzan, U.N., Capece, L., Marti, M.A., Estrin, D.A.
Formato:	JOUR
Materias:	Cytoglobin Heme protein Hexacoordination Molecular dynamics Neuroglobin Nonsymbiotic hemoglobins Plant hemoglobins Rice hemoglobin 1 Steered molecular dynamics dimer globin hemoglobin monomer rice hemoglobin 1 unclassified drug article circular dichroism controlled study crystal structure dimerization equilibrium constant hexacoordination equilibrium molecular dynamics nonhuman priority journal protein analysis protein function protein quaternary structure protein stability rice Globins Molecular Dynamics Simulation Oryza sativa Plant Proteins Protein Conformation Protein Multimerization Protein Structure, Quaternary Thermodynamics Animalia
Acceso en línea:	http://hdl.handle.net/20.500.12110/paper_08873585_v81_n5_p863_Morzan
Aporte de:	Biblioteca Digital - Facultad de Ciencias Exactas y Naturales (UBA) de Universidad de Buenos Aires

id	todo:paper_08873585_v81_n5_p863_Morzan
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spelling	todo:paper_08873585_v81_n5_p863_Morzan2023-10-03T15:40:53Z Quaternary structure effects on the hexacoordination equilibrium in rice hemoglobin rHb1: Insights from molecular dynamics simulations Morzan, U.N. Capece, L. Marti, M.A. Estrin, D.A. Cytoglobin Heme protein Hexacoordination Molecular dynamics Neuroglobin Nonsymbiotic hemoglobins Plant hemoglobins Rice hemoglobin 1 Steered molecular dynamics dimer globin hemoglobin monomer rice hemoglobin 1 unclassified drug article circular dichroism controlled study crystal structure dimerization equilibrium constant hexacoordination equilibrium molecular dynamics nonhuman priority journal protein analysis protein function protein quaternary structure protein stability rice Globins Molecular Dynamics Simulation Oryza sativa Plant Proteins Protein Conformation Protein Multimerization Protein Structure, Quaternary Thermodynamics Animalia Nonsymbiotic hemoglobins (nsHbs) form a widely distributed class of plant proteins, which function remains unknown. Despite the fact that class 1 plant nonsymbiotic hemoglobins are hexacoordinate (6c) heme proteins (hxHbs), their hexacoordination equilibrium constants are much lower than in hxHbs from animals or bacteria. In addition, they are characterized by having very high oxygen affinities and low oxygen dissociation rate constants. Rice hemoglobin 1 (rHb1) is a class 1 nonsymbiotic hemoglobin. It crystallizes as a fully associated homodimer with both subunits in 6c state, but showing slightly different conformations, thus leading to an asymmetric crystallographic homodimer. The residues that constitute the dimeric interface are conserved among all nsHbs, suggesting that the quaternary structure could be relevant to explain the chemical behavior and biological function of this family of proteins. In this work, we analyze the molecular basis that determine the hexacoordination equilibrium in rHb1. Our results indicate that dynamical features of the quaternary structure significantly affect the hexacoordination process. Specifically, we observe that the pentacoordinate state is stabilized in the dimer with respect to the isolated monomers. Moreover, the dimer behaves asymmetrically, in a negative cooperative scheme. The results presented in this work are fully consistent with our previous hypothesis about the key role played by the nature of the CD region in determining the coordination state of globins. © 2013 Wiley Periodicals, Inc. Fil:Morzan, U.N. 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:Marti, 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. JOUR info:eu-repo/semantics/openAccess http://creativecommons.org/licenses/by/2.5/ar http://hdl.handle.net/20.500.12110/paper_08873585_v81_n5_p863_Morzan
institution	Universidad de Buenos Aires
institution_str	I-28
repository_str	R-134
collection	Biblioteca Digital - Facultad de Ciencias Exactas y Naturales (UBA)
topic	Cytoglobin Heme protein Hexacoordination Molecular dynamics Neuroglobin Nonsymbiotic hemoglobins Plant hemoglobins Rice hemoglobin 1 Steered molecular dynamics dimer globin hemoglobin monomer rice hemoglobin 1 unclassified drug article circular dichroism controlled study crystal structure dimerization equilibrium constant hexacoordination equilibrium molecular dynamics nonhuman priority journal protein analysis protein function protein quaternary structure protein stability rice Globins Molecular Dynamics Simulation Oryza sativa Plant Proteins Protein Conformation Protein Multimerization Protein Structure, Quaternary Thermodynamics Animalia
