Publications

2007

• Nanosecond T-jump experiment in poly(glutamic acid): A circular dichroism study
  
  • Mendonça Lucille
  • Hache François
  International Journal of Molecular Sciences, MDPI, 2007, 13 (2), pp.2239-2248. Poly(glutamic acid) has been studied with a nanosecond T-jump experiment. A new experimental set-up based on the frequency-quadrupling of an 82 MHz Titanium-Sapphire laser allows rapid CD measurements to be performed. Combining time-resolved absorption and circular dichroism at 204 and 220 nm, we are able to measure precisely the unfolding relaxation time as well as the helical fraction evolution. We show that only CD at 220 nm is relevant to observe the unfolding of an alpha helix whereas no change is observed for CD at 204 nm. Conversely, both absorptions yield information on the dynamics of the process. (10.3390/ijms13022239)
  DOI : 10.3390/ijms13022239
• Sinuosities in vascular structures
  
  • Masson Jean-Baptiste
  • Martin Jean-Louis
  European Physical Journal: Applied Physics, EDP Sciences, 2007, 40 (3), pp.351. In most organs, depending on the scale, the nature of the heart pump, the geometry and topology of the organ, some of the blood vessels tend to exhibit sinuous trajectories. We describe a part of this sinuous behavior, including partial biological and strong physical effects in a global physical framework. We will voluntarily focus on physical and topological effects. This study is performed on the vitelline membrane of the chicken embryo. Crossing angles, sinuosity, and the oscillation amplitude of the vascular system are analyzed. Surprisingly, the equation of river meandering dynamics is found to model the sinuosities in the vascular system, and an extension of this equation to non planar case is able to explain the effect of tissue global curvature on the vascular system. Results of this study could lead to a new understanding of the interplay between biological signaling and physical effects in determining the vascular pattern in different tissues. (10.1051/epjap:2007161)
  DOI : 10.1051/epjap:2007161
• Hypericin activates L-type Ca2+ channels in cardiac myocytes
  
  • Sauviat Martin-Pierre
  • Colas Anthony
  • J. Chauveau M.
  • C. Drapier J.
  • Négrerie Michel
  Journal of Natural Products, American Chemical Society, 2007, 70 (4), pp.510-514. (10.1021/np060309h)
  DOI : 10.1021/np060309h
• Magnetization-induced optical nonlinearity in ferromagnetic GaMnAs
  
  • Han K.-J.
  • Kim J.-H.
  • Yee K.-J.
  • Liu X.
  • Furdyna J.K.
  • Hache François
  Journal of Applied Physics, American Institute of Physics, 2007, 101 (6), pp.63519. We report the observation of a coherent nonlinear signal in pump-probe experiments on a ferromagnetic GaMnAs. The coherent signal, which is originating due to coherent interaction between pump and probe beams, depends on the polarization configuration of each beam and follows the sample magnetization as it changes with the applied magnetic field and/or the sample temperature. Cop. 2007 American Institute of Physics. (10.1063/1.2696930)
  DOI : 10.1063/1.2696930
• Nanosecond electron tunneling between the hemes in cytochrome bo(3)
  
  • Jasaitis Audrius
  • Johansson Mickael
  • Wikstrom Marten
  • Vos Marten H.
  • Verkhovsky Michael
  Proceedings of the National Academy of Sciences of the United States of America, National Academy of Sciences, 2007, 104 (52), pp.20811-20814. Biological electron transfer (eT) between redox-active cofactors is thought to occur by quantum-mechanical tunneling. However, in many cases the observed rate is limited by other reactions coupled to eT, such as proton transfer, conformational changes, or catalytic chemistry at an active site. A prominent example of this phenomenon is the eT between the heme groups of mitochondrial cytochrome c oxiclase, which has been reported to take place in several different time domains. The question of whether pure eT tunneling in the nanosecond regime between the heme groups can be observed has been the subject of some experimental controversy. Here, we report direct observations of eT between the heme groups of the quinol oxiclase cytochrome bo(3) from Escherichia coli, where the reaction is initiated by photolysis of carbon monoxide from heme o(3). eT from CO-dissociated ferrous heme o(3) to the low-spin ferric heme b takes place at a rate of (1.2 ns)(-1) at 20 degrees C as determined by optical spectroscopy. These results establish hemeheme electron tunneling in the bo(3) enzyme, a bacterial relative to the mitochondrial cytochrome c oxiclase. The properties of eT between the closely lying heme groups in the heme-copper oxidases are discussed in terms of the reorganization energy for the process, and two methods for assessing the rate of electron tunneling are presented. (10.1073/pnas.0709876105)
  DOI : 10.1073/pnas.0709876105
• Quantification of sudden light-induced polarization in bacteriorhodopsin by optical rectification
  
