Nos tutelles


Nos partenaires

Accueil > Publications

Publications Département B3S


  • J. Santolini, « What does "NO-Synthase" stand for ? », Frontiers in Bioscience (Landmark Edition), vol. 24, p. 133-171, janv. 2019.
    Résumé : Mammalian NO-Synthases (NOSs) are the enzymatic sources of Nitric Oxide (NO°), a paradigmatic gasotransmitter involved in many (patho)-physiological processes. The increasing number of available genomes led to the identification of hundreds of new NOS proteins throughout the kingdoms of life, calling for a global investigation of this family of proteins. These new NOSs are commonly believed to share the same structure, functioning and role as mammalian NOSs. The scope of this article is to highlight the singularity of these NOSs and to describe their complex structural and functional diversity. NOS appears as a unique enzymatic machinery that exhibits a complex Structure - Activity - Function relationship. Its sophisticated redox mechanism and enzymatic regulation, coupled to the vast biological chemistry of reactive nitrogen species, leads to a specific cross-talk between NOS catalysis and its biological environment that implies a complex evolution of NOS function. This paper addresses the relationship between structure, function and evolution of NOS proteins using three NOS model families and advocates for an integrative and interdisciplinary approach that combines modelling studies, structural characterization, and in vitro/in vivo functional investigations.
    Mots-clés : B3S, LSOD.


  • N. Abdollahi, A. Albani, E. Anthony, A. Baud, M. Cardon, R. Clerc, D. Czernecki, R. Conte, L. David, A. Delaune, S. Djerroud, P. Fourgoux, N. Guiglielmoni, J. Laurentie, N. Lehmann, C. Lochard, R. Montagne, V. Myrodia, V. Opuu, E. Parey, L. Polit, S. Privé, C. Quignot, M. Ruiz-Cuevas, M. Sissoko, N. Sompairac, A. Vallerix, V. Verrecchia, M. Delarue, R. Guérois, Y. Ponty, S. Sacquin-Mora, A. Carbone, C. Froidevaux, S. Le Crom, O. Lespinet, M. Weigt, S. Abboud, J. Bernardes, G. Bouvier, C. Dequeker, A. Ferré, P. Fuchs, G. Lelandais, P. Poulain, H. Richard, H. Schweke, E. Laine, et A. Lopes, « Meet-U: Educating through research immersion », PLoS computational biology, vol. 14, nᵒ 3, p. e1005992, mars 2018.
    Résumé : We present a new educational initiative called Meet-U that aims to train students for collaborative work in computational biology and to bridge the gap between education and research. Meet-U mimics the setup of collaborative research projects and takes advantage of the most popular tools for collaborative work and of cloud computing. Students are grouped in teams of 4-5 people and have to realize a project from A to Z that answers a challenging question in biology. Meet-U promotes "coopetition," as the students collaborate within and across the teams and are also in competition with each other to develop the best final product. Meet-U fosters interactions between different actors of education and research through the organization of a meeting day, open to everyone, where the students present their work to a jury of researchers and jury members give research seminars. This very unique combination of education and research is strongly motivating for the students and provides a formidable opportunity for a scientific community to unite and increase its visibility. We report on our experience with Meet-U in two French universities with master's students in bioinformatics and modeling, with protein-protein docking as the subject of the course. Meet-U is easy to implement and can be straightforwardly transferred to other fields and/or universities. All the information and data are available at
    Mots-clés : AMIG, B3S, BDG, BIM.

  • C. Adam, R. Guérois, A. Citarella, L. Verardi, F. Adolphe, C. Béneut, V. Sommermeyer, C. Ramus, J. Govin, Y. Couté, et V. Borde, « The PHD finger protein Spp1 has distinct functions in the Set1 and the meiotic DSB formation complexes », PLOS Genetics, vol. 14, nᵒ 2, p. e1007223, févr. 2018.

  • L. Ahmad, S. Plancqueel, V. Dubosclard, N. Lazar, W. Ghattas, I. Li de la Sierra-Gallay, H. van Tilbeurgh, et L. Salmon, « Crystal structure of phosphomannose isomerase from Candida albicans complexed with 5-phospho-d-arabinonhydrazide », FEBS letters, vol. 592, nᵒ 10, p. 1667-1680, mai 2018.
    Résumé : Type I phosphomannose isomerases (PMIs) are zinc-dependent monofunctional metalloenzymes catalysing the reversible isomerization of d-mannose 6-phosphate to d-fructose 6-phosphate. 5-Phospho-d-arabinonhydrazide (5PAHz), designed as an analogue of the enediolate high-energy intermediate, strongly inhibits PMI from Candida albicans (CaPMI). In this study, we report the 3D crystal structure of CaPMI complexed with 5PAHz at 1.85 Å resolution. The high-resolution structure suggests that Glu294 is the catalytic base that transfers a proton between the C1 and C2 carbon atoms of the substrate. Bidentate coordination of the inhibitor explains the stereochemistry of the isomerase activity, as well as the absence of both anomerase and C2-epimerase activities for Type I PMIs. A detailed mechanism of the reversible isomerization is proposed.
    Mots-clés : B3S, Candida albicans, enzyme mechanism, FAAM, inhibitor, phosphomannose isomerase, zinc metalloenzyme.

  • G. Annio, T. L. Jennings, O. Tagit, et N. Hildebrandt, « Sensitivity Enhancement of Förster Resonance Energy Transfer Immunoassays by Multiple Antibody Conjugation on Quantum Dots », Bioconjugate Chemistry, vol. 29, nᵒ 6, p. 2082-2089, juin 2018.
    Résumé : Quantum dots (QDs) are not only advantageous for color-tuning, improved brightness, and high stability, but their nanoparticle surfaces also allow for the attachment of many biomolecules. Because IgG antibodies (AB) are in the same size range of biocompatible QDs and the AB orientation after conjugation to the QD is often random, it is difficult to predict if few or many AB per QD will lead to an efficient AB-QD conjugate. This is particularly true for homogeneous Förster resonance energy transfer (FRET) sandwich immunoassays, for which the AB on the QD must bind a biomarker that needs to bind a second AB-FRET-conjugate. Here, we investigate the performance of Tb-to-QD FRET immunoassays against total prostate specific antigen (TPSA) by changing the number of AB per QD while leaving all the other assay components unchanged. We first characterize the AB-QD conjugation by various spectroscopic, microscopic, and chromatographic techniques and then quantify the TPSA immunoassay performance regarding sensitivity, limit of detection, and dynamic range. Our results show that an increasing conjugation ratio leads to significantly enhanced FRET immunoassays. These findings will be highly important for developing QD-based immunoassays in which the concentrations of both AB and QDs can significantly influence the assay performance.
    Mots-clés : B3S, NANO.

  • M. Bakail, S. Rodriguez-Marin, Z. Hegedüs, M. E. Perrin, F. Ochsenbein, et A. J. Wilson, « Recognition of ASF1 Using Hydrocarbon Constrained Peptides », Chembiochem: A European Journal of Chemical Biology, déc. 2018.
    Résumé : Inhibition of the histone H3-ASF1 (anti-silencing function 1) protein-protein interaction (PPI) represents a potential approach for treatment of numerous cancers. As an α-helix mediated PPI, constraint of the key histone H3 helix (residues 118-135) represents a strategy through which chemical probes might be elaborated to test this hypothesis. In this work variant H3118-135 peptides bearing pentenyl glycine residues at i and i + 4 positions were constrained by olefin metathesis. Biophysical analyses revealed that promotion of a bioactive helical conformation depends on the position at which the constraint is introduced, but that potency of binding towards ASF1 is unaffected by the constraint and instead that enthalpy-entropy compensation occurs.
    Mots-clés : AMIG, B3S, protein-protein interactions histone chaperonnes constrained peptides protein surface recognition chemical biology.

  • A. Barwinska-Sendra, A. Baslé, K. J. Waldron, et S. Un, « A charge polarization model for the metal-specific activity of superoxide dismutases », Physical chemistry chemical physics: PCCP, janv. 2018.
    Résumé : The pathogenicity of Staphylococcus aureus is enhanced by having two superoxide dismutases (SODs): a Mn-specific SOD and another that can use either Mn or Fe. Using 94 GHz electron-nuclear double resonance (ENDOR) and electron double resonance detected (ELDOR)-NMR we show that, despite their different metal-specificities, their structural and electronic similarities extend down to their active-site 1H- and 14N-Mn(ii) hyperfine interactions. However these interactions, and hence the positions of these nuclei, are different in the inactive Mn-reconstituted Escherichia coli Fe-specific SOD. Density functional theory modelling attributes this to a different angular position of the E. coli H171 ligand. This likely disrupts the Mn-H171-E170' triad causing a shift in charge and in metal redox potential, leading to the loss of activity. This is supported by the correlated differences in the Mn(ii) zero-field interactions of the three SOD types and suggests that the triad is important for determining metal specific activity.
    Mots-clés : B3S, BHFMR.

