H-bonding networks of the distal residues and water molecules in the active site of Thermobifida fusca hemoglobin

Autores
Nicoletti, Francesco P.; Droghetti, Enrica; Howes, Barry D.; Bustamante, Juan Pablo; Bonamore, Alessandra; Sciamanna, Natascia; Estrin, Dario Ariel; Feis, Alessandro; Boffi, Alberto; Smulevich, Giulietta
Año de publicación
2013
Idioma
inglés
Tipo de recurso
artículo
Estado
versión publicada
Descripción
The ferric form of truncated hemoglobin II from Thermobifida fusca (Tf-trHb) and its triple mutant WG8F-YB10F-YCD1F at neutral and alkaline pH, and in the presence of CN− have been characterized by resonance Raman spectroscopy, electron paramagnetic resonance spectroscopy, and molecular dynamics simulations. Tf-trHb contains three polar residues in the distal site, namely TrpG8, TyrCD1 and TyrB10. Whereas TrpG8 can act as a potential hydrogen-bond donor, the tyrosines can act as donors or acceptors. Ligand binding in heme-containing proteins is determined by a number of factors, including the nature and conformation of the distal residues and their capability to stabilize the heme-bound ligand via hydrogen-bonding and electrostatic interactions. Since both the RR Fe-OH− and Fe-CN− frequencies are very sensitive to the distal environment, detailed information on structural variations has been obtained. The hydroxyl ligand binds only the WT protein giving rise to two different conformers. In form 1 the anion is stabilized by H-bonds with TrpG8, TyrCD1 and a water molecule, in turn H-bonded to TyrB10. In form 2, H-bonding with TyrCD1 is mediated by a water molecule. Unlike the OH− ligand, CN− binds both WT and the triple mutant giving rise to two forms with similar spectroscopic characteristics. The overall results clearly indicate that H-bonding interactions both with distal residues and water molecules are important structural determinants in the active site of Tf-trHb.
Fil: Nicoletti, Francesco P.. Universita Degli Studi Di Firenze; Italia
Fil: Droghetti, Enrica. Universita Degli Studi Di Firenze; Italia
Fil: Howes, Barry D.. Universita Degli Studi Di Firenze; Italia
Fil: Bustamante, Juan Pablo. Consejo Nacional de Investigaciones Científicas y Técnicas. Oficina de Coordinación Administrativa Ciudad Universitaria. Instituto de Química, Física de Los Materiales, Medioambiente y Energía; Argentina. Universidad de Buenos Aires; Argentina
Fil: Bonamore, Alessandra. Universita Di Roma; Italia
Fil: Sciamanna, Natascia. Universita Di Roma; Italia
Fil: Estrin, Dario Ariel. Consejo Nacional de Investigaciones Científicas y Técnicas. Oficina de Coordinación Administrativa Ciudad Universitaria. Instituto de Química, Física de Los Materiales, Medioambiente y Energía; Argentina. Universidad de Buenos Aires; Argentina
Fil: Feis, Alessandro. Universita Degli Studi Di Firenze; Italia
Fil: Boffi, Alberto. Universita Di Roma; Italia. Centro Nazionale di Ricerca. Institute Pasteur; Italia
Fil: Smulevich, Giulietta. Universita Degli Studi Di Firenze; Italia
Materia
Resonance Raman
Molecular Dynamics Simulations
Thermobifida Fusca Hemoglobin
Hydroxyl Ligand
Cyanide Ligand
Nivel de accesibilidad
acceso abierto
Condiciones de uso
https://creativecommons.org/licenses/by-nc-sa/2.5/ar/
Repositorio
CONICET Digital (CONICET)
Institución
Consejo Nacional de Investigaciones Científicas y Técnicas
OAI Identificador
oai:ri.conicet.gov.ar:11336/7971
Acceder
id CONICETDig_8c15012009d71cf450647b2604d12c60
oai_identifier_str oai:ri.conicet.gov.ar:11336/7971
network_acronym_str CONICETDig
repository_id_str 3498
network_name_str CONICET Digital (CONICET)