  • Colonna Anne
  • Groma Geza
  • Martin Jean-Louis
  • Joffre Manuel
  • Vos Marten H.
  Journal of Physical Chemistry B, American Chemical Society, 2007, 111 (10), pp.2707-2710. Upon population of its excited state, the retinal chromophore in the membrane protein bacteriorhodopsin (bR) undergoes a sudden (less than 10 fs) change in dipole moment, Δμ, that can be visualized in a direct way by optical rectification of a broadband visible femtosecond light pulse to the infrared but has not been quantified in this way. Here we show that a transparent thick AgGaS2 crystal delivers infrared radiation with the same spectral profile as bR and is a suitable reference for quantifying conversion efficiency. Using this reference, we estimate the projection of Δμ on the membrane normal at 11 D, corresponding to the displacement of a full charge over approximately half the length of the retinal chromophore. This result may help to evaluate models describing the interplay between the initial polarization change and the subsequent isomerization of the retinal. (10.1021/jp0673462)
  DOI : 10.1021/jp0673462
• Counting the number of proteins coupled to single nanoparticles
  
  • Casanova Didier
  • Giaume Domitile
  • Moreau Mélanie
  • Martin Jean-Louis
  • Gacoin Thierry
  • Boilot Jean-Pierre
  • Alexandrou Antigoni
  Journal of the American Chemical Society, American Chemical Society, 2007, 129 (42), pp.12592-12593. We implemented amine coating of lanthanide-ion doped oxide luminescent nanoparticles and coupling to a protein labeled with an organic fluorophore. We exploited the stepwise photobleaching of the organic fluorophores and their initial emission to count the number of proteins coupled to single nanoparticles. We thus precisely measured the distribution of the protein−nanoparticle ratio and showed that its maximum is different from the average ratio determined from ensemble measurements. The accurate quantification of the biomolecule−particle coupling opens up the possibility of selecting finely controlled conjugates. (10.1021/ja0731975)
  DOI : 10.1021/ja0731975
• Molecular basis for nitric oxide dynamics and affinity with Alcaligenes xylosoxidans cytochrome c
  
  • Kruglik Sergei G.
  • Lambry Jean-Christophe
  • Cianetti Simona
  • Martin Jean-Louis
  • Eady Robert
  • Andrew Colin R.
  • Négrerie Michel
  Journal of Biological Chemistry, American Society for Biochemistry and Molecular Biology, 2007, 282, pp.5053. The bacterial heme protein cytochrome ć from Alcaligenes xylosoxidans (AXCP) reacts with nitric oxide (NO) to form a 5-coordinate ferrous nitrosyl heme complex. The crystal structure of ferrous nitrosyl AXCP has previously revealed that NO is bound in an unprecedented manner on the proximal side of the heme. To understand how the protein structure of AXCP controls NO dynamics, we performed absorption and Raman time-resolved studies at the heme level as well as a molecular computational dynamics study at the entire protein structure level. We found that after NO dissociation from the heme iron, the structure of the proximal heme pocket of AXCP confines NO close to the iron so that an ultrafast (7 ps) and complete (99 ± 1%) geminate rebinding occurs, whereas the proximal histidine does not rebind to the heme iron on the timescale of NO geminate rebinding. The distal side controls the initial NO binding, whereas the proximal heme pocket controls its release. These dynamic properties allow the trapping of NO within the protein core and represent an extreme behavior observed among heme proteins. (10.1074/jbc.M604327200)
  DOI : 10.1074/jbc.M604327200
• Accommodation of NO in the active site of mammalian and bacterial cytochrome c oxidase aa3
  