  • A. Belyy, I. Santecchia, L. Renault, B. Bourigault, D. Ladant, et U. Mechold, « The extreme C-terminus of the Pseudomonas aeruginosa effector ExoY is crucial for binding to its eukaryotic activator, F-actin », The Journal of Biological Chemistry, oct. 2018.
    Résumé : Bacterial nucleotidyl cyclase toxins are potent virulence factors that upon entry into eukaryotic cells are stimulated by endogenous cofactors to catalyse the production of large amounts of 3'5'-cyclic nucleoside monophosphates. The activity of the effector ExoY from Pseudomonas aeruginosa is stimulated by the filamentous form of actin (F-actin). Utilising yeast phenotype analysis, site-directed mutagenesis, functional biochemical assays and confocal microscopy, we demonstrate that the last 9 amino acids of the C-terminus of ExoY are crucial for the interaction with F-actin and, consequently, for ExoY's enzymatic activity in vitro and toxicity in a yeast model. We observed that isolated C-terminal sequences of P. aeruginosa ExoY, that had been fused to a carrier protein, bind to F-actin, and that synthetic peptides corresponding to the extreme ExoY C-terminus inhibit ExoY enzymatic activity in vitro and compete with the full-length enzyme for F-actin binding. Interestingly, we noted that various P. aeruginosa isolates of the PA14 family, including highly virulent strains, harbour ExoY variants with a mutation altering the C-terminus of this effector. We found that these naturally occurring ExoY variants display drastically reduced enzymatic activity and toxicity. Our findings shed light on the molecular basis of the ExoY-F-actin interaction, revealing that the extreme C terminus of ExoY is critical for binding to F-actin in target cells and that some P. aeruginosa isolates carry C-terminally mutated, low-activity ExoY variants.
    Mots-clés : ACTIN, B3S, ExoY, Pseudomonas aeruginosa (P. aeruginosa).

  • A. Berto, J. Yu, S. Morchoisne-Bolhy, C. Bertipaglia, R. Vallee, J. Dumont, F. Ochsenbein, R. Guerois, et V. Doye, « Disentangling the molecular determinants for Cenp-F localization to nuclear pores and kinetochores », EMBO reports, vol. 19, nᵒ 5, mai 2018.
    Résumé : Cenp-F is a multifaceted protein implicated in cancer and developmental pathologies. The Cenp-F C-terminal region contains overlapping binding sites for numerous proteins that contribute to its functions throughout the cell cycle. Here, we focus on the nuclear pore protein Nup133 that interacts with Cenp-F both at nuclear pores in prophase and at kinetochores in mitosis, and on the kinase Bub1, known to contribute to Cenp-F targeting to kinetochores. By combining in silico structural modeling and yeast two-hybrid assays, we generate an interaction model between a conserved helix within the Nup133 β-propeller and a short leucine zipper-containing dimeric segment of Cenp-F. We thereby create mutants affecting the Nup133/Cenp-F interface and show that they prevent Cenp-F localization to the nuclear envelope, but not to kinetochores. Conversely, a point mutation within an adjacent leucine zipper affecting the kinetochore targeting of Cenp-F KT-core domain impairs its interaction with Bub1, but not with Nup133, identifying Bub1 as the direct KT-core binding partner of Cenp-F. Finally, we show that Cenp-E redundantly contributes together with Bub1 to the recruitment of Cenp-F to kinetochores.
    Mots-clés : AMIG, B3S, Cenp‐F, in silico modeling, kinetochores, mitosin, nuclear pore.

  • A. Boussac, I. Ugur, A. Marion, M. Sugiura, V. R. I. Kaila, et A. W. Rutherford, « The low spin - high spin equilibrium in the S2-state of the water oxidizing enzyme », Biochimica Et Biophysica Acta, vol. 1859, nᵒ 5, p. 342-356, févr. 2018.
    Résumé : In Photosystem II (PSII), the Mn4CaO5-cluster of the active site advances through five sequential oxidation states (S0to S4) before water is oxidized and O2is generated. Here, we have studied the transition between the low spin (LS) and high spin (HS) configurations of S2using EPR spectroscopy, quantum chemical calculations using Density Functional Theory (DFT), and time-resolved UV-visible absorption spectroscopy. The EPR experiments show that the equilibrium between S2LSand S2HSis pH dependent, with a pKa ≈ 8.3 (n ≈ 4) for the native Mn4CaO5and pKa ≈ 7.5 (n ≈ 1) for Mn4SrO5. The DFT results suggest that exchanging Ca with Sr modifies the electronic structure of several titratable groups within the active site, including groups that are not direct ligands to Ca/Sr, e.g., W1/W2, Asp61, His332 and His337. This is consistent with the complex modification of the pKaupon the Ca/Sr exchange. EPR also showed that NH3addition reversed the effect of high pH, NH3-S2LSbeing present at all pH values studied. Absorption spectroscopy indicates that NH3is no longer bound in the S3TyrZstate, consistent with EPR data showing minor or no NH3-induced modification of S3and S0. In both Ca-PSII and Sr-PSII, S2HSwas capable of advancing to S3at low temperature (198 K). This is an experimental demonstration that the S2LSis formed first and advances to S3via the S2HSstate without detectable intermediates. We discuss the nature of the changes occurring in the S2LSto S2HStransition which allow the S2HSto S3transition to occur below 200 K. This work also provides a protocol for generating S3in concentrated samples without the need for saturating flashes.
    Mots-clés : B3S, DFT, EPR, Mn(4)CaO(5) cluster, Oxygen evolution, Photosystem II, PS2, Spin state.

  • M. Byrdin, C. Duan, D. Bourgeois, et K. Brettel, « A Long-Lived Triplet State Is the Entrance Gateway to Oxidative Photochemistry in Green Fluorescent Proteins », Journal of the American Chemical Society, vol. 140, nᵒ 8, p. 2897-2905, févr. 2018.
    Résumé : Though ubiquitously used as selective fluorescence markers in cellular biology, fluorescent proteins (FPs) still have not disclosed all of their surprising properties. One important issue, notably for single-molecule applications, is the nature of the triplet state, suggested to be the starting point for many possible photochemical reactions leading to phenomena such as blinking or bleaching. Here, we applied transient absorption spectroscopy to characterize dark states in the prototypical enhanced green fluorescent protein (EGFP) of hydrozoan origin and, for comparison, in IrisFP, a representative phototransformable FP of anthozoan origin. We identified a long-lived (approximately 5 ms) dark state that is formed with a quantum yield of approximately 1% and has pronounced absorption throughout the visible-NIR range (peak at around 900 nm). Detection of phosphorescence emission with identical kinetics and excitation spectrum allowed unambiguous identification of this state as the first excited triplet state of the deprotonated chromophore. This triplet state was further characterized by determining its phosphorescence emission spectrum, the temperature dependence of its decay kinetics and its reactivity toward oxygen and electron acceptors and donors. It is suggested that it is this triplet state that lies at the origin of oxidative photochemistry in green FPs, leading to phenomena such as so-called "oxidative redding", "primed photoconversion", or, in a manner similar to that previously observed for organic dyes, redox induced blinking control with the reducing and oxidizing system ("ROXS").
    Mots-clés : B3S, LPB.

  • M. Cardoso Dos Santos, J. Goetz, H. Bartenlian, K. - L. Wong, L. J. Charbonnière, et N. Hildebrandt, « Autofluorescence-Free Live-Cell Imaging Using Terbium Nanoparticles », Bioconjugate Chemistry, févr. 2018.

  • F. Celli, A. Petitalot, C. Samson, F. - X. Theillet, et S. Zinn-Justin, « H-1, C-13 and N-15 backbone resonance assignment of the lamin C-terminal region specific to prelamin A », Biomolecular Nmr Assignments, vol. 12, nᵒ 2, p. 225-229, oct. 2018.
    Résumé : Lamins are the main components of the nucleoskeleton. They form a protein meshwork that underlies the inner nuclear membrane. Mutations in the LMNA gene coding for A-type lamins (lamins A and C) cause a large panel of human diseases, referred to as laminopathies. These diseases include muscular dystrophies, lipodystrophies and premature aging diseases. Lamin A exhibits a C-terminal region that is different from lamin C and is post-translationally modified. It is produced as prelamin A and it is then farnesylated, cleaved, carboxymethylated and cleaved again in order to become mature lamin A. In patients with the severe Hutchinson-Gilford progeria syndrome, a specific single point mutation in LMNA leads to an aberrant splicing of the LMNA gene preventing the post-translational processing of prelamin A. This leads to the accumulation of a permanently farnesylated lamin A mutant lacking 50 amino acids named progerin. We here report the NMR H-1, N-15, (CO)-C-13, C-13 and C-13 chemical shift assignment of the C-terminal region that is specific to prelamin A, from amino acid 567 to amino acid 664. We also report the NMR H-1, N-15, (CO)-C-13, C-13 and C-13 chemical shift assignment of the C-terminal region of the progerin variant, from amino acid 567 to amino acid 614. Analysis of these chemical shift data confirms that both prelamin A and progerin C-terminal domains are largely disordered and identifies a common partially populated -helix from amino acid 576 to amino acid 585. This helix is well conserved from fishes to mammals.
    Mots-clés : B3S, INTGEN, Intrinsically disordered protein, mutations, networks, NMR spectroscopy, NMR spectroscopy, Nuclear envelope, Nucleoskeleton.

