Publications

2008

• Ligand dynamics and early signalling events in the heme domain of the sensor protein Dos from Escherichia coli
  
  • Yamashita Taku
  • Bouzhir-Sima Latifa
  • Lambry Jean-Christophe
  • Liebl Ursula
  • Vos Marten H.
  Journal of Biological Chemistry, American Society for Biochemistry and Molecular Biology, 2008, 283 (4), pp.2344-2352. In the heme-based sensor Dos from Escherichia coli, the ferrous heme is coordinated by His-77 and Met-95. The latter residue is replaced upon oxygen binding or oxidation of the heme. Here we investigate the early signaling processes upon dissociation of the distal ligand using ultrafast spectroscopy and site-directed mutagenesis. Geminate CO rebinding to the heme domain DosH appears insensitive to replacement of Met-95, in agreement with the notion that this residue is oriented out of the heme pocket in the presence of external ligands. A uniquely slow 35-ps phase in rebinding of the flexible methionine side chain after dissociation from ferrous DosH is completely abolished in rebinding of the more rigid histidine side chain in the M95H mutant protein, where only the 7-ps phase, common to all 6-coordinate heme proteins, is observed. Temperature-dependence studies indicate that all rebinding of internal and external ligands is essentially barrierless, but that CfigsO escape from the heme pocket is an activated process. Solvent viscosity studies combined with molecular dynamics simulations show that there are two configurations in the ferrous 6-coordinate protein, involving two isomers of the Met-95 side chain, of which the structural changes extend to the solvent-exposed backbone, which is part of the flexible FG loop. One of these configurations has considerable motional freedom in the Met-95-dissociated state. We suggest that this configuration corresponds to an early signaling intermediate state, is responsible for the slow rebinding, and allows small ligands in the protein to efficiently compete for binding with the heme. (10.1074/jbc.M708123200)
  DOI : 10.1074/jbc.M708123200
• Are cyanobacteria involved in Ciguatera Fish Poisoning-like outbreaks in New-Caledonia?
  
  • Laurent Dominique
  • Kerbrat A.S.
  • Daruis H.T.
  • Girard Emmanuelle
  • Golubic S.
  • Benoit Evelyne
  • Sauviat Martin-Pierre
  • Chinain M.
  • Molgó Jordi
  • Pauillac S.
  Harmful Algae, Elsevier, 2008, 7 (6), pp.827-838. From 2001 to 2005, numerous cases of seafood poisonings were reported in a tribe from Lifou (Loyalty Islands Province, New Caledonia) of which 35 were thoroughly examined. Observations outlined by the epidemiological and clinical data (including severity and rapid onset of certain symptoms following consumption of either giant clams (Tridacna spp.) or grazing and molluscivorous fish together with the apparent inefficacy of traditional remedies, were not in favour of a classical Ciguatera Fish Poisoning (CFP) outbreak. From 2005 onwards, an environmental offshore survey of the affected area was conducted. Screening of the damaged coral area revealed the presence of large populations of cyanobacteria identified as Hydrocoleum Kützing, but the absence of Gambierdiscus spp., the well-known dinoflagellate causative agent of CFP. In vivo and in vitro toxicological studies of extracts obtained from cyanobacteria and giant clams, strongly suggested the co-occurrence of ciguatoxin-like, anatoxin-like and paralytic shellfish toxins in these samples. These new findings shed new light on the complexity of the CFP symptomatology and treatment and also on the diversity and origin of the CFP toxins. Furthermore they provide new evidence of the overall variability of seafood poisonings following the ingestion of different sea products living in a marine environment where significant harmful populations of microalgae and cyanobacteria coexist. This is the first report on the involvement of cyanobacteria in CFP-like outbreaks following the consumption of giant clams or fish specimens. Consequently, it is recommended that CFP risk assessment programs now include monitoring of cyanobacteria besides the obvious screening of CFP-promoting dinoflagellates (10.1016/j.hal.2008.04.005)
  DOI : 10.1016/j.hal.2008.04.005
• Characterization of mid-infrared femtosecond pulses [Invited]
  