  • Pilet Eric
  • Nitschke Wolfgang
  • Liebl Ursula
  • Vos Marten H.
  Biochimica et Biophysica Acta (BBA) - Reviews on Bioenergetics, Elsevier, 2007, 1767 (5), pp.387-392. Following different reports on the stoichiometry and configuration of NO binding to mammalian and bacterial reduced cytochrome c oxidase aa3 (CcO), we investigated NO binding and dynamics in the active site of beef heart CcO as a function of NO concentration, using ultrafast transient absorption and EPR spectroscopy. We find that in the physiological range only one NO molecule binds to heme a3, and time-resolved experiments indicate that even transient binding to CuB does not occur. Only at very high (∼ 2 mM) concentrations a second NO is accommodated in the active site, although in a different configuration than previously observed for CcO from Paracoccus denitrificans [E. Pilet, W. Nitschke, F. Rappaport, T. Soulimane, J.-C. Lambry, U. Liebl and M.H. Vos. Biochemistry 43 (2004) 14118-14127], where we proposed that a second NO does bind to CuB. In addition, in the bacterial enzyme two NO molecules can bind already at NO concentrations of ∼ 1 μM. The unexpected differences highlighted in this study may relate to differences in the physiological relevance of the CcO-NO interactions in both species. (10.1016/j.bbabio.2007.03.001)
  DOI : 10.1016/j.bbabio.2007.03.001
• Génération de second harmonique optique par le collagène fibrillaire
  
  • Schanne-Klein Marie-Claire
  • Strupler Mathias
  Images de la Physique, 2007, pp.81. Le collagène est la protéine la plus importante en poids chez les mammifères et joue un rôle essentiel dans l'assemblage des tissus biologiques. La technique de microscopie optique par génération de second harmonique permet d'imager l'architecture tridimensionnelle des fibres de collagène et de mesurer avec une excellente sensibilité l'accumulation de ces fibres dans certaines pathologies.
• Excited-state absorption and circular dichroism of ruthenium(II) tris(phenanthroline) in the ultraviolet region
  
  • Niezborala Claire
  • Hache François
  Journal of Physical Chemistry A, American Chemical Society, 2007, 111 (32), pp.7732. Excitation of ruthenium(II) tris(phenanthroline) in the visible region results in the tranfer of an electron from the central atom toward one of the ligands. To probe this excited state, we have performed pump-induced absorption and circular dichroism in the ultraviolet wavelengths, in the intraligand p-p* transition region. On top of the bleaching of the ground state transitions, new structures appear in the absorption and CD spectra. Thanks to a classical calculation based on the polarizability theory, we can interpret these features as the result of a strong reduction of the excitonic coupling due to a blue shift of the p-p* transition in the reduced ligand accompanied by the onset of new excited-state transitions. Cop. 2007 American Chemical Society. (10.1021/jp0662092)
  DOI : 10.1021/jp0662092
• Erratum: Measuring the dynamics of circular dichroism in a pump-probe experiment with a Babinet-Soleil compensator
  
  • Niezborala Claire
  • Hache François
  Journal of the Optical Society of America B, Optical Society of America, 2007, 24 (4), pp.1012. Circular dichroism contains rich information on the conformation of molecules and, in particular, of biomolecules, and measuring its variation in a pump-probe experiment is very promising but also very challenging. We propose a new technique to measure pump-induced variation of the circular dichroism, which is based on the measurement of the probe ellipticity and its variation with the pump. This technique has the advantage that it does not require modulation of the probe polarization, which allows modulation of the pump intensity. We show theoretically and demonstrate experimentally that this technique is very sensitive and user friendly. We also show that it can be used to measure pump-induced change in the optical rotation, allowing for a complete characterization of pump-induced optical activity. Cop. 2006 Optical Society of America. (10.1364/JOSAB.24.001012)
  DOI : 10.1364/JOSAB.24.001012
• Direct observation of ligand transfer and bond formation in cytochrome c oxidase by using mid-infrared chirped-pulse upconversion
  
