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  • M. Amjadi, T. Hallaj, H. Asadollahi, Z. Song, M. de Frutos, and N. Hildebrandt, “Facile synthesis of carbon quantum dot/silver nanocomposite and its application for colorimetric detection of methimazole”, Sensors and Actuators B: Chemical, vol. 244, p. 425-432, 2017.

  • H. Azouaoui, C. Montigny, T. Dieudonné, P. Champeil, A. Jacquot, J. L. Vázquez-Ibar, P. Le Maréchal, J. Ulstrup, M. - R. Ash, J. A. Lyons, P. Nissen, and G. Lenoir, “A High and Phosphatidylinositol-4-phosphate (PI4P)-dependent ATPase Activity for the Drs2p/Cdc50p Flippase after Removal of its N- and C-terminal Extensions”, Journal of Biological Chemistry, p. jbc.M116.751487, Mar. 2017.
    Tags: autophosphorylation, B3S, Cdc50 protein, Flippase, inhibition mechanism, limited proteolysis, lipid-protein interaction, LPSM, phosphatidylserine, phosphoinositide.

  • A. Bahloul, E. Pepermans, B. Raynal, N. Wolff, F. Cordier, P. England, S. Nouaille, B. Baron, A. El-Amraoui, J. - P. Hardelin, D. Durand, and C. Petit, “Conformational switch of harmonin, a submembrane scaffold protein of the hair cell mechanoelectrical transduction machinery”, FEBS letters, 2017.
    Abstract: Mutations in the gene encoding harmonin, a multi-PDZ domain-containing submembrane protein, cause Usher syndrome type 1 (congenital deafness and balance disorder, as well as early-onset sight loss). The structure of the protein and biological activities of its three different classes of splice isoforms (a, b, and c) remain poorly understood. Combining biochemical and biophysical analyses, we show that harmonin-a1 can switch between open and closed conformations through intramolecular binding of its C-terminal PDZ-binding motif to its N-terminal supramodule NTD-PDZ1 and a flexible PDZ2-PDZ3 linker. This conformational switch presumably extends to most harmonin isoforms, and is expected to have an impact on the interaction with some binding partners, as shown here for cadherin-related 23, another component of the hair cell mechanoelectrical transduction machinery. This article is protected by copyright. All rights reserved.
    Tags: B3S, conformation switch, FAAM, PDZ domain, Usher syndrome.

  • E. Baquero, A. A. Albertini, H. Raux, A. Abou‐Hamdan, E. Boeri‐Erba, M. Ouldali, L. Buonocore, J. K. Rose, J. Lepault, S. Bressanelli, and Y. Gaudin, “Structural intermediates in the fusion‐associated transition of vesiculovirus glycoprotein”, The EMBO Journal, vol. 36, no. 5, p. 679-692, Mar. 2017.
    Tags: B3S, conformational change, glycoprotein, IMAPP, intermediate structures, membrane fusion, RHABDO, Vesiculovirus, VIRO, VIROEM.

  • L. Benkaidali, F. André, G. Moroy, B. Tangour, F. Maurel, and M. Petitjean, “The Cytochrome P450 3A4 Has Three Major Conformations: New Clues to Drug Recognition by this Promiscuous Enzyme”, Molecular Informatics, 2017.
    Abstract: We computed the channels of the 3A4 isoform of the cytochrome P450 3A4 (CYP) on the basis of 24 crystal structures extracted from the Protein Data Bank (PDB). We identified three major conformations (denoted C, O1 and O2) using an enhanced version of the CCCPP software that we developed for the present work, while only two conformations (C and O(2) ) are considered in the literature. We established the flowchart of definition of these three conformations in function of the structural and physicochemical parameters of the ligand. The channels are characterized with qualitative and quantitative parameters, and not only with their surrounding secondary structures as it is usually done in the literature.
    Tags: active site access channels, B3S, conformations, CYP 3A4 ligands, cytochromes P450, drug-drug interactions, LSOD.

