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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paper:paper_08873585_v81_n5_p863_Morzan2025-07-30T18:23:12Z Quaternary structure effects on the hexacoordination equilibrium in rice hemoglobin rHb1: Insights from molecular dynamics simulations Morzan, Uriel Nicolas Capece, Luciana Martí, Marcelo Adrián Estrin, Dario Ariel 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. 2013 https://bibliotecadigital.exactas.uba.ar/collection/paper/document/paper_08873585_v81_n5_p863_Morzan 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, Uriel Nicolas Capece, Luciana Martí, Marcelo Adrián Estrin, Dario Ariel 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. |
| author |
Morzan, Uriel Nicolas Capece, Luciana Martí, Marcelo Adrián Estrin, Dario Ariel |
| author_facet |
Morzan, Uriel Nicolas Capece, Luciana Martí, Marcelo Adrián Estrin, Dario Ariel |
| author_sort |
Morzan, Uriel Nicolas |
| 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 |
| publishDate |
2013 |
| url |
https://bibliotecadigital.exactas.uba.ar/collection/paper/document/paper_08873585_v81_n5_p863_Morzan http://hdl.handle.net/20.500.12110/paper_08873585_v81_n5_p863_Morzan |
| work_keys_str_mv |
AT morzanurielnicolas quaternarystructureeffectsonthehexacoordinationequilibriuminricehemoglobinrhb1insightsfrommoleculardynamicssimulations AT capeceluciana quaternarystructureeffectsonthehexacoordinationequilibriuminricehemoglobinrhb1insightsfrommoleculardynamicssimulations AT martimarceloadrian quaternarystructureeffectsonthehexacoordinationequilibriuminricehemoglobinrhb1insightsfrommoleculardynamicssimulations AT estrindarioariel quaternarystructureeffectsonthehexacoordinationequilibriuminricehemoglobinrhb1insightsfrommoleculardynamicssimulations |
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