spelling H-bonding networks of the distal residues and water molecules in the active site of Thermobifida fusca hemoglobinNicoletti, Francesco P.Droghetti, EnricaHowes, Barry D.Bustamante, Juan PabloBonamore, AlessandraSciamanna, NatasciaEstrin, Dario ArielFeis, AlessandroBoffi, AlbertoSmulevich, GiuliettaResonance RamanMolecular Dynamics SimulationsThermobifida Fusca HemoglobinHydroxyl LigandCyanide Ligandhttps://purl.org/becyt/ford/1.4https://purl.org/becyt/ford/1The ferric form of truncated hemoglobin II from Thermobifida fusca (Tf-trHb) and its triple mutant WG8F-YB10F-YCD1F at neutral and alkaline pH, and in the presence of CN− have been characterized by resonance Raman spectroscopy, electron paramagnetic resonance spectroscopy, and molecular dynamics simulations. Tf-trHb contains three polar residues in the distal site, namely TrpG8, TyrCD1 and TyrB10. Whereas TrpG8 can act as a potential hydrogen-bond donor, the tyrosines can act as donors or acceptors. Ligand binding in heme-containing proteins is determined by a number of factors, including the nature and conformation of the distal residues and their capability to stabilize the heme-bound ligand via hydrogen-bonding and electrostatic interactions. Since both the RR Fe-OH− and Fe-CN− frequencies are very sensitive to the distal environment, detailed information on structural variations has been obtained. The hydroxyl ligand binds only the WT protein giving rise to two different conformers. In form 1 the anion is stabilized by H-bonds with TrpG8, TyrCD1 and a water molecule, in turn H-bonded to TyrB10. In form 2, H-bonding with TyrCD1 is mediated by a water molecule. Unlike the OH− ligand, CN− binds both WT and the triple mutant giving rise to two forms with similar spectroscopic characteristics. The overall results clearly indicate that H-bonding interactions both with distal residues and water molecules are important structural determinants in the active site of Tf-trHb.Fil: Nicoletti, Francesco P.. Universita Degli Studi Di Firenze; ItaliaFil: Droghetti, Enrica. Universita Degli Studi Di Firenze; ItaliaFil: Howes, Barry D.. Universita Degli Studi Di Firenze; ItaliaFil: Bustamante, Juan Pablo. Consejo Nacional de Investigaciones Científicas y Técnicas. Oficina de Coordinación Administrativa Ciudad Universitaria. Instituto de Química, Física de Los Materiales, Medioambiente y Energía; Argentina. Universidad de Buenos Aires; ArgentinaFil: Bonamore, Alessandra. Universita Di Roma; ItaliaFil: Sciamanna, Natascia. Universita Di Roma; ItaliaFil: Estrin, Dario Ariel. Consejo Nacional de Investigaciones Científicas y Técnicas. Oficina de Coordinación Administrativa Ciudad Universitaria. Instituto de Química, Física de Los Materiales, Medioambiente y Energía; Argentina. Universidad de Buenos Aires; ArgentinaFil: Feis, Alessandro. Universita Degli Studi Di Firenze; ItaliaFil: Boffi, Alberto. Universita Di Roma; Italia. Centro Nazionale di Ricerca. Institute Pasteur; ItaliaFil: Smulevich, Giulietta. Universita Degli Studi Di Firenze; ItaliaElsevier Science2013-02info:eu-repo/semantics/articleinfo:eu-repo/semantics/publishedVersionhttp://purl.org/coar/resource_type/c_6501info:ar-repo/semantics/articuloapplication/pdfapplication/pdfhttp://hdl.handle.net/11336/7971Nicoletti, Francesco P.; Droghetti, Enrica; Howes, Barry D.; Bustamante, Juan Pablo; Bonamore, Alessandra; et al.; H-bonding networks of the distal residues and water molecules in the active site of Thermobifida fusca hemoglobin; Elsevier Science; Biochimica Et Biophysica Acta-proteins And Proteomics; 1834; 9; 2-2013; 315-3241570-9639enginfo:eu-repo/semantics/altIdentifier/url/http://www.doi.org/10.1016/j.bbapap.2013.02.033info:eu-repo/semantics/altIdentifier/url/http://www.sciencedirect.com/science/article/pii/S1570963913001040info:eu-repo/semantics/openAccesshttps://creativecommons.org/licenses/by-nc-sa/2.5/ar/reponame:CONICET Digital (CONICET)instname:Consejo Nacional de Investigaciones Científicas y Técnicas2025-09-29T10:15:44Zoai:ri.conicet.gov.ar:11336/7971instacron:CONICETInstitucionalhttp://ri.conicet.gov.ar/Organismo científico-tecnológicoNo correspondehttp://ri.conicet.gov.ar/oai/requestdasensio@conicet.gov.ar; lcarlino@conicet.gov.arArgentinaNo correspondeNo correspondeNo correspondeopendoar:34982025-09-29 10:15:44.932CONICET Digital (CONICET) - Consejo Nacional de Investigaciones Científicas y Técnicasfalse
dc.title.none.fl_str_mv H-bonding networks of the distal residues and water molecules in the active site of Thermobifida fusca hemoglobin
title H-bonding networks of the distal residues and water molecules in the active site of Thermobifida fusca hemoglobin
spellingShingle H-bonding networks of the distal residues and water molecules in the active site of Thermobifida fusca hemoglobin
Nicoletti, Francesco P.