  • D. A. Braun, J. Rao, G. Mollet, D. Schapiro, M. - C. Daugeron, W. Tan, O. Gribouval, O. Boyer, P. Revy, T. Jobst-Schwan, J. M. Schmidt, J. A. Lawson, D. Schanze, S. Ashraf, J. F. P. Ullmann, C. A. Hoogstraten, N. Boddaert, B. Collinet, G. Martin, D. Liger, S. Lovric, M. Furlano, I. C. Guerrera, O. Sanchez-Ferras, J. F. Hu, A. - C. Boschat, S. Sanquer, B. Menten, S. Vergult, N. De Rocker, M. Airik, T. Hermle, S. Shril, E. Widmeier, H. Y. Gee, W. - I. Choi, C. E. Sadowski, W. L. Pabst, J. K. Warejko, A. Daga, T. Basta, V. Matejas, K. Scharmann, S. D. Kienast, B. Behnam, B. Beeson, A. Begtrup, M. Bruce, G. - S. Ch'ng, S. - P. Lin, J. - H. Chang, C. - H. Chen, M. T. Cho, P. M. Gaffney, P. E. Gipson, C. - H. Hsu, J. A. Kari, Y. - Y. Ke, C. Kiraly-Borri, W. - M. Lai, E. Lemyre, R. O. Littlejohn, A. Masri, M. Moghtaderi, K. Nakamura, F. Ozaltin, M. Praet, C. Prasad, A. Prytula, E. R. Roeder, P. Rump, R. E. Schnur, T. Shiihara, M. D. Sinha, N. A. Soliman, K. Soulami, D. A. Sweetser, W. - H. Tsai, J. - D. Tsai, R. Topaloglu, U. Vester, D. H. Viskochil, N. Vatanavicharn, J. L. Waxler, K. J. Wierenga, M. T. F. Wolf, S. - N. Wong, S. A. Leidel, G. Truglio, P. C. Dedon, A. Poduri, S. Mane, R. P. Lifton, M. Bouchard, P. Kannu, D. Chitayat, D. Magen, B. Callewaert, H. van Tilbeurgh, M. Zenker, C. Antignac, and F. Hildebrandt, “Mutations in KEOPS-complex genes cause nephrotic syndrome with primary microcephaly”, Nature Genetics, 2017.
    Abstract: Galloway-Mowat syndrome (GAMOS) is an autosomal-recessive disease characterized by the combination of early-onset nephrotic syndrome (SRNS) and microcephaly with brain anomalies. Here we identified recessive mutations in OSGEP, TP53RK, TPRKB, and LAGE3, genes encoding the four subunits of the KEOPS complex, in 37 individuals from 32 families with GAMOS. CRISPR-Cas9 knockout in zebrafish and mice recapitulated the human phenotype of primary microcephaly and resulted in early lethality. Knockdown of OSGEP, TP53RK, or TPRKB inhibited cell proliferation, which human mutations did not rescue. Furthermore, knockdown of these genes impaired protein translation, caused endoplasmic reticulum stress, activated DNA-damage-response signaling, and ultimately induced apoptosis. Knockdown of OSGEP or TP53RK induced defects in the actin cytoskeleton and decreased the migration rate of human podocytes, an established intermediate phenotype of SRNS. We thus identified four new monogenic causes of GAMOS, describe a link between KEOPS function and human disease, and delineate potential pathogenic mechanisms.

