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

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.

[1]  A. Mozzarelli,et al.  Time-resolved methods in Biophysics. 2. Monitoring haem proteins at work with nanosecond laser flash photolysis , 2006, Photochemical & photobiological sciences : Official journal of the European Photochemistry Association and the European Society for Photobiology.

[2]  J. Miksovska,et al.  Volume and enthalpy profiles of CO rebinding to horse heart myoglobin , 2003, JBIC Journal of Biological Inorganic Chemistry.

[3]  C. Matthews,et al.  Analysis of kinetics using a hybrid maximum-entropy/nonlinear-least-squares method: application to protein folding. , 2002, Biophysical journal.

[4]  Andrea Ilari,et al.  Crystal structure and ligand binding properties of the truncated hemoglobin from Geobacillus stearothermophilus. , 2007, Archives of biochemistry and biophysics.

[5]  A. Feis,et al.  Protein relaxation in the photodissociation of myoglobin−CO complexes , 2003, Photochemical & photobiological sciences : Official journal of the European Photochemistry Association and the European Society for Photobiology.

[6]  A. Boffi,et al.  Sulfide binding properties of truncated hemoglobins. , 2010, Biochemistry.

[7]  K. Peters,et al.  A photoacoustic calorimetry study of horse carboxymyoglobin on the 10-nanosecond time scale. , 1993, Biophysical journal.

[8]  Peter J. Steinbach,et al.  Inferring Lifetime Distributions from Kinetics by Maximizing Entropy Using a Bootstrapped Model , 2002, J. Chem. Inf. Comput. Sci..

[9]  B. Wittenberg,et al.  Reaction of Mycobacterium tuberculosis Truncated Hemoglobin O with Hydrogen Peroxide , 2007, Journal of Biological Chemistry.

[10]  Martino Bolognesi,et al.  Truncated Hemoglobins: A New Family of Hemoglobins Widely Distributed in Bacteria, Unicellular Eukaryotes, and Plants* 210 , 2002, The Journal of Biological Chemistry.

[11]  C. Kirmaier,et al.  Time‐resolved and static optical properties of vibrationally excited porphyrins , 1991 .

[12]  Leonardo Boechi,et al.  Dioxygen affinity in heme proteins investigated by computer simulation. , 2006, Journal of inorganic biochemistry.

[13]  C. Kirmaier,et al.  Optical properties of metalloporphyrin excited states , 1989 .

[14]  N. Belogortseva,et al.  The contribution of heme propionate groups to the conformational dynamics associated with CO photodissociation from horse heart myoglobin. , 2007, Journal of inorganic biochemistry.

[15]  M. Sakakura,et al.  Dynamics of structure and energy of horse carboxymyoglobin after photodissociation of carbon monoxide. , 2001, Journal of the American Chemical Society.

[16]  Aleksandr V. Smirnov,et al.  Watching a Protein as it Functions with 150-ps Time-Resolved X-ray Crystallography , 2003, Science.

[17]  K. Peters,et al.  Time-resolved photoacoustic calorimetry: probing the energetics and dynamics of fast chemical and biochemical reactions. , 1988, Science.

[18]  J. Hofrichter,et al.  Protein reaction kinetics in a room-temperature glass , 1995, Science.

[19]  P. Foggi,et al.  Excited-state absorption and ultrafast relaxation dynamics of porphyrin, diprotonated porphyrin, and tetraoxaporphyrin dication. , 2008, The journal of physical chemistry. A.

[20]  C. M. Jones,et al.  Speed of intersubunit communication in proteins. , 1992, Biochemistry.

[21]  M. Head‐Gordon,et al.  Initial Steps of the Photodissociation of the CO Ligated Heme Group , 2003 .

[22]  C. M. Jones,et al.  Conformational relaxation and ligand binding in myoglobin. , 1994, Biochemistry.

[23]  J B Callis,et al.  Fast changes of enthalpy and volume on flash excitation of Chromatium chromatophores. , 1972, Biochimica et biophysica acta.

[24]  F. J. Luque,et al.  Nitric oxide reactivity with globins as investigated through computer simulation. , 2008, Methods in enzymology.

[25]  Y. Lecarpentier,et al.  Femtosecond photolysis of CO-ligated protoheme and hemoproteins: appearance of deoxy species with a 350-fsec time constant. , 1983, Proceedings of the National Academy of Sciences of the United States of America.

[26]  J. Olson,et al.  Kinetic Pathways and Barriers for Ligand Binding to Myoglobin* , 1996, The Journal of Biological Chemistry.