  • Lee Kevin F.
  • Kubarych Kevin J.
  • Bonvalet Adeline
  • Joffre Manuel
  Journal of the Optical Society of America B, Optical Society of America, 2008, 25 (6), pp.A54. We review different methods for characterizing mid-infrared femtosecond pulses, including linear methods such as electro-optic sampling, time-and frequency-domain interferometry and nonlinear self-referenced methods such as frequency-resolved optical gating (FROG) and spectral phase interferometry for direct electric-field reconstruction (SPIDER). Of particular interest are methods based on upconversion through non-linear mixing with chirped 800 nm pulses, enabling a complete measurement of mid-infrared pulses with visible-light spectrometers. Cop. 2008 Optical Society of America. (10.1364/JOSAB.25.000A54)
  DOI : 10.1364/JOSAB.25.000A54
• Collective behavior during the exit of a wetting liquid through a network of channels
  
  • Baroud Charles N.
  • Wang Xin C.
  • Masson Jean-Baptiste
  Journal of Colloid and Interface Science, Elsevier, 2008, 326 (2), pp.445. The exit of a wetting fluid from a thin microchannel into a sudden expansion is studied experimentally. In the case of the exit from a single channel, the advancing interface converges to a parabolic shape after an initial transient, in accordance with the lubrication limit analysis of a spreading drop. The experiments are then repeated for the exit from two parallel channels. At early times, the two exiting drops behave independently and display the same evolution as a single exiting droplet, while at late times we recover a single parabolic profile. The transition between the early and late states is due to the merging of the two drops, which is associated with a sudden increase in the flow rate. This is the signature of a collective effect which acts to redistribute the fluid spatially. Finally, the experiment is generalized to the case of seven parallel channels where a cascade of two-by-two mergings is observed, indicating that local interactions dominate the dynamics which lead to the global state of the system. Cop. 2008 Elsevier Inc. All rights reserved. (10.1016/j.jcis.2008.06.040)
  DOI : 10.1016/j.jcis.2008.06.040
• Second Harmonic Microscopy to Quantify Renal Interstitial Fibrosis and Arterial Remodeling
  
  • Strupler Mathias
  • Hernest Monica
  • Fligny Cécile
  • Martin Jean-Louis
  • Tharaux Pierre-Louis
  • Schanne-Klein Marie-Claire
  Journal of Biomedical Optics, Society of Photo-optical Instrumentation Engineers, 2008, 13 (5), pp.054041. Interstitial fibrosis is a powerful pejorative predictor of progression of nephropathies in a variety of chronic renal diseases. It is characterized by the depletion of kidney cells and their replacement by extracellular matrix, in particular, type-I fibrillar collagen, a protein scarce in normal interstitium. However, assessment of fibrosis remains a challenge in research and clinical pathology. We develop a novel methodology based on second harmonic generation SHG microscopy, and we image collagen fibers in human and mouse unstained kidneys. We take into account the variability in renal shape, and we develop automated image processing for quantitative scoring of thick murine tissues. This approach allows quantitative 3-D imaging of interstitial fibrosis and arterial remodeling with high accuracy. Moreover, SHG microscopy helps to raise pathophysiological questions. First, imaging of a large volume within a mouse kidney shows that progression of fibrosis is a heterogeneous process throughout the different renal compartments. Second, SHG from fibrillar collagens does not overlap with the glomerular tuft, despite patent clinical and experimental glomerulosclerosis. Since glomerulosclerosis involves SHG-silent nonfibrillar collagens, our work supports pathophysiological differences between interstitial fibrosis and glomerulosclerosis, a clearly nonfibrotic process. © 2008 Society of Photo-Optical Instrumentation Engineers (10.1117/1.2981830)
  DOI : 10.1117/1.2981830
• Third-harmonic generation microscopy with focus-engineered beams: a numerical study
  