  • C. Caillet-Saguy, A. Toto, R. Guerois, P. Maisonneuve, E. di Silvio, K. Sawyer, S. Gianni, and N. Wolff, “Regulation of the Human Phosphatase PTPN4 by the inter-domain linker connecting the PDZ and the phosphatase domains”, Scientific Reports, vol. 7, no. 1, p. 7875, 2017.
    Abstract: Human protein tyrosine phosphatase non-receptor type 4 (PTPN4) has been shown to prevent cell death. The active form of human PTPN4 consists of two globular domains, a PDZ (PSD-95/Dlg/ZO-1) domain and a phosphatase domain, tethered by a flexible linker. Targeting its PDZ domain abrogates this protection and triggers apoptosis. We previously demonstrated that the PDZ domain inhibits the phosphatase activity of PTPN4 and that the mere binding of a PDZ ligand is sufficient to release the catalytic inhibition. We demonstrate here that the linker connecting the PDZ domain and the phosphatase domain is involved in the regulation of the phosphatase activity in both PDZ-related inhibition and PDZ ligand-related activation events. We combined bioinformatics and kinetic studies to decipher the role of the linker in the PTPN4 activity. By comparing orthologous sequences, we identified a conserved patch of hydrophobic residues in the linker. We showed that mutations in this patch affect the regulation of the PTPN4 bidomain indicating that the PDZ-PDZ ligand regulation of PTPN4 is a linker-mediated mechanism. However, the mutations do not alter the binding of the PDZ ligand. This study strengthens the notion that inter-domain linker can be of functional importance in enzyme regulation of large multi-domain proteins.
    Tags: AMIG, B3S.

  • S. E. Cannella, V. Y. Ntsogo Enguéné, M. Davi, C. Malosse, A. C. Sotomayor Pérez, J. Chamot-Rooke, P. Vachette, D. Durand, D. Ladant, and A. Chenal, “Stability, structural and functional properties of a monomeric, calcium–loaded adenylate cyclase toxin, CyaA, from Bordetella pertussis”, Scientific Reports, vol. 7, p. 42065, Feb. 2017.

  • L. Cao, S. Cantos-Fernandes, and B. Gigant, “The structural switch of nucleotide-free kinesin”, Scientific Reports, vol. 7, p. 42558, Feb. 2017.

  • P. Cardol and A. Krieger-Liszkay, “From light capture to metabolic needs, oxygenic photosynthesis is an ever-expanding field of study in plants, algae and cyanobacteria”, Physiologia Plantarum, 2017.
    Abstract: Understanding of the molecular mechanisms of photosynthetic electron and proton transports and their regulation in plants and algae in response to changes in environmental conditions is an important issue for fundamental research on photosynthesis, and may extend even to practical applications by identifying important sites for improvement of photosynthesis. The significance and often centrality of regulatory mechanisms of photosynthetic electron transport is well established for processes in plant acclimation. In recent years, significant advancements have been achieved in understanding of regulatory processes such as dissipation of excess energy in the antenna systems, state transitions, cyclic electron flow, oxygen reduction by flavodiiron enzymes and many others.
    Tags: B3S, MROP.

  • M. - F. Carlier and S. Shekhar, “Global treadmilling coordinates actin turnover and controls the size of actin networks”, Nature Reviews Molecular Cell Biology, Mar. 2017.

  • V. Chaptal, F. Delolme, A. Kilburg, S. Magnard, C. Montigny, M. Picard, C. Prier, L. Monticelli, O. Bornert, M. Agez, S. Ravaud, C. Orelle, R. Wagner, A. Jawhari, I. Broutin, E. Pebay-Peyroula, J. - M. Jault, H. R. Kaback, M. le Maire, and P. Falson, “Quantification of Detergents Complexed with Membrane Proteins”, Scientific Reports, vol. 7, p. 41751, Feb. 2017.

  • J. - P. Charbonnier, E. M. van Rikxoort, A. A. A. Setio, C. M. Schaefer-Prokop, B. van Ginneken, and F. Ciompi, “Improving airway segmentation in computed tomography using leak detection with convolutional networks”, Medical Image Analysis, vol. 36, p. 52-60, 2017.

