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

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 sim...

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Autores principales:	Bustamante, Juan Pablo, Estrin, Dario Ariel
Publicado:	2013
Materias:	Cyanide ligand Hydrogen-bond Hydroxyl ligand Resonance Raman Truncated hemoglobin cyanide hydroxyl group ligand truncated hemoglobin tyrosine water heme hemoglobin hydroxide hydroxide ion myoglobin alkalinity article electron spin resonance hydrogen bond ligand binding molecular dynamics molecule nonhuman priority journal Raman spectrometry static electricity Thermobifida fusca 2-(N-morpholino)ethanesulfonic acid 5c 6c acidic surface variant of Tf-trHb containing two single site mutations Phe107Glu and Arg91Glu Actinomycetales ASV enzyme active site five-coordinate genetics high spin HS low spin LS Mb MD MES metabolism pH protein binding RR six-coordinate Tf trHb wild type WT electron paramagnetic resonance EPR Hb resonance Raman Catalytic Domain Cyanides Heme Hemoglobins Hydrogen Bonding Hydrogen-Ion Concentration Hydroxides Molecular Dynamics Simulation Protein Binding Spectrum Analysis, Raman Tyrosine Water
Acceso en línea:	https://bibliotecadigital.exactas.uba.ar/collection/paper/document/paper_15709639_v1834_n9_p1901_Nicoletti http://hdl.handle.net/20.500.12110/paper_15709639_v1834_n9_p1901_Nicoletti
Aporte de:	Biblioteca Digital - Facultad de Ciencias Exactas y Naturales (UBA) de Universidad de Buenos Aires

