1. H-bonding networks of the distal residues and water molecules in the active site of Thermobifida fusca hemoglobin
- Author
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Barry D. Howes, Darío A. Estrin, Alessandro Feis, Francesco P. Nicoletti, Natascia Sciamanna, Giulietta Smulevich, Alessandra Bonamore, Enrica Droghetti, Alberto Boffi, Juan Pablo Bustamante, Department of Chemistry 'Ugo Schiff', Università degli Studi di Firenze = University of Florence [Firenze] (UNIFI), Departamento de Química Inorgánica, Analítica y Química Física (DQIAQF), Facultad de Ciencias Exactas y Naturales [Buenos Aires] (FCEyN), Universidad de Buenos Aires [Buenos Aires] (UBA)-Universidad de Buenos Aires [Buenos Aires] (UBA), Department of Biochemical Sciences 'Rossi Fanelli', Institut Pasteur, Fondation Cenci Bolognetti - Istituto Pasteur Italia, Fondazione Cenci Bolognetti, Réseau International des Instituts Pasteur (RIIP)-Réseau International des Instituts Pasteur (RIIP)-Università degli Studi di Roma 'La Sapienza' = Sapienza University [Rome], and This work was supported by the Institute Pasteur Fondazione Cenci Bolognetti (A.Boffi), MIURFIRBRBFR08F41U_002(A.Bonamore),MIUR PRIN 2008BFj34 (A. Feis and A. Boffi), University of Buenos Aires (grantX074), CONICET and European Union FP7 project NOStress (D. Estrin), and the Italian Ministero dell'Istruzione, dell'Università e della Ricerca (MIUR), Direzione Generale per l'Internazionalizzazione della Ricerca, Progetti di Grande Rilevanza Italia-Argentina. We thank Dr Maria Fittipaldi for provision of EPR facilities and assistance in recording the spectra.
- Subjects
MESH: Hydrogen-Ion Concentration ,Físico-Química, Ciencia de los Polímeros, Electroquímica ,MESH: Catalytic Domain ,Spectrum Analysis, Raman ,01 natural sciences ,Biochemistry ,Analytical Chemistry ,law.invention ,MESH: Tyrosine ,Hemoglobins ,law ,Catalytic Domain ,Hydroxides ,MESH: Molecular Dynamics Simulation ,Electron paramagnetic resonance ,Conformational isomerism ,0303 health sciences ,010304 chemical physics ,biology ,Hydrogen bond ,Chemistry ,RESONANCE RAMAN ,Ciencias Químicas ,Hydrogen-Ion Concentration ,Ligand (biochemistry) ,CYANIDE LIGAND ,MESH: Hydroxides ,MESH: Hemoglobins ,MESH: Heme ,CIENCIAS NATURALES Y EXACTAS ,Protein Binding ,HYDROXYL LIGAND ,Stereochemistry ,Resonance Raman spectroscopy ,MOLECULAR DYNAMICS SIMULATIONS ,Biophysics ,Heme ,Molecular Dynamics Simulation ,THERMOBIFIDA FUSCA HEMOGLOBIN ,03 medical and health sciences ,MESH: Cyanides ,Actinomycetales ,0103 physical sciences ,MESH: Water ,Molecule ,MESH: Protein Binding ,[SDV.BBM]Life Sciences [q-bio]/Biochemistry, Molecular Biology ,MESH: Hydrogen Bonding ,Molecular Biology ,030304 developmental biology ,MESH: Spectrum Analysis, Raman ,Cyanides ,Water ,Active site ,Hydrogen Bonding ,MESH: Actinomycetales ,biology.protein ,Tyrosine ,Oxygen binding - Abstract
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
- Published
- 2013