  • Olivier Nicolas
  • Beaurepaire Emmanuel
  Optics Express, Optical Society of America - OSA Publishing, 2008, 16 (19), pp.14703-14715. We use a vector field model to analyze third-harmonic generation (THG) from model geometries (interfaces, slabs, periodic structures) illuminated by Hermite-Gaussian (HG) and Laguerre-Gaussian (LG) beams focused by a high NA lens. Calculations show that phase matching conditions are significantly affected by the tailoring of the field distribution near focus. In the case of an interface parallel to the optical axis illuminated by an odd HG mode, the emission patterns and signal level reflect the relative orientation of the interface and the focal field structure. In the case of slabs and periodic structures, the emission patterns reflect the interplay between focal field distribution (amplitude and phase) and sample structure. Forward-to-backward emission ratios using different beam shapes provide sub-wavelength information about sample spatial frequencies. © 2008 Optical Society of America (10.1364/OE.16.014703)
  DOI : 10.1364/OE.16.014703
• Flavin-dependent thymidylate synthase X limits chromosomal DNA replication
  
  • Escartin Frédéric
  • Skouloubris Stéphane
  • Liebl Ursula
  • Myllykallio Hannu
  Proceedings of the National Academy of Sciences of the United States of America, National Academy of Sciences, 2008, 105 (29), pp.9948-9952.
• Electron hopping through the 15 Å triple tryptophan molecular wire in DNA photolyase occurs within 30 ps
  
  • Lukacs Andras
  • Eker André P.M.
  • Byrdin Martin
  • Brettel Klaus
  • Vos Marten H.
  Journal of the American Chemical Society, American Chemical Society, 2008, 130 (44), pp.14394. DNA photolyase is a photoactive flavoprotein that contains three tryptophan residues between the FAD cofactor and the protein surface, the solvent-exposed Trp being located 14.8 Å from the flavin. Photoreduction of the neutral radical FADH* form to the catalytically active FADH- form occurs via electron transfer through this chain. The first step in this chain takes 30 ps, the second less than 4 ps. Using a combination of site-directed mutagenesis and femtosecond polarization spectroscopy to discriminate the spectroscopically indistinguishable Trp residues, we show that the third step occurs in less than 30 ps. This implies that the first photoreduction step is rate limiting and that the Trp chain effectively acts as molecular "wire" ensuring rapid and directed long-range charge translocation across the protein. This finding is important for the functioning of the large class of cryptochrome blue-light receptors, where the Trp chain is conserved. In DNA photolyase we make use of the natural photoactivation of the process, but more generally chains of aromatic amino acids may allow very fast long-range electron transfer also in nonphotoactive proteins. Copyright Cop. 2008 American Chemical Society. (10.1021/ja805261m)
  DOI : 10.1021/ja805261m
• Fast ligand and electron transfer dynamics in oxidases and cytochrome c
  
  • Vos Marten H.
  Biochimica et Biophysica Acta (BBA) - Reviews on Bioenergetics, Elsevier, 2008, 1777 (Supplement), pp.S66. The active site of heme-copper oxidases contains two cofactors, heme a3 and CuB, which can both bind external ligands as the substrate O2 and signalling molecules NO and CO, and which are both involved in electron transfer processes. Over the last few years we have exploited the fact that the heme-ligand bond can be dissociated by a short light pulse to explore the dynamics of CO and NO in the active site and the interaction between the two cofactors using ultrafast spectroscopic techniques. For example, we have time-resolved the CO transfer from heme a3 to CuB and shown that it occurs in a ballistic way in ∼ 500 fs, which presumably reflects rigidity of the active site. Heme a is located close to heme a3 (∼ 7 Å edge-to-edge) and acts as electron donor for the active site. Using mixed valence oxidases we have extended the 'reverse electron flow' technique to the ultrafast regime and demonstrated that this electron transfer process occurs in only 1.2 ns. The process is activationless and associated with a very low reorganization energy (< 200 meV), in contrast to common assumptions but in general agreement with the hydrophobic environment of the reactants. Finally, ligand dynamics in native and modified cytochrome c reflects the rigidity required for optimal electron transfer properties. (10.1016/j.bbabio.2008.05.259)
  DOI : 10.1016/j.bbabio.2008.05.259
• Ultrafast dynamics of ligands within heme proteins
  