  • H. - J. Chang, P. Mayonove, A. Zavala, A. De Visch, P. Minard, M. Cohen-Gonsaud, et J. Bonnet, « A Modular Receptor Platform To Expand the Sensing Repertoire of Bacteria », ACS synthetic biology, vol. 7, nᵒ 1, p. 166-175, janv. 2018.
    Résumé : Engineered bacteria promise to revolutionize diagnostics and therapeutics, yet many applications are precluded by the limited number of detectable signals. Here we present a general framework to engineer synthetic receptors enabling bacterial cells to respond to novel ligands. These receptors are activated via ligand-induced dimerization of a single-domain antibody fused to monomeric DNA-binding domains (split-DBDs). Using E. coli as a model system, we engineer both transmembrane and cytosolic receptors using a VHH for ligand detection and demonstrate the scalability of our platform by using the DBDs of two different transcriptional regulators. We provide a method to optimize receptor behavior by finely tuning protein expression levels and optimizing interdomain linker regions. Finally, we show that these receptors can be connected to downstream synthetic gene circuits for further signal processing. The general nature of the split-DBD principle and the versatility of antibody-based detection should support the deployment of these receptors into various hosts to detect ligands for which no receptor is found in nature.
    Mots-clés : B3S, MIP.

  • G. Chararalambidis, S. Das, A. Trapali, A. Quaranta, M. Orio, Z. Halime, P. Fertey, R. Guillot, A. Coutsolelos, W. Leibl, A. Aukauloo, et M. Sircoglou, « Water Molecules Gating a Photoinduced One Electron Two Protons Transfer in a Tyr/His model of Photosystem II », Angewandte Chemie (International Ed. in English), mai 2018.
    Résumé : In this report, we investigate on a biomimetic model of a H-bonded TyrZ/His190 pair covalently attached to a porphyrin sensitizer. Laser flash photolysis in presence of an external electron acceptor reveals the need of water molecules to unlock the light-induced oxidation of the phenol through an intramolecular pathway. Kinetics monitoring encompasses two fast phases with distinct spectral properties. The first phase is related to one-electron transfer from the phenol to the porphyrin radical cation coupled with a domino two-proton transfer leading to the ejection of a proton from the imidazole-phenol pair. The second phase concerns the convoy of the released proton to the porphyrin N4 coordinating cavity. Importantly, our study provides an unprecedented example of light induced electron transfer process in a TyrZ/His190 model of Photosystem II, evidencing the movement of both the phenol and imidazole protons along an isoenergetic pathway.
    Mots-clés : artificial photosynthesis, B3S, LPB, Proton Coupled Electron Transfer, TyrZ-His190 model.

  • C. Chen, L. Ao, Y. - T. Wu, V. Cifliku, M. C. Dos Santos, E. Bourrier, M. Delbianco, D. Parker, J. M. Zwier, L. Huang, et N. Hildebrandt, « Single-Nanoparticle Cell Barcoding by Tunable FRET from Lanthanides to Quantum Dots », Angewandte Chemie-International Edition, vol. 57, nᵒ 41, p. 13686-13690, oct. 2018.
    Résumé : Fluorescence barcoding based on nanoparticles provides many advantages for multiparameter imaging. However, creating different concentration-independent codes without mixing various nanoparticles and by using single-wavelength excitation and emission for multiplexed cellular imaging is extremely challenging. Herein, we report the development of quantum dots (QDs) with two different SiO2 shell thicknesses (6 and 12nm) that are coated with two different lanthanide complexes (Tb and Eu). FRET from the Tb or Eu donors to the QD acceptors resulted in four distinct photoluminescence (PL) decays, which were encoded by simple time-gated (TG) PL intensity detection in three individual temporal detection windows. The well-defined single-nanoparticle codes were used for live cell imaging and a one-measurement distinction of four different cells in a single field of view. This single-color barcoding strategy opens new opportunities for multiplexed labeling and tracking of cells.
    Mots-clés : B3S, biomolecules, biosensors, bright, europium complexes, FRET, Lanthanides, Lifetime, NANO.

  • C. Chen, C. Midelet, S. Bhuckory, N. Hildebrandt, et M. H. V. Werts, « Nanosurface Energy Transfer from Long-Lifetime Terbium Donors to Gold Nanoparticles », Journal of Physical Chemistry C, vol. 122, nᵒ 30, p. 17566-17574, août 2018.
    Résumé : Photoluminescence (PL) quenching by gold nanoparticles (AuNPs) is a frequently applied principle in nanobiosensing. The quenching is most often explained in terms of the Forster resonance energy-transfer (FRET) mechanism, and more rarely in terms of the nanosurface energy-transfer (NSET) mechanism. Although both consider nonradiative resonance energy transfer, there are significant differences in predictions of the strength and the distance-dependence of the quenching. Here, we investigate the energy transfer to AuNPs from a terbium(III)-complex (Tb) with a long (millisecond) PL decay time with the aim to provide a better understanding of the underlying energy-transfer process. The binding of Tb-labeled streptavidin (Tb-sAv) to biotinylated AuNPs (biot-AuNPs) was studied using light-scattering spectroscopy. Quenching of the PL of Tb-sAv upon binding to biotAuNPs of different diameters (5, 30, 50, 80 nm) was studied by time-resolved PL spectroscopy. Energy-transfer efficiencies were found to be practically independent of the AuNP size. Analysis according to FRET theory yielded donor-acceptor distances that were inconsistent and far beyond the expected Tb-AuNP distance. In contrast, the NSET model yielded a good agreement between the Tb-to-AuNP surface distance estimated from the geometry of the Tb-sAv/biotin-AuNP assembly (4.5 nm) and those calculated from PL lifetime analysis, which range from 4.0 to 6.3 nm. Our findings strongly suggest that NSET (and not FRET) is the operational mechanism in PL quenching by AuNPs, which is important information for the development, characterization, and application of nanobiosensors based on PL quenching by AuNPs.
    Mots-clés : B3S, binding, fluorescence, metal, microscopy, modulation, NANO, quantum dots, single, spectroscopy, surface-plasmon resonance.

  • J. - H. Chen, L. - J. Yu, A. Boussac, Z. - Y. Wang-Otomo, T. Kuang, et J. - R. Shen, « Properties and structure of a low-potential, penta-heme cytochrome c 552 from a thermophilic purple sulfur photosynthetic bacterium Thermochromatium tepidum », Photosynthesis Research, avr. 2018.
    Résumé : The thermophilic purple sulfur bacterium Thermochromatium tepidum possesses four main water-soluble redox proteins involved in the electron transfer behavior. Crystal structures have been reported for three of them: a high potential iron-sulfur protein, cytochrome c', and one of two low-potential cytochrome c 552 (which is a flavocytochrome c) have been determined. In this study, we purified another low-potential cytochrome c 552 (LPC), determined its N-terminal amino acid sequence and the whole gene sequence, characterized it with absorption and electron paramagnetic spectroscopy, and solved its high-resolution crystal structure. This novel cytochrome was found to contain five c-type hemes. The overall fold of LPC consists of two distinct domains, one is the five heme-containing domain and the other one is an Ig-like domain. This provides a representative example for the structures of multiheme cytochromes containing an odd number of hemes, although the structures of multiheme cytochromes with an even number of hemes are frequently seen in the PDB database. Comparison of the sequence and structure of LPC with other proteins in the databases revealed several characteristic features which may be important for its functioning. Based on the results obtained, we discuss the possible intracellular function of this LPC in Tch. tepidum.
    Mots-clés : B3S, Crystal structure, Cytochrome c, Electron transfer, Multiheme, PS2, Purple sulfur bacteria, Thermochromatium tepidum.

