Search

Your search keyword '"INTERNAL HYDROPHOBIC CAVITIES"' showing total 2 results
Start Over Descriptor "INTERNAL HYDROPHOBIC CAVITIES"
2 results on '"INTERNAL HYDROPHOBIC CAVITIES"'

1. Ligation Tunes Protein Reactivity in an Ancient Haemoglobin: Kinetic Evidence for an Allosteric Mechanism in Methanosarcina acetivorans Protoglobin

Author

Marco Nardini, Massimo Coletta, Paolo Ascenzi, Filip Desmet, Chiara Ciaccio, Cristiano Viappiani, Stefano Bruno, Luc Moens, Sabine Van Doorslaer, Sylvia Dewilde, Stefania Abbruzzetti, Martino Bolognesi, L. Tilleman, Abbruzzetti, S, Tilleman, L, Bruno, S, Viappiani, C, Desmet, F, Van Doorslaer, S, Coletta, M, Ciaccio, C, Ascenzi, Paolo, Nardini, M, Bolognesi, M, Moens, L, and Dewilde, S.

Subjects
HEME ENVIRONMENT, Stereochemistry, SILICA-GELS, Archaeal Proteins, Allosteric regulation, Kinetics, Biophysics, lcsh:Medicine, Plasma protein binding, Biochemistry, Dissociation (chemistry), Hemoglobins, Allosteric Regulation, BINDING, INTERNAL HYDROPHOBIC CAVITIES, Molecule, Globin, Ferrous Compounds, Methanosarcina acetivorans, Settore BIO/10, lcsh:Science, Biology, T STATE HEMOGLOBIN, Carbon Monoxide, Multidisciplinary, Photolysis, biology, Chemistry, Physics, lcsh:R, Proteins, Methanosarcina, biology.organism_classification, Recombinant Proteins, Enzymes, Globins, OXYGEN-AFFINITY, ARABIDOPSIS-THALIANA, lcsh:Q, GLOBIN-COUPLED SENSORS, Human medicine, Protein Multimerization, LIGAND MIGRATION, NEUROGLOBIN, Research Article, Protein Binding
Abstract

Protoglobin from Methanosarcina acetivorans (MaPgb) is a dimeric globin with peculiar structural properties such as a completely buried haem and two orthogonal tunnels connecting the distal cavity to the solvent. CO binding to and dissociation from MaPgb occur through a biphasic kinetics. We show that the heterogenous kinetics arises from binding to (and dissociation from) two tertiary conformations in ligation-dependent equilibrium. Ligation favours the species with high binding rate (and low dissociation rate). The equilibrium is shifted towards the species with low binding (and high dissociation) rates for the unliganded molecules. A quantitative model is proposed to describe the observed carbonylation kinetics.

Published
2012
Full Text
View/download PDF

2. Following ligand migration pathways from picoseconds to milliseconds in type II truncated hemoglobin from Thermobifida fusca

Author

Alessandro Feis, Alessandra Bonamore, Darío A. Estrin, Cristiano Viappiani, Stefania Abbruzzetti, Agnese Marcelli, Stefano Bruno, Cristina Gellini, Alberto Boffi, Paolo Foggi, Pier Remigio Salvi, Juan Pablo Bustamante, European Laboratory for Non-Linear Spectroscopy (LENS), Università degli Studi di Firenze = University of Florence [Firenze] (UNIFI), Department of Physics, University of Parma = Università degli studi di Parma [Parme, Italie], 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 Chemistry 'Ugo Schiff', 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], Department of Biochemistry and Molecular Biology, Istituto Nazionale di Ottica (INO), Consiglio Nazionale delle Ricerche (CNR), Dipartimento di Chimica [Perugia], and Università degli Studi di Perugia (UNIPG)