  • Vos Marten H.
  Biochimica et Biophysica Acta (BBA) - Reviews on Bioenergetics, Elsevier, 2008, 1777, pp.15-31. Physiological bond formation and bond breaking events between proteins and ligands and their immediate consequences are difficult to synchronize and study in general. However, diatomic ligands can be photodissociated from heme, and thus in heme proteins ligand release and rebinding dynamics and trajectories have been studied on timescales of the internal vibrations of the protein that drive many biochemical reactions, and longer. The rapidly expanding number of characterized heme proteins involved in a large variety of functions allows comparative dynamics-structure-function studies. In this review, an overview is given of recent progress in this field, and in particular on initial sensing processes in signaling proteins, and on ligand and electron transfer dynamics in oxidases and cytochromes. (10.1016/j.bbabio.2007.10.004)
  DOI : 10.1016/j.bbabio.2007.10.004
• Conformational changes in photoexcited (R)-(+)-1,1'-bi-2-naphthol studied by time-resolved circular dichroism
  
  • Niezborala Claire
  • Hache François
  Journal of the American Chemical Society, American Chemical Society, 2008, 130 (38), pp.12783-12786. Conformational changes following photoexcitation of (R)-(+)-1,1′-bi-2-naphthol are studied with a time-resolved circular dichroism (CD) experiment. Two wavelengths are investigated. For λ = 237 nm, we observe a bleaching of the ground-state absorption and a transient CD structure. Thanks to a coupled-oscillator calculation, we can attribute this effect to a decrease of the dihedral angle. For λ = 245 nm, excited-state absorption and CD are observed. All these effects are solvent-dependent. In particular, it is shown that dynamics is slower in a protic solvent, which is attributed to hydrogen-bonding of the hydroxy groups with the solvent. (10.1021/ja8039844)
  DOI : 10.1021/ja8039844
• Mechanical factors activate beta-catenin-dependent oncogene expression in APC1638N/+ mouse colon
  
  • Whitehead J.
  • Vignjevic Danijela
  • Fütterer C.
  • Beaurepaire Emmanuel
  • Robine Sylvie
  • Farge Emmanuel
  HFSP Journal, 2008, 2 (5), pp.286. catenin acts as a critical regulator of gastrointestinal homeostasis through its control of the Wnt signaling pathway, and genetic or epigenetic lesions which activate Wnt signaling are the primary feature of colon cancer. -catenin is also a key element of mechanotranscription pathways, leading to upregulation of master developmental gene expression during Drosophila gastrulation, or regulating mammalian bone development and maintenance. Here we investigate the impact of mechanical stimulation on the initiation of colon cancer. Myc and Twist1, two oncogenes regulated through -catenin, are expressed in response to transient compression in APC deficient "APC1638N/+... colon tissue explants, but not in wild-type colon explants. Mechanical stimulation of APC1638N/+ tissue leads to the phosphorylation of -catenin at tyrosine 654, the site of interaction with E-cadherin, as well as to increased nuclear localization of -catenin. The mechanical activation of Myc and Twist1 expression in APC1638N/+ colon can be prevented by blocking -catenin phosphorylation using Src kinase inhibitors. Microenvironmental signals are known to cooperate with genetic lesions to promote the nuclear -catenin accumulation which drives colon cancer. Here we demonstrate that when APC is limiting, mechanical strain, such as that associated with intestinal transit or tumor growth, can be interpreted by cells of preneoplastic colon tissue as a signal to initiate a -catenin dependent transcriptional program characteristic of cancer (10.2976/1.2955566)
  DOI : 10.2976/1.2955566
• Two photon-induced electron injection from a nanotrigger in native endothelial NO-synthase
  