  • M. Chevreuil, D. Law-Hine, J. Chen, S. Bressanelli, S. Combet, D. Constantin, J. Degrouard, J. Möller, M. Zeghal, et G. Tresset, « Nonequilibrium self-assembly dynamics of icosahedral viral capsids packaging genome or polyelectrolyte », Nature Communications, vol. 9, nᵒ 1, p. 3071, août 2018.
    Résumé : The survival of viruses partly relies on their ability to self-assemble inside host cells. Although coarse-grained simulations have identified different pathways leading to assembled virions from their components, experimental evidence is severely lacking. Here, we use time-resolved small-angle X-ray scattering to uncover the nonequilibrium self-assembly dynamics of icosahedral viral capsids packaging their full RNA genome. We reveal the formation of amorphous complexes via an en masse pathway and their relaxation into virions via a synchronous pathway. The binding energy of capsid subunits on the genome is moderate (~7kBT0, with kB the Boltzmann constant and T0 = 298 K, the room temperature), while the energy barrier separating the complexes and the virions is high (~ 20kBT0). A synthetic polyelectrolyte can lower this barrier so that filled capsids are formed in conditions where virions cannot build up. We propose a representation of the dynamics on a free energy landscape.
    Mots-clés : B3S, cryoelectron microscopy, disassembly, IMAPP, kinetic pathway, mechanism, Modeling, nanoparticles, pathway, plant-virus, protein, reconstruction, rna, templates, time-resolved small-angle X-ray scattering, Virus, virus-like particles.

  • R. R. Choubeh, E. Wientjes, P. C. Struik, D. Kirilovsky, et H. van Amerongen, « State transitions in the cyanobacterium Synechococcus elongatus 7942 involve reversible quenching of the photosystem II core », Biochimica Et Biophysica Acta-Bioenergetics, vol. 1859, nᵒ 10, p. 1059-1066, oct. 2018.
    Résumé : Cyanobacteria use chlorophyll and phycobiliproteins to harvest light. The resulting excitation energy is delivered to reaction centers (RCs), where photochemistry starts. The relative amounts of excitation energy arriving at the RCs of photosystem I (PSI) and II (PSII) depend on the spectral composition of the light. To balance the excitations in both photosystems, cyanobacteria perform state transitions to equilibrate the excitation energy. They go to state I if PSI is preferentially excited, for example after illumination with blue light (light I), and to state II after illumination with green-orange light (light II) or after dark adaptation. In this study, we performed 77-K time-resolved fluorescence spectroscopy on wild-type Synechococcus elongatus 7942 cells to measure how state transitions affect excitation energy transfer to PSI and PSII in different light conditions and to test the various models that have been proposed in literature. The time-resolved spectra show that the PSII core is quenched in state II and that this is not due to a change in excitation energy transfer from PSII to PSI (spill-over), either direct or indirect via phycobilisomes.
    Mots-clés : B3S, cells, Cyanobacteria, excitation-energy, less mutant, MROP, photosynthesis, Photosystem II, phycobilisome, picosecond fluorescence spectroscopy, porphyridium-cruentum, State transitions, synechococcus sp, synechocystis pcc 6803, Time-resolved fluorescence spectroscopy, wild-type.

  • M. David, C. Lebrun, T. Duguet, F. Talmont, R. Beech, S. Orlowski, F. André, R. K. Prichard, et A. Lespine, « Structural model, functional modulation by ivermectin and tissue localization of Haemonchus contortus P-glycoprotein-13 », International Journal for Parasitology. Drugs and Drug Resistance, vol. 8, nᵒ 1, p. 145-157, avr. 2018.
    Résumé : Haemonchus contortus, one of the most economically important parasites of small ruminants, has become resistant to the anthelmintic ivermectin. Deciphering the role of P-glycoproteins in ivermectin resistance is desirable for understanding and overcoming this resistance. In the model nematode, Caenorhabditis elegans, P-glycoprotein-13 is expressed in the amphids, important neuronal structures for ivermectin activity. We have focused on its ortholog in the parasite, Hco-Pgp-13. A 3D model of Hco-Pgp-13, presenting an open inward-facing conformation, has been constructed by homology with the Cel-Pgp-1 crystal structure. In silico docking calculations predicted high affinity binding of ivermectin and actinomycin D to the inner chamber of the protein. Following in vitro expression, we showed that ivermectin and actinomycin D modulated Hco-Pgp-13 ATPase activity with high affinity. Finally, we found in vivo Hco-Pgp-13 localization in epithelial, pharyngeal and neuronal tissues. Taken together, these data suggest a role for Hco-Pgp-13 in ivermectin transport, which could contribute to anthelmintic resistance.
    Mots-clés : ABC transporters, B3S, Haemonchus contortus, Homology modeling, Ivermectin, LPSM, LSOD, Nematode, P-glycoprotein.

  • A. De Muyt, A. Pyatnitskaya, J. Andréani, L. Ranjha, C. Ramus, R. Laureau, A. Fernandez-Vega, D. Holoch, E. Girard, J. Govin, R. Margueron, Y. Couté, P. Cejka, R. Guérois, et V. Borde, « A meiotic XPF–ERCC1-like complex recognizes joint molecule recombination intermediates to promote crossover formation », Genes & Development, vol. 32, nᵒ 3-4, p. 283-296, févr. 2018.

  • Z. Edoo, L. Iannazzo, F. Compain, I. Li de la Sierra Gallay, H. van Tilbeurgh, M. Fonvielle, F. Bouchet, E. Le Run, J. - L. Mainardi, M. Arthur, M. Ethève-Quelquejeu, et J. - E. Hugonnet, « Synthesis of Avibactam Derivatives and Activity on β-Lactamases and Peptidoglycan Biosynthesis Enzymes of Mycobacteria », Chemistry (Weinheim an Der Bergstrasse, Germany), vol. 24, nᵒ 32, p. 8081-8086, juin 2018.
    Résumé : There is a renewed interest for β-lactams for treating infections due to Mycobacterium tuberculosis and M. abscessus because their β-lactamases are inhibited by classical (clavulanate) or new generation (avibactam) inhibitors, respectively. Here, access to an azido derivative of the diazabicyclooctane (DBO) scaffold of avibactam for functionalization by the Huisgen-Sharpless cycloaddition reaction is reported. The amoxicillin-DBO combinations were active, indicating that the triazole ring is compatible with drug penetration (minimal inhibitory concentration of 16 μg mL-1 for both species). Mechanistically, β-lactamase inhibition was not sufficient to account for the potentiation of amoxicillin by DBOs. Thus, the latter compounds were investigated as inhibitors of l,d-transpeptidases (Ldts), which are the main peptidoglycan polymerases in mycobacteria. The DBOs acted as slow-binding inhibitors of Ldts by S-carbamoylation indicating that optimization of DBOs for Ldt inhibition is an attractive strategy to obtain drugs selectively active on mycobacteria.
    Mots-clés : Avibactam, Azabicyclo Compounds, B3S, beta-Lactamase Inhibitors, beta-Lactamases, FAAM, l,d-transpeptidases, Mycobacterium abscessus, Mycobacterium tuberculosis, Peptidoglycan, β-lactamase.

  • J. B. Fernandes, M. Duhamel, M. Seguéla-Arnaud, N. Froger, C. Girard, S. Choinard, V. Solier, N. De Winne, G. De Jaeger, K. Gevaert, P. Andrey, M. Grelon, R. Guerois, R. Kumar, et R. Mercier, « FIGL1 and its novel partner FLIP form a conserved complex that regulates homologous recombination », PLOS Genetics, vol. 14, nᵒ 4, p. e1007317, avr. 2018.

  • D. Georgess, P. Spuul, C. Le Clainche, D. Le Nihouannen, I. Fremaux, T. Dakhli, D. M. Delannoy López, D. Deffieux, P. Jurdic, S. Quideau, et E. Génot, « Anti-osteoclastic effects of C-glucosidic ellagitannins mediated by actin perturbation », European Journal of Cell Biology, sept. 2018.
    Résumé : Actin subunits assemble into actin filaments whose dynamics and three-dimensional architectures are further regulated by a variety of cellular factors to establish the functional actin cytoskeleton. The C-glucosidic ellagitannin vescalagin and its simpler analogue vescalin, affect both the dynamics and the ultrastructure of the actin cytoskeleton by directly binding to F-actin. Herein, we show that in vitro, the two compounds induce the formation of distinct F-actin networks characterized by different superstructures and dynamics. In living mature osteoclasts, highly specialized bone-degrading cells that constantly remodel their cytoskeleton, vescalagin and vescalin alter actin dynamics at podosomes and compromise the integrity of the podosome belt that forms the bone-degrading apparatus. Both compounds target the bone-resorbing activity at concentrations that preserve osteoclastic maturation and survival and with no detectable impact on the behaviour of bone-forming osteoblastic cells. This anti-osteoclastic activity of vescalagin and vescalin reveals the potential of targeting actin dynamics as a new therapeutic opportunity and, in this case, as a plausible approach for the local treatment of osteoporosis.
    Mots-clés : ACTIN, Actin dynamics, B3S, Cytoskeleton, Medicinal biology, Osteoclast biology, Podosomes, Polyphenol sciences.