[27]  Dario A. Estrin,et al.  Comparing and combining implicit ligand sampling with multiple steered molecular dynamics to study ligand migration processes in heme proteins , 2011, J. Comput. Chem..

[28]  F. Spyrakis,et al.  The reactivity with CO of AHb1 and AHb2 from Arabidopsis thaliana is controlled by the distal HisE7 and internal hydrophobic cavities. , 2007, Journal of the American Chemical Society.

[29]  R. Eldik,et al.  Volume profile analysis of the formation and dissociation of carboxymyoglobin. Comparison with the corresponding oxymyoglobin system , 1991 .

[30]  K. Yoshihara,et al.  Dissociation and Recombination between Ligands and Heme in a CO-sensing Transcriptional Activator CooA , 2000, The Journal of Biological Chemistry.

[31]  Jan M. Kriegl,et al.  Ligand binding and protein dynamics in neuroglobin , 2002, Proceedings of the National Academy of Sciences of the United States of America.

[32]  Holger Gohlke,et al.  The Amber biomolecular simulation programs , 2005, J. Comput. Chem..

[33]  Michael L. Johnson,et al.  Numerical computer methods , 1992 .

[34]  A. Mozzarelli,et al.  Evidence for two geminate rebinding states following laser photolysis of R state hemoglobin encapsulated in wet silica gels. , 2005, The journal of physical chemistry. B.

[35]  Junmei Wang,et al.  How well does a restrained electrostatic potential (RESP) model perform in calculating conformational energies of organic and biological molecules? , 2000, J. Comput. Chem..

[36]  D. Estrin,et al.  Heme pocket structural properties of a bacterial truncated hemoglobin from Thermobifida fusca. , 2010, Biochemistry.

[37]  C. Kirmaier,et al.  Picosecond photodissociation of six-coordinate iron(II) porphyrins , 1985 .

[38]  J. Friedman,et al.  Ultrafast heme–ligand recombination in truncated hemoglobin HbO from Mycobacterium tuberculosis: A ligand cage , 2012 .

[39]  J. L. Martin,et al.  Femtosecond processes in proteins. , 1999, Biochimica et biophysica acta.

[40]  R. Miller,et al.  Vibrational energy relaxation and structural dynamics of heme proteins. , 1991, Annual review of physical chemistry.

[41]  S. Franzen,et al.  Evidence for sub-picosecond heme doming in hemoglobin and myoglobin: a time-resolved resonance Raman comparison of carbonmonoxy and deoxy species. , 1995, Biochemistry.

[42]  P. Kallio,et al.  Nitric oxide detoxification--a new era for bacterial globins in biotechnology? , 2005, Trends in biotechnology.

[43]  J. Goodman,et al.  Simultaneous determination of photoreaction dynamics and energetics using pulsed, time-resolved photoacoustic calorimetry , 1985 .

[44]  David Dantsker,et al.  Reactions of Mycobacterium tuberculosis truncated hemoglobin O with ligands reveal a novel ligand-inclusive hydrogen bond network. , 2003, Biochemistry.

[45]  Y. Mizutani,et al.  Direct observation of cooling of heme upon photodissociation of carbonmonoxy myoglobin. , 1997, Science.

[46]  F. Spyrakis,et al.  Ligand migration through the internal hydrophobic cavities in human neuroglobin , 2009, Proceedings of the National Academy of Sciences.

[47]  M. Wilson,et al.  Geminate carbon monoxide rebinding to a c-type haem. , 2005, Dalton transactions.

[48]  M. Lim,et al.  Femtosecond Near-IR Absorbance Study of Photoexcited Myoglobin: Dynamics of Electronic and Thermal Relaxation , 1996 .

[49]  F Javier Luque,et al.  Structural determinants of ligand migration in Mycobacterium tuberculosis truncated hemoglobin O , 2008, Proteins.

[50]  P. Foggi,et al.  S1 → Sn and S2 → Sn Absorption of Azulene: Femtosecond Transient Spectra and Excited State Calculations , 2003 .

[51]  D. Estrin,et al.  Fluoride as a probe for H-bonding interactions in the active site of heme proteins: the case of Thermobifida fusca hemoglobin. , 2011, Journal of the American Chemical Society.

[52]  M. Martí,et al.  Unraveling the molecular basis for ligand binding in truncated hemoglobins: The trHbO Bacillus subtilis case , 2010, Proteins.

[53]  Tammy Grogan,et al.  PICOSECOND REACTION OF PICKET FENCE HEME WITH O2 AND CO : GEMINATE RECOMBINATION IN THE SOLVENT CAGE , 1994 .