  • Beaumont Edward
  • Lambry Jean-Christophe
  • Robin A.-C.
  • Martasek P.
  • Blanchard-Desce M.
  • Slama-Schwok Anny
  ChemPhysChem, Wiley-VCH Verlag, 2008, 9 (16), pp.2325. We have recently designed a nanotrigger (NT), a photoactive molecule addressing the NADPH sites of proteins. This nanotrigger has a 103 times larger two-photon cross-section compared to the ubiquitous NADPH cofactor. In this work, we tested whether two-photon excitation of the bound NT to NADPH sites may be used to initiate enzymatic catalysis by appropriate electron injection. To establish proof of principle, we monitored the ultrafast absorption of NT bound to the fully active endothelial NO-Synthase (eNOS) following excitation by one and two-photons at 405 and 810 nm, respectively. Electron injection from NT* to FAD in eNOS initiated the catalytic cycle in 15±3 ps at both exciting wavelengths. The data proved for the first time that electron transfer can be promoted by two-photon excitation. We also show that the nanotrigger decays faster in homogeneous solvents than in the NADPH site of proteins, suggesting that hindered environments modified the natural decay of NT. The nanotrigger provides a convenient way of synchronizing an ensemble of proteins in solution with a femtosecond laser pulse. The ability of NT to initiate NOS catalysis by two-photon excitation may be exploited for controlled and localized release of free NO in cells with enhanced spatial and temporal resolution. Cop. 2008 Wiley-VCH Verlag GmbH & Co. KGaA. (10.1002/cphc.200800411)
  DOI : 10.1002/cphc.200800411
• Processus ultra-rapides dans les hémoprotéines [Ultrafast processes in heme proteins]
  
  • Vos Marten H.
  L'Actualité Chimique, Société chimique de France (SCF), 2008, 317 (52), pp.55. Les hémoprotéines sont impliquées dans une grande diversité de fonctions biologiques qui incluent transport et stockage d'oxygène, catalyse, transfert d'électron et signalisation. Le fer de l'hème peut être lié aux acides aminés et également aux molécules diatomiques (O2, NO, CO). Ces liaisons peuvent être rompues par une impulsion lumineuse avec un rendement élevé. En utilisant des techniques de spectroscopie optique ultrarapide, cette propriété donne la possibilité unique d'étudier la dynamique structurelle et électronique de l'hème et de son environnement protéique à l'échelle femtoseconde-picoseconde, c'est-à-dire à l'échelle même des vibrations internes de la macromolécule. Cet article décrit des développements récents dans ce domaine, en particulier l'implication de mouvements concertés hème-protéine dans des réactions balistiques de transfert de ligands et la possibilité de suivre des étapes intermédiaires de propagation d'un " signal " au sein de protéines de signalisation. Heme proteins contribute to a large variety of biological functions including transport and storage of oxygen, catalysis, electron transfer and signalling. The iron atom in the heme can bind amino acids and also diatomic molecules (O-2, NO, CO). These bonds can efficiently be broken by a light pulse. Using ultrafast optical spectroscopy techniques, this property allows the study of structural and electronic dynamics in the heme and its proteic environment at femtosecond-picosecond time scales, i.e. at the time scale of internal vibrations of the macromolecular systems. This review describes recent progress in this domain, specifically the role of concerted movements of the heme-protein system in ballistic ligand transfer reactions as well as the real-time monitoring of signal propagation within signalling proteins.
• Nanofluidics in the Debye Layer at Hydrophilic and Hydrophobic Surfaces
  
  • Bouzigues Cédric
  • Tabeling Paul
  • Bocquet L.
  Physical Review Letters, American Physical Society, 2008, 101, pp.114503. By using evanescent waves, we study equilibrium and dynamical properties of liquid-solid interfaces in the Debye layer for hydrophilic and hydrophobic surfaces. We measure velocity profiles and nanotracer concentration and diffusion profiles between 20 and 300 nm from the walls in pressure-driven and electro-osmotic flows. We extract electrostatic and zeta potentials and determine hydrodynamic slip lengths with 10 nm accuracy. The spectacular amplification of the zeta potential resulting from hydrodynamic slippage allows us to clarify for the first time the dynamic origin of the zeta potential. (10.1103/PhysRevLett.101.114503)
  DOI : 10.1103/PhysRevLett.101.114503
• Tissue deformation modulates Twist expression to determine anterior midgut differentiation in Drosophila embryos
  