  • P. Gotico, A. Del Vecchio, D. Audisio, A. Quaranta, Z. Halime, W. Leibl, et A. Aukauloo, « Visible-Light-Driven Reduction of CO2 to CO and Its Subsequent Valorization in Carbonylation Chemistry and C-13 Isotope Labeling », Chemphotochem, vol. 2, nᵒ 8, p. 715-719, août 2018.
    Résumé : A convenient and safe approach in valorizing carbon monoxide (CO) produced from the photocatalytic reduction of carbon dioxide (CO2) has been investigated. Visible light was used to drive an optimized photocatalytic reduction using a ruthenium trisbipyridine complex as a sensitizer and a rhenium bipyridyl carbonyl complex as a catalyst to perform an efficient reduction of CO2 to CO, which was then simultaneously utilized in a palladium-catalyzed aminocarbonylation reaction at room temperature. This approach provides safe handling of the produced CO which also opens the way for a more efficient application of C-13-isotope and C-14-radioisotope-labeled CO2 in pharmaceutically relevant drug labeling.
    Mots-clés : artificial photosynthesis, B3S, carbon dioxide, carbon-dioxide, carbonylation, continuous-flow, formic-acid, highly efficient, homogeneous catalysts, isotopic labeling, LPB, metal-complexes, photocatalysis, photocatalytic reduction, photochemical reduction, photoredox catalysis, rhenium(i) complex.

  • J. Guo, X. Qiu, C. Mingoes, J. R. Deschamps, K. Susumu, I. L. Medintz, et N. Hildebrandt, « Conformational Details of Quantum Dot-DNA Resolved by Förster Resonance Energy Transfer Lifetime Nanoruler », ACS nano, déc. 2018.
    Résumé : DNA-nanoparticle conjugates are important tools in nanobiotechnology. Knowing the orientation, function, and length of DNA on nanoparticle surfaces at low nanomolar concentrations under physiological conditions is therefore of great interest. Here, we investigate the conformation of a 31 nucleotides (nt) long DNA attached to a semiconductor quantum dot (QD) via FRET (Förster resonance energy transfer) from Tb-DNA probes hybridized to different positions on the QD-DNA. Precise Tb-to-QD distance determination from 7 to 14 nm along 26 nt of the peptide-appended QD-DNA were realized by time-resolved FRET spectroscopy. The FRET nanoruler measured linear single-stranded (ssDNA) and double-stranded (dsDNA) extensions of ~0.15 and ~0.31 nm per base, reflecting the different conformations. Comparison with biomolecular modeling confirmed the denser conformation of ssDNA and a possibly more flexible orientation on the QD surface, whereas the dsDNA was fully extended with radial orientation. The temporally distinct photoluminescence decays of the different DNA-FRET-configurations were used for prototypical DNA hybridization assays that demonstrated the large potential for extended temporal multiplexing. The extensive experimental and theoretical analysis of 11 different distances/configurations of the same QD-DNA conjugate provided important information of DNA conformation on nanoparticle surfaces and will be an important benchmark for the development and optimization of DNA-nanobiosensors.
    Mots-clés : B3S, NANO.

  • M. - H. Ha-Thi, V. - T. Pham, T. Pino, V. Maslova, A. Quaranta, C. Lefumeux, W. Leibl, et A. Aukauloo, « Photoinduced electron transfer in a molecular dyad by nanosecond pump-pump-probe spectroscopy », Photochemical & Photobiological Sciences, vol. 17, nᵒ 7, p. 903-909, juill. 2018.
    Résumé : The design of robust and inexpensive molecular photocatalysts for the conversion of abundant stable molecules like H2O and CO2 into an energetic carrier is one of the major fundamental questions for scientists nowadays. The outstanding challenge is to couple single photoinduced charge separation events with the sequential accumulation of redox equivalents at the catalytic unit for performing multielectronic catalytic reactions. Herein, double excitation by nanosecond pump-pump-probe experiments was used to interrogate the photoinduced charge transfer and charge accumulation on a molecular dyad composed of a porphyrin chromophore and a ruthenium-based catalyst in the presence of a reversible electron acceptor. An accumulative charge transfer state is unattainable because of rapid reverse electron transfer to the photosensitizer upon the second excitation and the low driving force of the forward photodriven electron transfer reaction. Such a method allows the fundamental understanding of the relaxation mechanism after two sequential photon absorptions, deciphering the undesired electron transfer reactions that limit the charge accumulation efficiency. This study is a step toward the improvement of synthetic strategies of molecular photocatalysts for light-induced charge accumulation and more generally, for solar energy conversion.
    Mots-clés : accumulative charge separation, artificial photosynthesis, B3S, catalytic water oxidation, co2, complex, LPB, photocatalysts, photosensitizer, photosystem-ii, reduction, solar-energy.

  • D. Harris, A. Wilson, F. Muzzopappa, N. N. Sluchanko, T. Friedrich, E. G. Maksimov, D. Kirilovsky, et N. Adir, « Structural rearrangements in the C-terminal domain homolog of Orange Carotenoid Protein are crucial for carotenoid transfer », Communications Biology, vol. 1, p. 125, 2018.
    Résumé : A recently reported family of soluble cyanobacterial carotenoproteins, homologs of the C-terminal domain (CTDH) of the photoprotective Orange Carotenoid Protein, is suggested to mediate carotenoid transfer from the thylakoid membrane to the Helical Carotenoid Proteins, which are paralogs of the N-terminal domain of the OCP. Here we present the three-dimensional structure of a carotenoid-free CTDH variant from Anabaena (Nostoc) PCC 7120. This CTDH contains a cysteine residue at position 103. Two dimer-forming interfaces were identified, one stabilized by a disulfide bond between monomers and the second between each monomer's β-sheets, both compatible with small-angle X-ray scattering data and likely representing intermediates of carotenoid transfer processes. The crystal structure revealed a major positional change of the C-terminal tail. Further mutational analysis revealed the importance of the C-terminal tail in both carotenoid uptake and delivery. These results have allowed us to suggest a detailed model for carotenoid transfer via these soluble proteins.
    Mots-clés : B3S, MROP.

  • N. Hildebrandt et O. Tagit, « Colloidal Nanoparticles for Signal Enhancement in Optical Diagnostic Assays », Journal of Nanoscience and Nanotechnology, vol. 18, nᵒ 10, p. 6671-6679, oct. 2018.
    Résumé : The use of nanotechnologies for the development of highly sensitive and affordable diagnostic assays has significantly improved the ability to detect and characterize multiple types of biomarkers. Semiconductor and metal nanoparticles with unique optical properties have been successfully integrated within biomarker detection schemes for the generation and enhancement of optical signals in label-based and label-free assays. Highly sensitive label-based diagnostics has been realized particularly via using quantum dots (QDs) as labeling probes. Similarly, many label-free techniques that are emerging as potential complements to label-based approaches benefit from signal enhancement strategies using e.g., metal nanoparticles. This review presents a concise overview of recent advances in diagnostic assays that utilize nanoparticles for the generation and enhancement of optical signals in fluorescence- and surface plasmon resonance-based techniques. Advanced diagnostic assays that utilize nanoparticles provide major improvements in detection sensitivity, which can potentially meet the challenging requirements of clinical diagnostics.
    Mots-clés : B3S, NANO.

  • G. Hutinet, A. Besle, O. Son, S. McGovern, R. Guerois, M. - A. Petit, F. Ochsenbein, et F. Lecointe, « Sak4 of Phage HK620 Is a RecA Remote Homolog With Single-Strand Annealing Activity Stimulated by Its Cognate SSB Protein », Frontiers in Microbiology, vol. 9, p. 743, 2018.
    Résumé : Bacteriophages are remarkable for the wide diversity of proteins they encode to perform DNA replication and homologous recombination. Looking back at these ancestral forms of life may help understanding how similar proteins work in more sophisticated organisms. For instance, the Sak4 family is composed of proteins similar to the archaeal RadB protein, a Rad51 paralog. We have previously shown that Sak4 allowed single-strand annealing in vivo, but only weakly compared to the phage λ Redβ protein, highlighting putatively that Sak4 requires partners to be efficient. Here, we report that the purified Sak4 of phage HK620 infecting Escherichia coli is a poorly efficient annealase on its own. A distant homolog of SSB, which gene is usually next to the sak4 gene in various species of phages, highly stimulates its recombineering activity in vivo. In vitro, Sak4 binds single-stranded DNA and performs single-strand annealing in an ATP-dependent way. Remarkably, the single-strand annealing activity of Sak4 is stimulated by its cognate SSB. The last six C-terminal amino acids of this SSB are essential for the binding of Sak4 to SSB-covered single-stranded DNA, as well as for the stimulation of its annealase activity. Finally, expression of sak4 and ssb from HK620 can promote low-level of recombination in vivo, though Sak4 and its SSB are unable to promote strand exchange in vitro. Regarding its homology with RecA, Sak4 could represent a link between two previously distinct types of recombinases, i.e., annealases that help strand exchange proteins and strand exchange proteins themselves.
    Mots-clés : AMIG, annealase, B3S, bacteriophage, Rad51 paralog, RecA, recombineering, Sak4, SSB, strand exchange protein.