  • Treuffet Johanne
  • Kubarych Kevin J.
  • Lambry Jean-Christophe
  • Pilet Eric
  • Masson Jean-Baptiste
  • Martin Jean-Louis
  • Vos Marten H.
  • Joffre Manuel
  • Alexandrou Antigoni
  Proceedings of the National Academy of Sciences of the United States of America, National Academy of Sciences, 2007, 104 (40), pp.15705. We have implemented the recently demonstrated technique of chirped-pulse upconversion of midinfrared femtosecond pulses into the visible in a visible pump-midinfrared probe experiment for high-resolution, high-sensitivity measurements over a broad spectral range. We have succeeded in time-resolving the CO ligand transfer process from the heme Fe to the neighboring Cu B atom in the bimetallic active site of mammalian cytochrome c oxidase, which was known to proceed in <1 ps, using the full CO vibrational signature of Fe-CO bond breaking and CuB-CO bond formation. Our differential transmission results show a delayed onset of the appearance of the CuB-bound species (200 fs), followed by a 450-fs exponential rise. Trajectories calculated by using molecular-dynamics simulations with a Morse potential for the CuB-C interaction display a similar behavior. Both experimental and calculated data strongly suggest a ballistic contribution to the transfer process. Cop. 2007 by The National Academy of Sciences of the USA. (10.1073/pnas.0703279104)
  DOI : 10.1073/pnas.0703279104
• Three-dimensional investigation and scoring of extracellular matrix remodeling during lung fibrosis using multiphoton microscopy
  
  • Pena Ana-Maria
  • Fabre Aurelie J
  • Débarre Delphine
  • Marchal-Somme J.
  • Crestani Bruno
  • Martin Jean-Louis
  • Beaurepaire Emmanuel
  • Schanne-Klein Marie-Claire
  Microscopy Research and Technique, Wiley, 2007, 70 (2), pp.162-170. The organization of collagen during fibrotic processes is poorly characterized because of the lack of appropriate methodologies. Here we show that multimodal multiphoton microscopy provides novel insights into lung fibrosis. We characterize normal and fibrotic pulmonary tissue in the bleomycin model, and show that second-harmonic generation by fibrillar collagen reveals the micrometer-scale three-dimensional spatial distribution of the fibrosis. We find that combined two-photon excited fluorescence and second-harmonic imaging of unstained lung tissue allows separating the inflammatory and fibrotic steps in this pathology, underlining characteristic features of fibroblastic foci in human Idiopathic Pulmonary Fibrosis samples. Finally, we propose phenomenological scores of lung fibrosis and we show that they unambiguously sort out control and treated mice, with a better sensitivity and reproducibility in the subpleural region. These results should be readily generalized to other organs, as an accurate method to assess extracellular matrix remodeling during fibrosis. Microsc. Res. Tech., 2007. © 2006 Wiley-Liss, Inc. (10.1002/jemt.20400)
  DOI : 10.1002/jemt.20400
• Highly sensitive pH measurements using a transistor composed of a large array of parallel silicon nanowires
  
  • Lehoucq Gaëlle
  • Bondavalli Paolo
  • Xavier Stéphane
  • Legagneux Pierre
  • Abbyad Paul
  • Baroud Charles N.
  • Pribat Didier
  Sensors and Actuators B: Chemical, Elsevier, 2007, 171-172, pp.127-134. Silicon nanowire field-effect transistors (SiNW FETs) have emerged as good candidates for ultra-sensitive electrical detection of biological species, presenting a label-free alternative to colorimetry and fluorescence techniques. Here, a top-down approach has been used to fabricate the SiNW FETs using silicon-on-insulator (SOI) substrates. As in previous work, a change of the transistor conductance according to the pH of the solution is observed on a large pH interval [3-10.5], even for small variations of 0.1 pH units. The influence of several physico-chemical parameters such as gate voltage and buffer salinity, usually not adequately taken into account in previous papers, is discussed to achieve a better understanding of the detection phenomena. (10.1016/j.snb.2012.01.054)
  DOI : 10.1016/j.snb.2012.01.054
• Discovery of intracellular heme-binding protein HrtR, which controls heme efflux by the conserved HrtB-HrtA transporter in Lactococcus lactis
  
