Following Ligand Migration Pathways from Picoseconds to Milliseconds in Type II Truncated Hemoglobin from Thermobifida fusca

Year: 2012

Authors: Marcelli A., Abbruzzetti S., Bustamante JP., Feis A., Bonamore A., Boffi A., Gellini C., Salvi PR., Estrin DA., Bruno S., Viappiani C., Foggi P.

Autors Affiliation: LENS, European Lab Nonlinear Spect, Florence, Italy; Univ Parma, Dept Phys, I-43100 Parma, Italy; Univ Buenos Aires, Fac Ciencias Exactas & Nat, Dept Quim Inorgan Analit & Quim Fis, INQUIMAE CONICET, Buenos Aires, DF, Argentina; Univ Florence, Dept Chem Ugo Schiff, Florence, Italy; Univ Roma La Sapienza, Dept Biochem Sci, Fdn Cenci Bolognetti, Ist Pasteur, I-00185 Rome, Italy; Univ Parma, Dept Biochem & Mol Biol, I-43100 Parma, Italy; Univ Perugia, Dept Chem, I-06100 Perugia, Italy; INO CNR, Florence, Italy

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 similar 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 similar to 2 ns representing almost 60% of the overall reaction. An additional, small amplitude geminate recombination was identified at similar to 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 similar to 3 to similar 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.

Journal/Review: PLOS ONE

Volume: 7 (7)      Pages from: e39884  to: e39884

More Information: The authors acknowledge the Italian Ministero dell\’Istruzione, dell\’Universita e della Ricerca (PRIN 2008, 2008BFJ34R, Azioni Integrate Italia Spagna 2009, IT10L1M59M, and FIRB 2008 to Alessandra Bonamore), Ministero degli Affari Esteri, Direzione generale per la promozione del sistema Paese (Progetti di Grande Rilevanza, Italia-Argentina 2011-2013) and Istituto Pasteur Fondazione Cenci Bolognetti. One of the authors, A.M., wishes to acknowledge the grant financial support by Regione Toscana under the project EPHODS (POR FSE 2007-2013 obiettivo 2 Asse IV). The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.
KeyWords: carbon monoxide; truncated hemoglobin, article; bacterium; binding affinity; binding kinetics; binding site; complex formation; controlled study; enthalpy; entropy; ligand binding; molecular dynamics; molecular recognition; nonhuman; photoacoustic spectroscopy; photolysis; protein binding; quantum yield; steady state; temperature sensitivity; Thermobifida fusca, Actinomycetales; Carbon Monoxide; Kinetics; Ligands; Photolysis; Protein Binding; Time Factors; Truncated Hemoglobins, Thermobifida fusca
DOI: 10.1371/journal.pone.0039884

ImpactFactor: 3.730
Citations: 21
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