  • W. Jalby, D. Kuck, A. D. Malony, M. Masella, A. Mazouz, et M. Popov, « The Long and Winding Road Toward Efficient High-Performance Computing », Proceedings of the Ieee, vol. 106, nᵒ 11, p. 1985-2003, nov. 2018.
    Résumé : The major challenge to Exaflop computing, and more generally, efficient high-end computing, is in finding the best "matches" between advanced hardware capabilities and the software used to program applications, so that top performance will be achieved. Several benchmarks show very disappointing performance progress over the last decade, clearly indicating a mismatch between hardware and software. To remedy this problem, it is important that key performance enablers at the software level-autotuning, performance analysis tools, full application optimization-are understood. For each area, we highlight major limitations and most promising approaches to reaching better performance and energy levels. Finally, we conclude by analyzing hardware and software design, trying to pave the way for more tightly integrated hardware and software codesign.
    Mots-clés : Autotuning, B3S, benchmarking, code, design, hardware design, implementation, INTGEN, molecular dynamics, molecular-dynamics, performance evaluation tools.

  • N. Jamin, M. Garrigos, C. Jaxel, A. Frelet-Barrand, et S. Orlowski, « Ectopic Neo-Formed Intracellular Membranes in Escherichia coli: A Response to Membrane Protein-Induced Stress Involving Membrane Curvature and Domains », Biomolecules, vol. 8, nᵒ 3, p. 88, sept. 2018.
    Résumé : Bacterial cytoplasmic membrane stress induced by the overexpression of membrane proteins at high levels can lead to formation of ectopic intracellular membranes. In this review, we report the various observations of such membranes in Escherichia coli, compare their morphological and biochemical characterizations, and we analyze the underlying molecular processes leading to their formation. Actually, these membranes display either vesicular or tubular structures, are separated or connected to the cytoplasmic membrane, present mono- or polydispersed sizes and shapes, and possess ordered or disordered arrangements. Moreover, their composition differs from that of the cytoplasmic membrane, with high amounts of the overexpressed membrane protein and altered lipid-to-protein ratio and cardiolipin content. These data reveal the importance of membrane domains, based on local specific lipid-protein and protein-protein interactions, with both being crucial for local membrane curvature generation, and they highlight the strong influence of protein structure. Indeed, whether the cylindrically or spherically curvature-active proteins are actively curvogenic or passively curvophilic, the underlying molecular scenarios are different and can be correlated with the morphological features of the neo-formed internal membranes. Delineating these molecular mechanisms is highly desirable for a better understanding of protein-lipid interactions within membrane domains, and for optimization of high-level membrane protein production in E. coli.
    Mots-clés : atp synthase, B3S, bacterial-membranes, cell-membrane, chemotaxis receptor tsr, cytoplasmic membrane, Escherichia coli, fumarate reductase, intracellular membranes, intracytoplasmic membrane, lipid rafts, LPSM, membrane curvature, membrane domains, membrane protein overexpression, phospholipid-synthesis, sn-glycerol-3-phosphate acyltransferase, tubules, vesicles.

  • S. M. Kapetanaki, M. J. Burton, J. Basran, C. Uragami, P. C. E. Moody, J. S. Mitcheson, R. Schmid, N. W. Davies, P. Dorlet, M. H. Vos, N. M. Storey, et E. Raven, « A mechanism for CO regulation of ion channels », Nature Communications, vol. 9, nᵒ 1, p. 907, 2018.
    Résumé : Despite being highly toxic, carbon monoxide (CO) is also an essential intracellular signalling molecule. The mechanisms of CO-dependent cell signalling are poorly defined, but are likely to involve interactions with heme proteins. One such role for CO is in ion channel regulation. Here, we examine the interaction of CO with KATP channels. We find that CO activates KATP channels and that heme binding to a CXXHX16H motif on the SUR2A receptor is required for the CO-dependent increase in channel activity. Spectroscopic and kinetic data were used to quantify the interaction of CO with the ferrous heme-SUR2A complex. The results are significant because they directly connect CO-dependent regulation to a heme-binding event on the channel. We use this information to present molecular-level insight into the dynamic processes that control the interactions of CO with a heme-regulated channel protein, and we present a structural framework for understanding the complex interplay between heme and CO in ion channel regulation.
    Mots-clés : B3S, LSOD.

  • A. Khadhraoui, P. Gotico, B. Boitrel, W. Leibl, Z. Halime, et A. Aukauloo, « Local ionic liquid environment at a modified iron porphyrin catalyst enhances the electrocatalytic performance of CO2 to CO reduction in water », Chemical Communications, vol. 54, nᵒ 82, p. 11630-11633, oct. 2018.
    Résumé : In this study we report a strategy to attach methylimidazolium fragments as ionic liquid units on an established iron porphyrin catalyst for the selective reduction of CO2 to CO. Importantly, we found that the tetra-methylimidazolium containing porphyrin exhibits an exalted electrocatalytic activity at low overpotential in water precluding the need for an external proton donor.
    Mots-clés : B3S, benchmarking, carbon-dioxide, co2-to-co electrochemical conversion, complex, driven, efficient, electroreduction, fe, LMB, molecular catalysts, systems.

  • F. Kong, A. Burlacot, Y. Liang, B. Legeret, S. Alseekh, Y. Brotman, A. R. Fernie, A. Krieger-Liszkay, F. Beisson, G. Peltier, et Y. Li-Beisson, « Interorganelle Communication: Peroxisomal MALATE DEHYDROGENASE 2 Connects Lipid Catabolism to Photosynthesis through Redox Coupling in Chlamydomonas », The Plant Cell, juill. 2018.
    Résumé : Plants and algae must tightly coordinate photosynthetic electron transport and metabolic activities given that they often face fluctuating light and nutrient conditions. The exchange of metabolites and signaling molecules between organelles is thought to be central to this regulation but evidence for this is still fragmentary. Here we show that knocking out the peroxisome-located MALATE DEHYDROGENASE 2 (MDH2) of Chlamydomonas reinhardtii results in dramatic alterations not only in peroxisomal fatty acid breakdown but also in chloroplast starch metabolism and photosynthesis. mdh2 mutants accumulated 50% more storage lipid and two-fold more starch than wild type during nitrogen deprivation. In parallel, mdh2 showed increased PSII yield and photosynthetic CO2 fixation. Metabolite analyses revealed a >60% reduction in malate, together with increased levels of NADPH and H2O2 in mdh2. Similar phenotypes were found upon high light exposure. Furthermore, based on the lack of starch accumulation in a knock-out mutant of the H2O2-producing peroxisomal ACYL-COA OXIDASE 2 and on the effects of H2O2 supplementation, we propose that peroxisome-derived H2O2 acts as a regulator of chloroplast metabolism. We conclude that peroxisomal MDH2 helps photoautotrophs cope with nitrogen scarcity and high light by transmitting the redox state of the peroxisome to the chloroplast by means of malate shuttle- and H2O2-based redox signaling.
    Mots-clés : B3S, MROP.

