Back to Search
Start Over
H-bonding networks of the distal residues and water molecules in the active site of Thermobifida fusca hemoglobin
- Source :
- BBA-Biochimica et Biophysica Acta, BBA-Biochimica et Biophysica Acta, Elsevier, 2013, 1834 (9), pp.1901-9. ⟨10.1016/j.bbapap.2013.02.033⟩
- Publication Year :
- 2013
- Publisher :
- HAL CCSD, 2013.
-
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
- 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
Subjects
Details
- Language :
- English
- ISSN :
- 00063002
- Database :
- OpenAIRE
- Journal :
- BBA-Biochimica et Biophysica Acta, BBA-Biochimica et Biophysica Acta, Elsevier, 2013, 1834 (9), pp.1901-9. ⟨10.1016/j.bbapap.2013.02.033⟩
- Accession number :
- edsair.doi.dedup.....e820143440b15fab93cad3bdc74e3e14