[54]  A. Mozzarelli,et al.  Determination of microscopic rate constants for CO binding and migration in myoglobin encapsulated in silica gels. , 2005, The journal of physical chemistry. B.

[55]  A. Nadra,et al.  Modeling heme proteins using atomistic simulations. , 2006, Physical chemistry chemical physics : PCCP.

[56]  Victor Guallar,et al.  Ligand Migration in the Truncated Hemoglobin-II from Mycobacterium tuberculosis , 2009, Journal of Biological Chemistry.

[57]  C. Viappiani,et al.  Kinetics of proton release after flash photolysis of 1-(2-nitrophenyl)ethyl sulfate (caged sulfate) in aqueous solution. , 2005, Journal of the American Chemical Society.

[58]  L. Kiger,et al.  Heme photolysis occurs by ultrafast excited state metal-to-ring charge transfer. , 2001, Biophysical journal.

[59]  S. Sligar,et al.  Analysis of the kinetic barriers for ligand binding to sperm whale myoglobin using site-directed mutagenesis and laser photolysis techniques. , 1990, The Journal of biological chemistry.

[60]  J. Petrich,et al.  Photophysics and reactivity of heme proteins: a femtosecond absorption study of hemoglobin, myoglobin, and protoheme. , 1988, Biochemistry.

[61]  Femtosecond biology. , 1992, Annual review of biophysics and biomolecular structure.

[62]  E. Henry,et al.  [8] Singular value decomposition: Application to analysis of experimental data , 1992 .

[63]  D. Barrick,et al.  Investigations of Heme Protein Absorption Line Shapes, Vibrational Relaxation, and Resonance Raman Scattering on Ultrafast Time Scales † , 2003 .

[64]  S. Braslavsky,et al.  Time-resolved photothermal and photoacoustic methods applied to photoinduced processes in solution , 1992 .

[65]  J. Miksovska,et al.  Time resolved thermodynamics of ligand binding to heme proteins , 2007 .

[66]  L. Libertini,et al.  Analysis of photoacoustic waveforms using the nonlinear least squares method. , 1992, Biophysical chemistry.

[67]  R. Hochstrasser,et al.  Energy dissipation and relaxation processes in deoxy myoglobin after photoexcitation in the Soret region , 2000 .

[68]  L. Moens,et al.  Diversity of Globin Function: Enzymatic, Transport, Storage, and Sensing* , 2008, Journal of Biological Chemistry.

[69]  M. H. Vos.  Ultrafast dynamics of ligands within heme proteins. , 2008, Biochimica et biophysica acta.

[70]  P. Champion,et al.  Measurements of the photodissociation quantum yields of MbNO and MbO(2) and the vibrational relaxation of the six-coordinate heme species. , 2002, Journal of the American Chemical Society.

[71]  M. Lim,et al.  Modulating carbon monoxide binding affinity and kinetics in myoglobin: the roles of the distal histidine and the heme pocket docking site , 1997, JBIC Journal of Biological Inorganic Chemistry.

[72]  Veronica Morea,et al.  A novel thermostable hemoglobin from the actinobacterium Thermobifida fusca , 2005, The FEBS journal.

[73]  M. Kubo,et al.  Ultrafast dynamics of diatomic ligand binding to nitrophorin 4. , 2010, Journal of the American Chemical Society.

[74]  K. Schulten,et al.  Imaging the migration pathways for O2, CO, NO, and Xe inside myoglobin. , 2006, Biophysical journal.

[75]  F. J. Luque,et al.  Theoretical study of the truncated hemoglobin HbN: exploring the molecular basis of the NO detoxification mechanism. , 2005, Journal of the American Chemical Society.

[76]  Cristiano Viappiani,et al.  Time-resolved photothermal methods: accessing time-resolved thermodynamics of photoinduced processes in chemistry and biology , 2003, Photochemical & photobiological sciences : Official journal of the European Photochemistry Association and the European Society for Photobiology.

[77]  R. A. Goldbeck,et al.  Water and ligand entry in myoglobin: Assessing the speed and extent of heme pocket hydration after CO photodissociation , 2006, Proceedings of the National Academy of Sciences of the United States of America.

[78]  E. Ippen,et al.  Time-resolved spectroscopy of hemoglobin and its complexes with subpicosecond optical pulses. , 1976, Science.

[79]  J. Miksovska,et al.  Time resolved thermodynamics associated with ligand photorelease in heme peroxidases and globins: Open access channels versus gated ligand release. , 2011, Biochimica et biophysica acta.