  • P. E. Konold, I. H. M. van Stokkum, F. Muzzopappa, A. Wilson, M. L. Groot, D. Kirilovsky, et J. T. M. Kennis, « Photoactivation mechanism, timing of protein secondary structure dynamics and carotenoid translocation in the Orange Carotenoid Protein », Journal of the American Chemical Society, déc. 2018.
    Résumé : The Orange Carotenoid Protein (OCP) is a two-domain photoactive protein that noncovalently binds an echinenone (ECN) carotenoid and mediates photoprotection in cyanobacteria. In the dark, OCP assumes an orange, inactive state known as OCPO; blue light illumination results in the red active state, known as OCPR. The OCPR state is characterized by large-scale structural changes that involve dissociation and separation of C-terminal and N-terminal domains accompanied by carotenoid translocation into the N-terminal domain. The mechanistic and dynamic-structural relations between photon absorption and formation of the OCPR state have remained largely unknown. Here, we employ a combination of time-resolved UV-visible and (polarized) mid-infrared spectroscopy to assess the electronic and structural dynamics of the carotenoid and the protein secondary structure, from femtoseconds to 0.5 milliseconds. We identify a hereto unidentified carotenoid excited state in OCP, the so-called S* state, which we propose to play a key role in breaking conserved hydrogen-bond interactions between carotenoid and aromatic amino acids in the binding pocket. We arrive at a comprehensive reaction model where the hydrogen-bond rupture with conserved aromatic side chains at the carotenoid β1-ring in picoseconds occurs at a low yield of <1 %, whereby the β1-ring retains a trans configuration with respect to the conjugated π-electron chain. This event initiates structural changes at the N-terminal domain in 1 μs, which allow the carotenoid to translocate into the N-terminal domain in 10 μs. We identified infrared signatures of helical elements that dock on the C-terminal domain β-sheet in the dark and unfold in the light to allow domain separation. These helical elements do not move within the experimental range of 0.5 ms, indicating that domain separation occurs on longer timescales, lagging carotenoid translocation by at least 2 decades of time.
    Mots-clés : B3S, MROP.

  • A. Krieger-Liszkay et S. Thomine, « Importing Manganese into the Chloroplast: Many Membranes to Cross », Molecular Plant, vol. 11, nᵒ 9, p. 1109-1111, août 2018.
    Mots-clés : arabidopsis, B3S, BIOCELL, cells, homeostasis, MINION, MROP, photosynthesis, photosystem-ii, protein.

  • H. Kubota-Kawai, R. Mutoh, K. Shinmura, P. Sétif, M. M. Nowaczyk, M. Rögner, T. Ikegami, H. Tanaka, et G. Kurisu, « X-ray structure of an asymmetrical trimeric ferredoxin–photosystem I complex », Nature Plants, vol. 4, nᵒ 4, p. 218-224, 2018.

  • P. Lafite, F. Andre, J. P. Graves, D. C. Zeldin, P. M. Dansette, et D. Mansuy, « Role of Arginine 117 in Substrate Recognition by Human Cytochrome P450 2J2 », International Journal of Molecular Sciences, vol. 19, nᵒ 7, p. 2066, juill. 2018.
    Résumé : The influence of Arginine 117 of human cytochrome P450 2J2 in the recognition of ebastine and a series of terfenadone derivatives was studied by site-directed mutagenesis. R117K, R117E, and R117L mutants were produced, and the behavior of these mutants in the hydroxylation of ebastine and terfenadone derivatives was compared to that of wild-type CYP2J2. The data clearly showed the importance of the formation of a hydrogen bond between R117 and the keto group of these substrates. The data were interpreted on the basis of 3D homology models of the mutants and of dynamic docking of the substrates in their active site. These modeling studies also suggested the existence of a R117-E222 salt bridge between helices B' and F that would be important for maintaining the overall folding of CYP2J2.
    Mots-clés : arachidonic-acid metabolism, B3S, CYP2J2, LSOD.

  • F. Lallemand, A. Petitalot, S. Vacher, L. de Koning, K. Taouis, B. S. Lopez, S. Zinn-Justin, N. Dalla-Venezia, W. Chemlali, A. Schnitzler, R. Lidereau, I. Bieche, et S. M. Caputo, « Involvement of the FOXO6 transcriptional factor in breast carcinogenesis », Oncotarget, vol. 9, nᵒ 7, p. 7464-7475, janv. 2018.
    Résumé : In mammals, FOXO transcriptional factors form a family of four members (FOXO1, 3, 4, and 6) involved in the modulation proliferation, apoptosis, and carcinogenesis. The role of the FOXO family in breast cancer remains poorly elucidated. According to the cellular context and the stage of the disease, FOXOs can have opposite effects on carcinogenesis. To study the role of FOXOs in breast carcinogenesis in more detail, we examined their expression in normal tissues, breast cell lines, and a large series of breast tumours of human origin. We found a very low physiological level ofFOXO6expression in normal adult tissues and high levels of expression in foetal brain.FOXOgene expressions fluctuate specifically in breast cancer cells compared to normal cells, suggesting that these genes may have different roles in breast carcinogenesis. For the first time, we have shown that, among the variousFOXOgenes, onlyFOXO6was frequently highly overexpressed in breast cell lines and tumours. We also found that inhibition of the endogenous expression of FOXO6 by a specific siRNA inhibited the growth of the human breast cell lines MDA-MB-468 and HCC-38. FACS and Western blot analysis showed that inhibition of endogenous expression of FOXO6 induced accumulation of cells in G0/G1 phase of the cell cycle, but not apoptosis. These results tend to demonstrate that the overexpression of the humanFOXO6gene that we highlighted in the breast tumors stimulates breast carcinogenesis by activating breast cancer cell proliferation.
    Mots-clés : B3S, cervical squamous cell carcinoma, endometrial adenocarcinoma, gynecological cancers, INTGEN, prognosis, uc.189.

  • S. Leach, N. C. Jones, S. V. Hoffmann, et S. Un, « VUV Absorption Spectra of Gas-Phase Quinoline in the 3.5-10.7 eV Photon Energy Range », The Journal of Physical Chemistry. A, juill. 2018.
    Résumé : The absorption spectrum of quinoline was measured in the gas phase between 3.5 and 10.7 eV using a synchrotron photon source. A large number of sharp and broad spectral features were observed, some of which have plasmon-type collective π-electron modes contributing to their intensities. Eight valence electronic transitions were assigned, considerably extending the number of π-π* transitions previously observed mainly in solution. The principal factor in solution red-shifts is found to be the Lorentz-Lorenz polarizability parameter. Rydberg bands, observed for the first time, are analyzed into eight different series, converging to the D0 ground and two excited electronic states, namely, D3 and D4, of the quinoline cation. The R1 series limit is 8.628 eV for the first ionization energy of quinoline, a value more precise than previously published. This value, combined with cation electronic transition data, provides precise energies, respectively, 10.623 and 11.355 eV, for the D3 and D4 states. The valence transition assignments are based on density functional theory (DFT) calculations as well as on earlier Pariser-Parr-Pople (P-P-P) self-consistent field linear combination of atomic orbitals molecular orbital results. The relative quality of the P-P-P and DFT data is discussed. Both are far from spectroscopic accuracy concerning electronic excited states but were nevertheless useful for our assignments. Our time-dependent DFT calculations of quinoline are excellent for its ground-state properties such as geometry, rotational constants, dipole moment, and vibrational frequencies, which agree well with experimental observations. Vibrational components of the valence and Rydberg transitions mainly involve C-H bend and C═C and C═N stretch modes. Astrophysical applications of the vacuum UV absorption of quinoline are briefly discussed.
    Mots-clés : B3S, BHFMR.

  • L. Lecoq, S. Wang, T. Wiegand, S. Bressanelli, M. Nassal, B. H. Meier, et A. Böckmann, « Localizing Conformational Hinges by NMR: Where Do Hepatitis B Virus Core Proteins Adapt for Capsid Assembly? », Chemphyschem: A European Journal of Chemical Physics and Physical Chemistry, vol. 19, nᵒ 11, p. 1336-1340, juin 2018.
    Résumé : The hepatitis B virus (HBV) icosahedral nucleocapsid is assembled from 240 chemically identical core protein molecules and, structurally, comprises four groups of symmetrically nonequivalent subunits. We show here that this asymmetry is reflected in solid-state NMR spectra of the capsids, in which peak splitting is observed for a subset of residues. We compare this information to dihedral angle variations from available 3D structures and also to computational predictions of "dynamic" domains and molecular hinges. We find that although, at the given resolution, dihedral angles variations directly obtained from the X-ray structures are not precise enough to be interpreted, the chemical-shift information from NMR correlates, and interestingly goes beyond, information from bioinformatics approaches. Our study reveals the high sensitivity with which NMR can detect the residues allowing the subtle conformational adaptations needed in lattice formation. Our findings are important for understanding the formation and modulation of protein assemblies in general.
    Mots-clés : asymmetric unit, B3S, core protein, hepatitis B virus, IMAPP, nucleocapsid, solid-state NMR.