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spelling	paper:paper_15709639_v1834_n9_p1901_Nicoletti2023-06-08T16:24:17Z H-bonding networks of the distal residues and water molecules in the active site of Thermobifida fusca hemoglobin Bustamante, Juan Pablo Estrin, Dario Ariel Cyanide ligand Hydrogen-bond Hydroxyl ligand Resonance Raman Truncated hemoglobin cyanide hydroxyl group ligand truncated hemoglobin tyrosine water cyanide heme hemoglobin hydroxide hydroxide ion myoglobin truncated hemoglobin alkalinity article electron spin resonance hydrogen bond ligand binding molecular dynamics molecule nonhuman priority journal Raman spectrometry static electricity Thermobifida fusca 2-(N-morpholino)ethanesulfonic acid 5c 6c acidic surface variant of Tf-trHb containing two single site mutations Phe107Glu and Arg91Glu Actinomycetales ASV Cyanide ligand enzyme active site five-coordinate genetics high spin HS hydrogen bond Hydrogen-bond Hydroxyl ligand low spin LS Mb MD MES metabolism pH protein binding Resonance Raman RR six-coordinate Tf Thermobifida fusca trHb wild type WT Thermobifida fusca 2-(N-morpholino)ethanesulfonic acid 5c 6c acidic surface variant of Tf-trHb containing two single site mutations Phe107Glu and Arg91Glu ASV Cyanide ligand electron paramagnetic resonance EPR five-coordinate Hb hemoglobin high spin HS Hydrogen-bond Hydroxyl ligand low spin LS Mb MD MES molecular dynamics myoglobin Resonance Raman resonance Raman RR six-coordinate Tf Thermobifida fusca trHb truncated hemoglobin Truncated hemoglobin wild type WT Actinomycetales Catalytic Domain Cyanides Heme Hemoglobins Hydrogen Bonding Hydrogen-Ion Concentration Hydroxides Molecular Dynamics Simulation Protein Binding Spectrum Analysis, Raman Tyrosine Water 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 residuesin 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, inturn 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. This article is part of a Special Issue entitled: Oxygen Binding and Sensing Proteins. © 2013 Elsevier B.V. All rights reserved. Fil:Bustamante, J.P. 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_15709639_v1834_n9_p1901_Nicoletti http://hdl.handle.net/20.500.12110/paper_15709639_v1834_n9_p1901_Nicoletti
institution	Universidad de Buenos Aires
institution_str	I-28
repository_str	R-134
collection	Biblioteca Digital - Facultad de Ciencias Exactas y Naturales (UBA)
topic	Cyanide ligand Hydrogen-bond Hydroxyl ligand Resonance Raman Truncated hemoglobin cyanide hydroxyl group ligand truncated hemoglobin tyrosine water cyanide heme hemoglobin hydroxide hydroxide ion myoglobin truncated hemoglobin alkalinity article electron spin resonance hydrogen bond ligand binding molecular dynamics molecule nonhuman priority journal Raman spectrometry static electricity Thermobifida fusca 2-(N-morpholino)ethanesulfonic acid 5c 6c acidic surface variant of Tf-trHb containing two single site mutations Phe107Glu and Arg91Glu Actinomycetales ASV Cyanide ligand enzyme active site five-coordinate genetics high spin HS hydrogen bond Hydrogen-bond Hydroxyl ligand low spin LS Mb MD MES metabolism pH protein binding Resonance Raman RR six-coordinate Tf Thermobifida fusca trHb wild type WT Thermobifida fusca 2-(N-morpholino)ethanesulfonic acid 5c 6c acidic surface variant of Tf-trHb containing two single site mutations Phe107Glu and Arg91Glu ASV Cyanide ligand electron paramagnetic resonance EPR five-coordinate Hb hemoglobin high spin HS Hydrogen-bond Hydroxyl ligand low spin LS Mb MD MES molecular dynamics myoglobin Resonance Raman resonance Raman RR six-coordinate Tf Thermobifida fusca trHb truncated hemoglobin Truncated hemoglobin wild type WT Actinomycetales Catalytic Domain Cyanides Heme Hemoglobins Hydrogen Bonding Hydrogen-Ion Concentration Hydroxides Molecular Dynamics Simulation Protein Binding Spectrum Analysis, Raman Tyrosine Water
spellingShingle	Cyanide ligand Hydrogen-bond Hydroxyl ligand Resonance Raman Truncated hemoglobin cyanide hydroxyl group ligand truncated hemoglobin tyrosine water cyanide heme hemoglobin hydroxide hydroxide ion myoglobin truncated hemoglobin alkalinity article electron spin resonance hydrogen bond ligand binding molecular dynamics molecule nonhuman priority journal Raman spectrometry static electricity Thermobifida fusca 2-(N-morpholino)ethanesulfonic acid 5c 6c acidic surface variant of Tf-trHb containing two single site mutations Phe107Glu and Arg91Glu Actinomycetales ASV Cyanide ligand enzyme active site five-coordinate genetics high spin HS hydrogen bond Hydrogen-bond Hydroxyl ligand low spin LS Mb MD MES metabolism pH protein binding Resonance Raman RR six-coordinate Tf Thermobifida fusca trHb wild type WT Thermobifida fusca 2-(N-morpholino)ethanesulfonic acid 5c 6c acidic surface variant of Tf-trHb containing two single site mutations Phe107Glu and Arg91Glu ASV Cyanide ligand electron paramagnetic resonance EPR five-coordinate Hb hemoglobin high spin HS Hydrogen-bond Hydroxyl ligand low spin LS Mb MD MES molecular dynamics myoglobin Resonance Raman resonance Raman RR six-coordinate Tf Thermobifida fusca trHb truncated hemoglobin Truncated hemoglobin wild type WT Actinomycetales Catalytic Domain Cyanides Heme Hemoglobins Hydrogen Bonding Hydrogen-Ion Concentration Hydroxides Molecular Dynamics Simulation Protein Binding Spectrum Analysis, Raman Tyrosine Water Bustamante, Juan Pablo Estrin, Dario Ariel H-bonding networks of the distal residues and water molecules in the active site of Thermobifida fusca hemoglobin
topic_facet	Cyanide ligand Hydrogen-bond Hydroxyl ligand Resonance Raman Truncated hemoglobin cyanide hydroxyl group ligand truncated hemoglobin tyrosine water cyanide heme hemoglobin hydroxide hydroxide ion myoglobin truncated hemoglobin alkalinity article electron spin resonance hydrogen bond ligand binding molecular dynamics molecule nonhuman priority journal Raman spectrometry static electricity Thermobifida fusca 2-(N-morpholino)ethanesulfonic acid 5c 6c acidic surface variant of Tf-trHb containing two single site mutations Phe107Glu and Arg91Glu Actinomycetales ASV Cyanide ligand enzyme active site five-coordinate genetics high spin HS hydrogen bond Hydrogen-bond Hydroxyl ligand low spin LS Mb MD MES metabolism pH protein binding Resonance Raman RR six-coordinate Tf Thermobifida fusca trHb wild type WT Thermobifida fusca 2-(N-morpholino)ethanesulfonic acid 5c 6c acidic surface variant of Tf-trHb containing two single site mutations Phe107Glu and Arg91Glu ASV Cyanide ligand electron paramagnetic resonance EPR five-coordinate Hb hemoglobin high spin HS Hydrogen-bond Hydroxyl ligand low spin LS Mb MD MES molecular dynamics myoglobin Resonance Raman resonance Raman RR six-coordinate Tf Thermobifida fusca trHb truncated hemoglobin Truncated hemoglobin wild type WT Actinomycetales Catalytic Domain Cyanides Heme Hemoglobins Hydrogen Bonding Hydrogen-Ion Concentration Hydroxides Molecular Dynamics Simulation Protein Binding Spectrum Analysis, Raman Tyrosine Water
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 residuesin 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, inturn 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. This article is part of a Special Issue entitled: Oxygen Binding and Sensing Proteins. © 2013 Elsevier B.V. All rights reserved.
author	Bustamante, Juan Pablo Estrin, Dario Ariel
author_facet	Bustamante, Juan Pablo Estrin, Dario Ariel
author_sort	Bustamante, Juan Pablo
title	H-bonding networks of the distal residues and water molecules in the active site of Thermobifida fusca hemoglobin
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
publishDate	2013
url	https://bibliotecadigital.exactas.uba.ar/collection/paper/document/paper_15709639_v1834_n9_p1901_Nicoletti http://hdl.handle.net/20.500.12110/paper_15709639_v1834_n9_p1901_Nicoletti
work_keys_str_mv	AT bustamantejuanpablo hbondingnetworksofthedistalresiduesandwatermoleculesintheactivesiteofthermobifidafuscahemoglobin AT estrindarioariel hbondingnetworksofthedistalresiduesandwatermoleculesintheactivesiteofthermobifidafuscahemoglobin
_version_	1768545207206281216

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

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