  • Desprat Nicolas
  • Supatto Willy
  • Pouille Philippe-Alexandre
  • Beaurepaire Emmanuel
  • Farge Emmanuel
  Developmental Cell, Elsevier, 2008, 15 (3), pp.470-477. Mechanical deformations associated with embryonic morphogenetic movements have been suggested to actively participate in the signaling cascades regulating developmental gene expression. Here we develop an appropriate experimental approach to ascertain the existence and the physiological relevance of this phenomenon. By combining the use of magnetic tweezers with in vivo laser ablation, we locally control physiologically relevant deformations in wild-type Drosophila embryonic tissues. We demonstrate that the deformations caused by germ band extension upregulate Twist expression in the stomodeal primordium. We find that stomodeal compression triggers Src42A-dependent nuclear translocation of Armadillo/β-catenin, which is required for Twist mechanical induction in the stomodeum. Finally, stomodeal-specific RNAi-mediated silencing of Twist during compression impairs the differentiation of midgut cells, resulting in larval lethality. These experiments show that mechanically induced Twist upregulation in stomodeal cells is necessary for subsequent midgut differentiation. DEVBIO (10.1016/j.devcel.2008.07.009)
  DOI : 10.1016/j.devcel.2008.07.009
• Contrast generation and signal epidetection in THG microscopy of turbid media
  
  • Débarre Delphine
  • Olivier Nicolas
  • Beaurepaire Emmanuel
  , 2008.
• Low-loss polymers for terahertz applications
  
  • Podzorov Alexander
  • Gallot Guilhem
  Applied optics, Optical Society of America, 2008, 47, pp.3254.
• Anomalies in the disappearance of the extraordinary electromagnetic transmission in subwavelength hole arrays
  
  • Masson Jean-Baptiste
  • Podzorov Alexander
  • Gallot Guilhem
  Optics Express, Optical Society of America - OSA Publishing, 2008, 16, pp.4719.
• Organic functionalization of luminescent oxide nanoparticles towards their application as biological probes
  
  • Giaume Domitille
  • Poggi Mélanie
  • Casanova Didier
  • Mialon Geneviève
  • Lahlil Khalid
  • Alexandrou Antigoni
  • Gacoin Thierry
  • Boilot Jean-Pierre
  Langmuir, American Chemical Society, 2008, 24 (19), pp.11018. Luminescent inorganic nanoparticles are now widely studied for their applications as biological probes for in vitro or in vivo experiments. The functionalization of the particles is a key step toward these applications, since it determines the control of the coupling between the particles and the biological species of interest. This paper is devoted to the case of rare earth doped oxide nanoparticles and their functionalization through their surface encapsulation with a functional polysiloxane shell. The first step of the process is the adsorption of silicate ions that will act as a primary layer for the further surface polymerization of the silane, either aminopropyltriethoxysilane (APTES) or glycidoxypropyltrimethoxysilane (GPTMS). The amino- or epoxy- functions born by the silane allow the versatile coupling of the particles with bio-organic species following the chemistry that is commonly used in biochips. Special attention is paid to the careful characterization of each step of the functionalization process, especially concerning the average number of organic functions that are available for the final coupling of the particles with proteins. The surface density of amino or epoxy functions was found to be 0.4 and 1.9 functions per square nanometer for GPTMS and APTES silanized particles, respectively. An example of application of the amino-functionalized particles is given for the coupling with α-bungarotoxins. The average number (up to 8) and the distribution of the number of proteins per particle are given, showing the potentialities of the functionalization process for the labeling of biological species. (10.1021/la8015468)
  DOI : 10.1021/la8015468