Resonance Raman
Molecular Dynamics Simulations
Thermobifida Fusca Hemoglobin
Hydroxyl Ligand
Cyanide Ligand
title_short H-bonding networks of the distal residues and water molecules in the active site of Thermobifida fusca hemoglobin
title_full H-bonding networks of the distal residues and water molecules in the active site of Thermobifida fusca hemoglobin
title_fullStr H-bonding networks of the distal residues and water molecules in the active site of Thermobifida fusca hemoglobin
title_full_unstemmed H-bonding networks of the distal residues and water molecules in the active site of Thermobifida fusca hemoglobin
title_sort H-bonding networks of the distal residues and water molecules in the active site of Thermobifida fusca hemoglobin
dc.creator.none.fl_str_mv Nicoletti, Francesco P.
Droghetti, Enrica
Howes, Barry D.
Bustamante, Juan Pablo
Bonamore, Alessandra
Sciamanna, Natascia
Estrin, Dario Ariel
Feis, Alessandro
Boffi, Alberto
Smulevich, Giulietta
author Nicoletti, Francesco P.
author_facet Nicoletti, Francesco P.
Droghetti, Enrica
Howes, Barry D.
Bustamante, Juan Pablo
Bonamore, Alessandra
Sciamanna, Natascia
Estrin, Dario Ariel
Feis, Alessandro
Boffi, Alberto
Smulevich, Giulietta
author_role author
author2 Droghetti, Enrica
Howes, Barry D.
Bustamante, Juan Pablo
Bonamore, Alessandra
Sciamanna, Natascia
Estrin, Dario Ariel
Feis, Alessandro
Boffi, Alberto
Smulevich, Giulietta
author2_role author
author
author
author
author
author
author
author
author
dc.subject.none.fl_str_mv Resonance Raman
Molecular Dynamics Simulations
Thermobifida Fusca Hemoglobin
Hydroxyl Ligand
Cyanide Ligand
topic Resonance Raman
Molecular Dynamics Simulations
Thermobifida Fusca Hemoglobin
Hydroxyl Ligand
Cyanide Ligand
purl_subject.fl_str_mv https://purl.org/becyt/ford/1.4
https://purl.org/becyt/ford/1
dc.description.none.fl_txt_mv The ferric form of truncated hemoglobin II from Thermobifida fusca (Tf-trHb) and its triple mutant WG8F-YB10F-YCD1F at neutral and alkaline pH, and in the presence of CN− have been characterized by resonance Raman spectroscopy, electron paramagnetic resonance spectroscopy, and molecular dynamics simulations. Tf-trHb contains three polar residues in the distal site, namely TrpG8, TyrCD1 and TyrB10. Whereas TrpG8 can act as a potential hydrogen-bond donor, the tyrosines can act as donors or acceptors. Ligand binding in heme-containing proteins is determined by a number of factors, including the nature and conformation of the distal residues and their capability to stabilize the heme-bound ligand via hydrogen-bonding and electrostatic interactions. Since both the RR Fe-OH− and Fe-CN− frequencies are very sensitive to the distal environment, detailed information on structural variations has been obtained. The hydroxyl ligand binds only the WT protein giving rise to two different conformers. In form 1 the anion is stabilized by H-bonds with TrpG8, TyrCD1 and a water molecule, in turn H-bonded to TyrB10. In form 2, H-bonding with TyrCD1 is mediated by a water molecule. Unlike the OH− ligand, CN− binds both WT and the triple mutant giving rise to two forms with similar spectroscopic characteristics. The overall results clearly indicate that H-bonding interactions both with distal residues and water molecules are important structural determinants in the active site of Tf-trHb.