spellingShingle	Cytoglobin Heme protein Hexacoordination Molecular dynamics Neuroglobin Nonsymbiotic hemoglobins Plant hemoglobins Rice hemoglobin 1 Steered molecular dynamics dimer globin hemoglobin monomer rice hemoglobin 1 unclassified drug article circular dichroism controlled study crystal structure dimerization equilibrium constant hexacoordination equilibrium molecular dynamics nonhuman priority journal protein analysis protein function protein quaternary structure protein stability rice Globins Molecular Dynamics Simulation Oryza sativa Plant Proteins Protein Conformation Protein Multimerization Protein Structure, Quaternary Thermodynamics Animalia Morzan, U.N. Capece, L. Marti, M.A. Estrin, D.A. Quaternary structure effects on the hexacoordination equilibrium in rice hemoglobin rHb1: Insights from molecular dynamics simulations
topic_facet	Cytoglobin Heme protein Hexacoordination Molecular dynamics Neuroglobin Nonsymbiotic hemoglobins Plant hemoglobins Rice hemoglobin 1 Steered molecular dynamics dimer globin hemoglobin monomer rice hemoglobin 1 unclassified drug article circular dichroism controlled study crystal structure dimerization equilibrium constant hexacoordination equilibrium molecular dynamics nonhuman priority journal protein analysis protein function protein quaternary structure protein stability rice Globins Molecular Dynamics Simulation Oryza sativa Plant Proteins Protein Conformation Protein Multimerization Protein Structure, Quaternary Thermodynamics Animalia
description	Nonsymbiotic hemoglobins (nsHbs) form a widely distributed class of plant proteins, which function remains unknown. Despite the fact that class 1 plant nonsymbiotic hemoglobins are hexacoordinate (6c) heme proteins (hxHbs), their hexacoordination equilibrium constants are much lower than in hxHbs from animals or bacteria. In addition, they are characterized by having very high oxygen affinities and low oxygen dissociation rate constants. Rice hemoglobin 1 (rHb1) is a class 1 nonsymbiotic hemoglobin. It crystallizes as a fully associated homodimer with both subunits in 6c state, but showing slightly different conformations, thus leading to an asymmetric crystallographic homodimer. The residues that constitute the dimeric interface are conserved among all nsHbs, suggesting that the quaternary structure could be relevant to explain the chemical behavior and biological function of this family of proteins. In this work, we analyze the molecular basis that determine the hexacoordination equilibrium in rHb1. Our results indicate that dynamical features of the quaternary structure significantly affect the hexacoordination process. Specifically, we observe that the pentacoordinate state is stabilized in the dimer with respect to the isolated monomers. Moreover, the dimer behaves asymmetrically, in a negative cooperative scheme. The results presented in this work are fully consistent with our previous hypothesis about the key role played by the nature of the CD region in determining the coordination state of globins. © 2013 Wiley Periodicals, Inc.
format	JOUR
author	Morzan, U.N. Capece, L. Marti, M.A. Estrin, D.A.
author_facet	Morzan, U.N. Capece, L. Marti, M.A. Estrin, D.A.
author_sort	Morzan, U.N.
title	Quaternary structure effects on the hexacoordination equilibrium in rice hemoglobin rHb1: Insights from molecular dynamics simulations
title_short	Quaternary structure effects on the hexacoordination equilibrium in rice hemoglobin rHb1: Insights from molecular dynamics simulations
title_full	Quaternary structure effects on the hexacoordination equilibrium in rice hemoglobin rHb1: Insights from molecular dynamics simulations
title_fullStr	Quaternary structure effects on the hexacoordination equilibrium in rice hemoglobin rHb1: Insights from molecular dynamics simulations
title_full_unstemmed	Quaternary structure effects on the hexacoordination equilibrium in rice hemoglobin rHb1: Insights from molecular dynamics simulations
title_sort	quaternary structure effects on the hexacoordination equilibrium in rice hemoglobin rhb1: insights from molecular dynamics simulations
url	http://hdl.handle.net/20.500.12110/paper_08873585_v81_n5_p863_Morzan
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Quaternary structure effects on the hexacoordination equilibrium in rice hemoglobin rHb1: Insights from molecular dynamics simulations

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