  • L. Lecoq, S. Wang, T. Wiegand, S. Bressanelli, M. Nassal, B. H. Meier, et A. Böckmann, « Solid-state [13C-15N] NMR resonance assignment of hepatitis B virus core protein », Biomolecular NMR assignments, vol. 12, nᵒ 1, p. 205-214, avr. 2018.
    Résumé : Each year, nearly 900,000 deaths are due to serious liver diseases caused by chronic hepatitis B virus infection. The viral particle is composed of an outer envelope and an inner icosahedral nucleocapsid formed by multiple dimers of a ~ 20 kDa self-assembling core protein (Cp). Here we report the solid-state 13C and 15N resonance assignments of the assembly domain, Cp149, of the core protein in its capsid form. A secondary chemical shift analysis of the 140 visible residues suggests an overall alpha-helical three-dimensional fold matching that derived for Cp149 from the X-ray crystallography of the capsid, and from solution-state NMR of the Cp149 dimer. Interestingly, however, at three distinct regions the chemical shifts in solution differ significantly between core proteins in the capsid state versus in the dimer state, strongly suggesting the respective residues to be involved in capsid assembly.
    Mots-clés : AMIG, Assignments, B3S, Core protein, Hepatitis B virus, IMAPP, Nucleocapsid, Solid-state NMR.

  • G. Lenoir, T. Dieudonné, A. Lamy, M. Lejeune, J. - L. Vazquez-Ibar, et C. Montigny, « Screening of Detergents for Stabilization of Functional Membrane Proteins », Current Protocols in Protein Science, vol. 93, nᵒ 1, p. e59, août 2018.
    Résumé : Membrane protein studies usually require use of detergents to extract and isolate proteins from membranes and manipulate them in a soluble context for their functional or structural characterization. However, solubilization with detergent may interfere with MP stability and may directly affect MP function or structure. Moreover, detergent properties can be affected such as critical micellar concentration (CMC) can be affected by the experimental conditions. Consequently, the experimenter must pay attention to both the protein and the behavior of the detergent. This article provides a convenient protocol for estimating the CMC of detergents in given experimental conditions. Then, it presents two protocols aimed at monitoring the function of a membrane protein in the presence of detergent. Such experiments may help to test various detergents for their inactivating or stabilizing effects on long incubation times, ranging from few hours to some days. © 2018 by John Wiley & Sons, Inc.
    Mots-clés : B3S, detergents, Drs2p/Cdc50p, lipids, LMNG, LPSM, membrane protein, SERCA1a, stabilization.

  • X. Liang, C. Guo, S. Liu, Z. Dang, Y. Wei, X. Yi, et S. Abel, « Cosolubilization of phenanthrene and pyrene in surfactant micelles: Experimental and atomistic simulations studies », Journal of Molecular Liquids, vol. 263, p. 1-9, août 2018.
    Résumé : Solubilization of mixed phenanthrene (PHE) and pyrene (PYR) in Triton X-100 (TX), sodium dodecyl sulfate (SDS) and mixed TX-SDS surfactant solutions were done to observe their cosolubilization effect. Moreover, molecular dynamics (MD) simulations were performed to reveal how polycyclic aromatic hydrocarbons (PAHs) coexist in the micelle. Cosolubilization of PHE and PYR exhibited synergism along with decreasing synergistic extent with increasing SDS in mixed micelle. MD simulations verified the distribution of PHE and PYR in the shell and core regions of pure SDS and mixed SDS-TX micelles (with molar ratio of 1: 1), which were chosen as the representative systems for simulation study. The movement of PHE and PYR inside the micelle along with their different probability to contact with SDS non‑hydrogen atoms in pure SDS and mixed SDS-TX solubilization systems suggests the different solubilization sites of the two PAHs inside the micelle leading to their coexistence in the micelle. This study implies the significance of considering cosolubilization effects between PAH mixtures in determining surfactant concentration for environmental remediation.
    Mots-clés : B3S, Cosolubilization, LBMS, Molecular dynamics simulations, Phenanthrene, Pyrene, Surfactant.

  • A. Litvinov, A. Feintuch, S. Un, et D. Goldfarb, « Triple resonance EPR spectroscopy determines the Mn2+ coordination to ATP », Journal of Magnetic Resonance, vol. 294, p. 143-152, sept. 2018.
    Résumé : Mn2+ often serves as a paramagnetic substitute to Mg2+, providing means for exploring the close environment of Mg2+ in many biological systems where it serves as an essential co-factor. This applies to proteins with ATPase activity, where the ATP hydrolysis requires the binding of Mg2+-ATP to the ATPase active site. In this context, it is important to distinguish between the Mn2+ coordination mode with free ATP in solution as compared to the protein bound case. In this work, we explore the Mn2+ complexes with ATP, the non-hydrolysable ATP analog, AMPPNP, and ADP free in solution. Using W-band P-31 electron-nuclear double resonance (ENDOR) we obtained information about the coordination to the phosphates, whereas from electron-electron double resonance (ELDOR) - detected NMR (EDNMR) we determined the coordination to an adenosine nitrogen. The coordination to these ligands has been reported earlier, but whether the nitrogen and phosphate coordination is within the same nucleotide molecules or different ones is still under debate. By applying the correlation technique, THYCOS (triple hyperfine correlation spectroscopy), and measuring N-15-P-31 correlations we establish that in Mn-ATP in solution both phosphates and a nitrogen are coordinated to the Mn2+ ion. We also carried out DFT calculations to substantiate this finding. In addition, we expanded the understanding of the THYCOS experiment by comparing it to 2D-EDNMR for Mn-55-P-31 correlation experiments and through simulations of THYCOS and 2D-EDNMR spectra with N-15-P-31 correlations. (C) 2018 Elsevier Inc. All rights reserved.
    Mots-clés : adenosine 5-triphosphate, atp, B3S, BHFMR, crystal-structure, divalent metal, ELDOR detected NMR, eldor-detected nmr, endor, gaussian-type basis, High field EPR, metal-ion-binding, Mn2+ ion, Mn2+-ATP, molecular-orbital methods, nuclear-magnetic-resonance, organic-molecules, ternary complexes, thycos.

  • M. J. Llansola-Portoles, K. Redeckas, S. Streckaité, C. Ilioaia, A. A. Pascal, A. Telfer, M. Vengris, L. Valkunas, et B. Robert, « Lycopene crystalloids exhibit singlet exciton fission in tomatoes », Physical Chemistry Chemical Physics, vol. 20, nᵒ 13, p. 8640-8646, 2018.

  • E. Ma, P. Dupaigne, L. Maloisel, R. Guerois, E. Le Cam, et E. Coïc, « Rad52-Rad51 association is essential to protect Rad51 filaments against Srs2, but facultative for filament formation », eLife, vol. 7, juill. 2018.
    Résumé : Homology search and strand exchange mediated by Rad51 nucleoprotein filaments are key steps of the homologous recombination process. In budding yeast, Rad52 is the main mediator of Rad51 filament formation, thereby playing an essential role. The current model assumes that Rad51 filament formation requires the interaction between Rad52 and Rad51. However, we report here that Rad52 mutations that disrupt this interaction do not affect γ-ray- or HO endonuclease-induced gene conversion frequencies. In vivo and in vitro studies confirmed that Rad51 filaments formation is not affected by these mutations. Instead, we found that Rad52-Rad51 association makes Rad51 filaments toxic in Srs2-deficient cells after exposure to DNA damaging agents, independently of Rad52 role in Rad51 filament assembly. Importantly, we also demonstrated that Rad52 is essential for protecting Rad51 filaments against dissociation by the Srs2 DNA translocase. Our findings open new perspectives in the understanding of the role of Rad52 in eukaryotes.
    Mots-clés : AMIG, B3S, biochemistry, chemical biology, chromosomes, gene expression, genome stability, homologous recombination, Rad51, Rad52, S. cerevisiae, Saccharomyces cerevisiae, Srs2.

  • A. Mahuzier, A. Shihavuddin, C. Fournier, P. Lansade, M. Faucourt, N. Menezes, A. Meunier, M. Garfa-Traoré, M. - F. Carlier, R. Voituriez, A. Genovesio, N. Spassky, et N. Delgehyr, « Ependymal cilia beating induces an actin network to protect centrioles against shear stress », Nature Communications, vol. 9, nᵒ 1, p. 2279, juin 2018.
    Résumé : Multiciliated ependymal cells line all brain cavities. The beating of their motile cilia contributes to the flow of cerebrospinal fluid, which is required for brain homoeostasis and functions. Motile cilia, nucleated from centrioles, persist once formed and withstand the forces produced by the external fluid flow and by their own cilia beating. Here, we show that a dense actin network around the centrioles is induced by cilia beating, as shown by the disorganisation of the actin network upon impairment of cilia motility. Moreover, disruption of the actin network, or specifically of the apical actin network, causes motile cilia and their centrioles to detach from the apical surface of ependymal cell. In conclusion, cilia beating controls the apical actin network around centrioles; the mechanical resistance of this actin network contributes, in turn, to centriole stability.
    Mots-clés : ACTIN, B3S.

0 | 50 | 100 | 150 | 200 | 250 | 300 | 350 | 400

--- Exporter la sélection au format

par webmaster - publié le , mis à jour le