Access and Binding of H2S to Hemeproteins: The Case of HbI of Lucina pectinata
Hydrogen sulfide (H2S) was recently discovered as a gasotransmitter, capable of coordinating to the heme iron of hemeproteins. H2S is unique for its ability to render varying concentrations of the nucleophilic conjugate bases (HS- or S2-), either as free or bound species with expected outcomes on it...
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2016
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paper:paper_15206106_v120_n36_p9642_Boubeta2023-06-08T16:19:11Z Access and Binding of H2S to Hemeproteins: The Case of HbI of Lucina pectinata Boubeta, Fernando Martin Bari, Sara Elizabeth Estrin, Dario Ariel Boechi, Leonardo Ligands Molecules Active site Binding process Bound species Clustered water Coordinated ligands Heme-proteins Lucina pectinata Nucleophilic conjugate basis Bins hemoglobin hemoprotein hydrogen sulfide animal binding site bivalve chemistry conformation molecular dynamics Animals Binding Sites Bivalvia Hemeproteins Hemoglobins Hydrogen Sulfide Molecular Conformation Molecular Dynamics Simulation Hydrogen sulfide (H2S) was recently discovered as a gasotransmitter, capable of coordinating to the heme iron of hemeproteins. H2S is unique for its ability to render varying concentrations of the nucleophilic conjugate bases (HS- or S2-), either as free or bound species with expected outcomes on its further reactivity. There is no direct evidence about which species (H2S, HS-, or S2-) coordinates to the iron. We performed computer simulations to address the migration and binding processes of H2S species to the hemoglobin I of Lucina pectinata, which exhibits the highest affinity for the substrate measured to date. We found that H2S is the most favorable species in the migration from the bulk to the active site, through an internal pathway of the protein. After the coordination of H2S, an array of clustered water molecules modifies the active site environment, and assists in the subsequent deprotonation of the ligand, forming Fe(III)-SH-. The feasibility of the second deprotonation of the coordinated ligand is also discussed. © 2016 American Chemical Society. Fil:Boubeta, F.M. Universidad de Buenos Aires. Facultad de Ciencias Exactas y Naturales; Argentina. Fil:Bari, S.E. 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_15206106_v120_n36_p9642_Boubeta http://hdl.handle.net/20.500.12110/paper_15206106_v120_n36_p9642_Boubeta |
| institution |
Universidad de Buenos Aires |
| institution_str |
I-28 |
| repository_str |
R-134 |
| collection |
Biblioteca Digital - Facultad de Ciencias Exactas y Naturales (UBA) |
| topic |
Ligands Molecules Active site Binding process Bound species Clustered water Coordinated ligands Heme-proteins Lucina pectinata Nucleophilic conjugate basis Bins hemoglobin hemoprotein hydrogen sulfide animal binding site bivalve chemistry conformation molecular dynamics Animals Binding Sites Bivalvia Hemeproteins Hemoglobins Hydrogen Sulfide Molecular Conformation Molecular Dynamics Simulation |
| spellingShingle |
Ligands Molecules Active site Binding process Bound species Clustered water Coordinated ligands Heme-proteins Lucina pectinata Nucleophilic conjugate basis Bins hemoglobin hemoprotein hydrogen sulfide animal binding site bivalve chemistry conformation molecular dynamics Animals Binding Sites Bivalvia Hemeproteins Hemoglobins Hydrogen Sulfide Molecular Conformation Molecular Dynamics Simulation Boubeta, Fernando Martin Bari, Sara Elizabeth Estrin, Dario Ariel Boechi, Leonardo Access and Binding of H2S to Hemeproteins: The Case of HbI of Lucina pectinata |
| topic_facet |
Ligands Molecules Active site Binding process Bound species Clustered water Coordinated ligands Heme-proteins Lucina pectinata Nucleophilic conjugate basis Bins hemoglobin hemoprotein hydrogen sulfide animal binding site bivalve chemistry conformation molecular dynamics Animals Binding Sites Bivalvia Hemeproteins Hemoglobins Hydrogen Sulfide Molecular Conformation Molecular Dynamics Simulation |
| description |
Hydrogen sulfide (H2S) was recently discovered as a gasotransmitter, capable of coordinating to the heme iron of hemeproteins. H2S is unique for its ability to render varying concentrations of the nucleophilic conjugate bases (HS- or S2-), either as free or bound species with expected outcomes on its further reactivity. There is no direct evidence about which species (H2S, HS-, or S2-) coordinates to the iron. We performed computer simulations to address the migration and binding processes of H2S species to the hemoglobin I of Lucina pectinata, which exhibits the highest affinity for the substrate measured to date. We found that H2S is the most favorable species in the migration from the bulk to the active site, through an internal pathway of the protein. After the coordination of H2S, an array of clustered water molecules modifies the active site environment, and assists in the subsequent deprotonation of the ligand, forming Fe(III)-SH-. The feasibility of the second deprotonation of the coordinated ligand is also discussed. © 2016 American Chemical Society. |
| author |
Boubeta, Fernando Martin Bari, Sara Elizabeth Estrin, Dario Ariel Boechi, Leonardo |
| author_facet |
Boubeta, Fernando Martin Bari, Sara Elizabeth Estrin, Dario Ariel Boechi, Leonardo |
| author_sort |
Boubeta, Fernando Martin |
| title |
Access and Binding of H2S to Hemeproteins: The Case of HbI of Lucina pectinata |
| title_short |
Access and Binding of H2S to Hemeproteins: The Case of HbI of Lucina pectinata |
| title_full |
Access and Binding of H2S to Hemeproteins: The Case of HbI of Lucina pectinata |
| title_fullStr |
Access and Binding of H2S to Hemeproteins: The Case of HbI of Lucina pectinata |
| title_full_unstemmed |
Access and Binding of H2S to Hemeproteins: The Case of HbI of Lucina pectinata |
| title_sort |
access and binding of h2s to hemeproteins: the case of hbi of lucina pectinata |
| publishDate |
2016 |
| url |
https://bibliotecadigital.exactas.uba.ar/collection/paper/document/paper_15206106_v120_n36_p9642_Boubeta http://hdl.handle.net/20.500.12110/paper_15206106_v120_n36_p9642_Boubeta |
| work_keys_str_mv |
AT boubetafernandomartin accessandbindingofh2stohemeproteinsthecaseofhbioflucinapectinata AT barisaraelizabeth accessandbindingofh2stohemeproteinsthecaseofhbioflucinapectinata AT estrindarioariel accessandbindingofh2stohemeproteinsthecaseofhbioflucinapectinata AT boechileonardo accessandbindingofh2stohemeproteinsthecaseofhbioflucinapectinata |
| _version_ |
1768546739229294592 |