Subjects
Time Factors, lcsh:Medicine, Photochemistry, Molecular Dynamics, Ligands, 01 natural sciences, Biochemistry, Biophysics Simulations, Physical Chemistry, purl.org/becyt/ford/1 [https], Computational Chemistry, FLASH PHOTOLYSIS, TRANSIENT ABSORTION AND OPTOACOUSTIC SPECTROSCOPY, MESH: Ligands, Biomacromolecule-Ligand Interactions, lcsh:Science, HEME-PROTEINS, 0303 health sciences, Carbon Monoxide, Multidisciplinary, Hemoproteins, MESH: Kinetics, Chemistry, Ciencias Químicas, Truncated Hemoglobins, VIBRATIONAL-RELAXATION, Ligand (biochemistry), Femtochemistry, Physicochemical Properties, Reaction Dynamics, Picosecond, Flash photolysis, MYCOBACTERIUM-TUBERCULOSIS, TIME-RESOLVED THERMODYNAMICS, MESH: Carbon Monoxide, CIENCIAS NATURALES Y EXACTAS, Recombination, Research Article, Protein Binding, MESH: Photolysis, PHOTOINDUCED PROCESSES, Absorption spectroscopy, Kinetics, MOLECULAR DYNAMICS SIMULATIONS, Biophysics, 010402 general chemistry, CO PHOTODISSOCIATION, 03 medical and health sciences, Ultrafast laser spectroscopy, Actinomycetales, purl.org/becyt/ford/1.4 [https], INTERNAL HYDROPHOBIC CAVITIES, MESH: Protein Binding, THERMOBIFIDA FUSCA TRUNCATED HEMOGLOBIN, Spettroscopia, dinamica di proteine, emoproteine batteriche, assorbimento transiente, laser flash photolysis, dinamica molecolare, fotoacustica, [SDV.BBM]Life Sciences [q-bio]/Biochemistry, Molecular Biology, CARBON-MONOXIDE, Biology, 030304 developmental biology, Photolysis, Otras Ciencias Químicas, Photodissociation, lcsh:R, MESH: Time Factors, Proteins, Computational Biology, 0104 chemical sciences, MESH: Actinomycetales, HORSE HEART MYOGLOBIN, Chemical Properties, LIGAND MIGRATION PATHWAYS, MESH: Truncated Hemoglobins, lcsh:Q, PHOTOACOUSTIC CALORIMETRY, TIME-RESOLVED THERMODYNAMICS, INTERNAL HYDROPHOBIC CAVITIES, HORSE HEART MYOGLOBIN, HEME-PROTEINS, MYCOBACTERIUM-TUBERCULOSIS, CARBON-MONOXIDE, PHOTOACOUSTIC CALORIMETRY, VIBRATIONAL-RELAXATION, PHOTOINDUCED PROCESSES, CO PHOTODISSOCIATION
Abstract

CO recombination kinetics has been investigated in the type II truncated hemoglobin from Thermobifida fusca (Tf-trHb) over more than 10 time decades (from 1 ps to 100 ms) by combining femtosecond transient absorption, nanosecond laser flash photolysis and optoacoustic spectroscopy. Photolysis is followed by a rapid geminate recombination with a time constant of 2 ns representing almost 60% of the overall reaction. An additional, small amplitude geminate recombination was identified at 100 ns. Finally, CO pressure dependent measurements brought out the presence of two transient species in the second order rebinding phase, with time constants ranging from 3 to 100 ms. The available experimental evidence suggests that the two transients are due to the presence of two conformations which do not interconvert within the time frame of the experiment. Computational studies revealed that the plasticity of protein structure is able to define a branched pathway connecting the ligand binding site and the solvent. This allowed to build a kinetic model capable of describing the complete time course of the CO rebinding kinetics to Tf-trHb. Fil: Marcelli, Agnese. European Laboratory for Non-Linear Spectroscopy; Italia Fil: Abbruzzetti, Stefania. Università di Parma; 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. Universidad de Buenos Aires. Facultad de Ciencias Exactas y Naturales. Instituto de Química, Física de los Materiales, Medioambiente y Energía; Argentina Fil: Feis, Alessandro. University of Florence; Italia Fil: Bonamore, Alessandra. Università degli studi di Roma "La Sapienza"; Italia Fil: Boffi, Alberto. Università degli studi di Roma "La Sapienza"; Italia Fil: Gellini, Cristina. University of Florence; Italia Fil: Salvi, Pier R.. University of Florence; 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. Universidad de Buenos Aires. Facultad de Ciencias Exactas y Naturales. Instituto de Química, Física de los Materiales, Medioambiente y Energía; Argentina Fil: Bruno, Stefano. Università di Parma; Italia Fil: Viappiani, Cristiano. Università di Parma; Italia Fil: Foggi, Paolo. European Laboratory for Non-Linear Spectroscopy; Italia. University of Perugia; Italia

Published
2012
Full Text
View/download PDF

Catalog

Books, media, physical & digital resources
See catalog results