Fil: Nicoletti, Francesco P.. Universita Degli Studi Di Firenze; Italia
Fil: Droghetti, Enrica. Universita Degli Studi Di Firenze; Italia
Fil: Howes, Barry D.. Universita Degli Studi Di Firenze; Italia
Fil: Bustamante, Juan Pablo. Consejo Nacional de Investigaciones Científicas y Técnicas. Oficina de Coordinación Administrativa Ciudad Universitaria. Instituto de Química, Física de Los Materiales, Medioambiente y Energía; Argentina. Universidad de Buenos Aires; Argentina
Fil: Bonamore, Alessandra. Universita Di Roma; Italia
Fil: Sciamanna, Natascia. Universita Di Roma; Italia
Fil: Estrin, Dario Ariel. Consejo Nacional de Investigaciones Científicas y Técnicas. Oficina de Coordinación Administrativa Ciudad Universitaria. Instituto de Química, Física de Los Materiales, Medioambiente y Energía; Argentina. Universidad de Buenos Aires; Argentina
Fil: Feis, Alessandro. Universita Degli Studi Di Firenze; Italia
Fil: Boffi, Alberto. Universita Di Roma; Italia. Centro Nazionale di Ricerca. Institute Pasteur; Italia
Fil: Smulevich, Giulietta. Universita Degli Studi Di Firenze; Italia
description The ferric form of truncated hemoglobin II from Thermobifida fusca (Tf-trHb) and its triple mutant WG8F-YB10F-YCD1F at neutral and alkaline pH, and in the presence of CN− have been characterized by resonance Raman spectroscopy, electron paramagnetic resonance spectroscopy, and molecular dynamics simulations. Tf-trHb contains three polar residues in the distal site, namely TrpG8, TyrCD1 and TyrB10. Whereas TrpG8 can act as a potential hydrogen-bond donor, the tyrosines can act as donors or acceptors. Ligand binding in heme-containing proteins is determined by a number of factors, including the nature and conformation of the distal residues and their capability to stabilize the heme-bound ligand via hydrogen-bonding and electrostatic interactions. Since both the RR Fe-OH− and Fe-CN− frequencies are very sensitive to the distal environment, detailed information on structural variations has been obtained. The hydroxyl ligand binds only the WT protein giving rise to two different conformers. In form 1 the anion is stabilized by H-bonds with TrpG8, TyrCD1 and a water molecule, in turn H-bonded to TyrB10. In form 2, H-bonding with TyrCD1 is mediated by a water molecule. Unlike the OH− ligand, CN− binds both WT and the triple mutant giving rise to two forms with similar spectroscopic characteristics. The overall results clearly indicate that H-bonding interactions both with distal residues and water molecules are important structural determinants in the active site of Tf-trHb.
publishDate 2013
dc.date.none.fl_str_mv 2013-02
dc.type.none.fl_str_mv info:eu-repo/semantics/article
info:eu-repo/semantics/publishedVersion
http://purl.org/coar/resource_type/c_6501
info:ar-repo/semantics/articulo
format article
status_str publishedVersion
dc.identifier.none.fl_str_mv http://hdl.handle.net/11336/7971
Nicoletti, Francesco P.; Droghetti, Enrica; Howes, Barry D.; Bustamante, Juan Pablo; Bonamore, Alessandra; et al.; H-bonding networks of the distal residues and water molecules in the active site of Thermobifida fusca hemoglobin; Elsevier Science; Biochimica Et Biophysica Acta-proteins And Proteomics; 1834; 9; 2-2013; 315-324
1570-9639
url http://hdl.handle.net/11336/7971
identifier_str_mv Nicoletti, Francesco P.; Droghetti, Enrica; Howes, Barry D.; Bustamante, Juan Pablo; Bonamore, Alessandra; et al.; H-bonding networks of the distal residues and water molecules in the active site of Thermobifida fusca hemoglobin; Elsevier Science; Biochimica Et Biophysica Acta-proteins And Proteomics; 1834; 9; 2-2013; 315-324
1570-9639
dc.language.none.fl_str_mv eng
language eng
dc.relation.none.fl_str_mv info:eu-repo/semantics/altIdentifier/url/http://www.doi.org/10.1016/j.bbapap.2013.02.033
info:eu-repo/semantics/altIdentifier/url/http://www.sciencedirect.com/science/article/pii/S1570963913001040
dc.rights.none.fl_str_mv info:eu-repo/semantics/openAccess
https://creativecommons.org/licenses/by-nc-sa/2.5/ar/
eu_rights_str_mv openAccess
rights_invalid_str_mv https://creativecommons.org/licenses/by-nc-sa/2.5/ar/
dc.format.none.fl_str_mv application/pdf
application/pdf
dc.publisher.none.fl_str_mv Elsevier Science
publisher.none.fl_str_mv Elsevier Science
dc.source.none.fl_str_mv reponame:CONICET Digital (CONICET)
instname:Consejo Nacional de Investigaciones Científicas y Técnicas
reponame_str CONICET Digital (CONICET)
collection CONICET Digital (CONICET)
instname_str Consejo Nacional de Investigaciones Científicas y Técnicas
repository.name.fl_str_mv CONICET Digital (CONICET) - Consejo Nacional de Investigaciones Científicas y Técnicas
repository.mail.fl_str_mv dasensio@conicet.gov.ar; lcarlino@conicet.gov.ar
_version_ 1844614095788048384
score 13.070432

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