  • Lechardeur Delphine
  • Cesselin Bénédicte
  • Liebl Ursula
  • Vos Marten H.
  • Fernandez Annabelle
  • Brun Celia
  • Gruss Alexandra
  • Gaudu Philippe
  Cellular and Molecular Life Sciences, Springer Verlag, 2007, 64 (1), pp.96-103. Most commensal and food bacteria lack heme biosynthesis genes. For several of them, the capture of environmental heme is a means of activating aerobic respiration metabolism. Our previous studies in the Gram-positive bacterium Lactococcus lactis showed that heme exposure strongly induced expression of a single operon, called here hrtRBA, encoding an ortholog of the conserved membrane heme-regulated transporter (hrt) and a unique transcriptional regulator we named HrtR. We show that HrtR expressed as a fusion protein is a heme-binding protein. Heme iron interaction with HrtR is non-covalent, hexacoordinated and involves two histidines, His-72 and His-149. HrtR specifically binds a 15 nt palindromic sequence in the hrtRBA promoter region, which is needed for hrtRBA repression. HrtR-DNA binding is abolished by heme addition, which activates expression of the HrtB-HrtA (HrtBA) transporter in vitro and in vivo. The use of HrtR as an intracellular heme sensor appears to be conserved among numerous commensal bacteria, in contrast with numerous Gram-positive pathogens that use an extracellular heme-sensing system, HssRS, to regulate hrt. Finally, we show for the first time that HrtBA permease controls heme toxicity by its direct and specific efflux. The use of an intracellular heme sensor to control heme efflux constitutes a novel paradigm for bacterial heme homeostasis. (10.1074/jbc.M111.297531)
  DOI : 10.1074/jbc.M111.297531
• Comment on "Coherent control of retinal isomerization in bacteriorhodopsin
  
  • Joffre Manuel
  Science, American Association for the Advancement of Science (AAAS), 2007, 317, pp.1137011.
• True near field versus contrast near field imaging. II. imaging with a probe
  
  • Masson Jean-Baptiste
  • Gallot Guilhem
  Optics Express, Optical Society of America - OSA Publishing, 2007, 15 (6), pp.3078. In this letter, we extend the results previously found in near field imaging with aperture [Opt. Express 14, 11566 (2006)], where we demonstrated that interaction between light and sample can be divided into two main areas: the true near field and the contrast near field domain. Here, we show that in near field with a probe, the same division of space exists, and thus we show that a much simpler way to model theses experiments can be given. Cop. 2007 Optical Society of America. (10.1364/OE.15.003078)
  DOI : 10.1364/OE.15.003078
• Subpicosecond Oxygen Trapping in the Heme Pocket of the Oxygen Sensor FixL Observed by Time-Resolved Resonance Raman Spectroscopy
  
  • Kruglik Sergei G.
  • Jasaitis Audrius
  • Hola Klara
  • Yamashita Taku
  • Liebl Ursula
  • Martin Jean-Louis
  • Vos Marten H.
  Proceedings of the National Academy of Sciences of the United States of America, National Academy of Sciences, 2007, 104 (18), pp.7408-7413. Dissociation of oxygen from the heme domain of the bacterial oxygen sensor protein FixL constitutes the first step in hypoxia-induced signaling. In the present study, the photodissociation of the heme-O2 bond was used to synchronize this event, and time-resolved resonance Raman (TR(3)) spectroscopy with subpicosecond time resolution was implemented to characterize the heme configuration of the primary photoproduct. TR(3) measurements on heme-oxycomplexes are highly challenging and have not yet been reported. Whereas in all other known six-coordinated heme protein complexes with diatomic ligands, including the oxymyoglobin reported here, heme iron out-of-plane motion (doming) occurs faster than 1 ps after iron-ligand bond breaking; surprisingly, no sizeable doming is observed in the oxycomplex of the Bradyrhizobium japonicum FixL sensor domain (FixLH). This assessment is deduced from the absence of the iron-histidine band around 217 cm(-1) as early as 0.5 ps. We suggest that efficient ultrafast oxygen rebinding to the heme occurs on the femtosecond time scale, thus hindering heme doming. Comparing WT oxy-FixLH, mutant proteins FixLH-R220H and FixLH-R220Q, the respective carbonmonoxy-complexes, and oxymyoglobin, we show that a hydrogen bond of the terminal oxygen atom with the residue in position 220 is responsible for the observed behavior; in WT FixL this residue is arginine, crucially implicated in signal transmission. We propose that the rigid O2 configuration imposed by this residue, in combination with the hydrophobic and constrained properties of the distal cavity, keep dissociated oxygen in place. These results uncover the origin of the "oxygen cage" properties of this oxygen sensor protein. (10.1073/pnas.0700445104)
  DOI : 10.1073/pnas.0700445104
• Distal Val346Ile mutation in inducible NO synthase promotes substrate-dependent NO confinement
  
  • Beaumont Edward
  • Lambry Jean-Christophe
  • Wang Z.-Q.
  • Stuehr D.J.
  • Martin Jean-Louis
  • Slama-Schwok Anny
  Biochemistry, American Chemical Society, 2007, 46 (47), pp.13533. The function of inducible NO synthase (WT iNOS) depends on the release of NO from the ferric heme before the enzyme is reduced. Key parameters controlling ligand dynamics include the distal and proximal heme pocket amino acids, as well as the inner solvent molecules. In this work, we tested how a point mutation in the distal heme side of WT iNOS affected the geminate rebinding of NO by ultrafast kinetics and molecular dynamics simulations. The mutation sequestered much of the photodissociated NO close to the heme compared to WT iNOS, with a main picosecond phase accounting for 78% of the rebinding to the arginine-bound Val346Ile protein. Consequently, the probability of NO release from Val346Ile decreased as compared to that from WT iNOS, provided the substrate binding site is filled. These data are rationalized by a steric effect of the Ile methyl group inducing events mediated by the substrate, transmitted via the propionates to the NO and the protein. This model is consistent with the role of the H-bonding network involving the heme, the substrate, and the BH4 cofactor in controlling NO release, with a key role of the heme propionates [Gautier et al. (2006) Nitric Oxide 15, 312]. These data support the effect of Val346Ile mutation in decreasing NO release and slowing down NO synthesis compared to WT iNOS determined by single turnover catalysis [Wang et al. (2004) J. Biol. Chem. 279, 19018]. Cop. 2007 American Chemical Society. (10.1021/bi701567h)
  DOI : 10.1021/bi701567h
• Ligand dynamics in an electron-transfer protein: picosecond geminate recombination of carbon monoxide to heme in mutant forms of cytochrome c
  
  • Silkstone Gary
  • Jasaitis Audrius
  • Wilson M. T.
  • Vos Marten H.
  Journal of Biological Chemistry, American Society for Biochemistry and Molecular Biology, 2007, 282, pp.1638-1649. Substitution of the heme coordination residue Met-80 of the electron transport protein yeast iso-1-cytochrome c allows external ligands like CO to bind and thus increase the effective redox potential. This mutation, in principle, turns the protein into a quasi-native photoactivable electron donor. We have studied the kinetic and spectral characteristics of geminate recombination of heme and CO in a series of single M80X (X = Ala, Ser, Asp, Arg) mutants, using femtosecond transient absorption spectroscopy. In these proteins, all geminate recombination occurs on the picosecond and early nanosecond time scale, in a multiphasic manner, in which heme relaxation takes place on the same time scale. The extent of geminate recombination varies from >99% (Ala, Ser) to ∼70% (Arg), the latter value being in principle low enough for electron injection studies. The rates and extent of the CO geminate recombination phases are much higher than in functional ligand-binding proteins like myoglobin, presumably reflecting the rigid and hydrophobic properties of the heme environment, which are optimized for electron transfer. Thus, the dynamics of CO recombination in cytochrome c are a tool for studying the heme pocket, in a similar way as NO in myoglobin. We discuss the differences in the CO kinetics between the mutants in terms of the properties of the heme environment and strategies to enhance the CO escape yield. Experiments on double mutants in which Phe-82 is replaced by Asp or Gly as well as the M80D substitution indicate that such steric changes substantially increase the motional freedom-dissociated CO. (10.1074/jbc.M605760200)
  DOI : 10.1074/jbc.M605760200