  • A. Chevrel, A. Mesneau, D. Sanchez, L. Celma, S. Quevillon-Cheruel, A. Cavagnino, S. Nessler, I. Li de la Sierra-Gallay, H. van Tilbeurgh, P. Minard, M. Valerio-Lepiniec, and A. Urvoas, “Alpha Repeat proteins (αRep) as expression and crystallization helpers”, Journal of Structural Biology, 2017.
    Abstract: We have previously described a highly diverse library of artificial repeat proteins based on thermostable HEAT-like repeats, named αRep. αReps binding specifically to proteins difficult to crystallize have been selected and in several examples, they made possible the crystallization of these proteins. To further simplify the production and crystallization experiments we have explored the production of chimeric protein corresponding to covalent association between the targets and their specific binders strengthened by a linker. Although chimeric proteins with expression partners are classically used to enhance expression these fusions cannot usually be used for crystallization. With specific expression partners like a cognate αRep this is no longer true, and chimeric proteins can be expressed purified and crystallized. αRep selection by phage display suppose that at least a small amount of the target protein should be produced to be used as a bait for selection and this might, in some cases, be difficult. We have therefore transferred the αRep library in a new construction adapted to selection by protein complementation assay (PCA). This new procedure allows to select specific binders by direct interaction with the target in the cytoplasm of the bacteria and consequently does not require preliminary purification of target protein. αRep binders selected by PCA or by phage display can be used to enhance expression, stability, solubility and crystallogenesis of proteins that are otherwise difficult to express, purify and/or crystallize.
    Tags: artificial repeat proteins, B3S, Crystallization helper, FAAM, Fusion protein, MIP, Protein complementation assay, Protein library.

  • M. Clémancey, T. Cantat, G. Blondin, J. - M. Latour, P. Dorlet, and G. Lefèvre, “Structural Insights into the Nature of Fe(0) and Fe(I) Low-Valent Species Obtained upon the Reduction of Iron Salts by Aryl Grignard Reagents”, Inorganic Chemistry, vol. 56, no. 7, p. 3834-3848, 2017.
    Abstract: Mechanistic studies of the reduction of Fe(III) and Fe(II) salts by aryl Grignard reagents in toluene/tetrahydrofuran mixtures in the absence of a supporting ligand, as well as structural insights regarding the nature of the low-valent iron species obtained at the end of this reduction process, are reported. It is shown that several reduction pathways can be followed, depending on the starting iron precursor. We demonstrate, moreover, that these pathways lead to a mixture of Fe(0) and Fe(I) complexes regardless of the nature of the precursor. Mössbauer and (1)H NMR spectroscopies suggest that diamagnetic 16-electron bisarene complexes such as (η(4)-C6H5Me)2Fe(0) can be formed as major species (85% of the overall iron quantity). The formation of a η(6)-arene-ligated low-spin Fe(I) complex as a minor species (accounting for ca. 15% of the overall iron quantity) is attested by Mössbauer spectroscopy, as well as by continuous-wave electron paramagnetic resonance (EPR) and pulsed-EPR (HYSCORE) spectroscopies. The nature of the Fe(I) coordination sphere is discussed by means of isotopic labeling experiments and density functional theory calculations. It is shown that the most likely low-spin Fe(I) candidate obtained in these systems is a diphenylarene-stabilized species [(η(6)-C6H5Me)Fe(I)Ph2](-) exhibiting an idealized C2v topology. This enlightens the nature of the lowest valence states accommodated by iron during the reduction of Fe(III) and Fe(II) salts by aryl Grignard reagents in the absence of any additional coligand, which so far remained rather unknown. The reactivity of these low-valent Fe(I) and Fe(0) complexes in aryl-heteroaryl Kumada cross-coupling conditions has also been investigated, and it is shown that the zerovalent Fe(0) species can be used efficiently as a precursor in this reaction, whereas the Fe(I) oxidation state does not exhibit any reactivity.
    Tags: B3S, LSOD.

  • P. Cuniasse, P. Tavares, E. V. Orlova, and S. Zinn-Justin, “Structures of biomolecular complexes by combination of NMR and cryoEM methods”, Current Opinion in Structural Biology, vol. 43, p. 104-113, 2017.

  • L. Dhers, N. Pietrancosta, L. Ducassou, B. Ramassamy, J. Dairou, M. Jaouen, F. André, D. Mansuy, and J. - L. Boucher, “Spectral and 3D model studies of the interaction of orphan human cytochrome P450 2U1 with substrates and ligands”, Biochimica et Biophysica Acta (BBA) - General Subjects, vol. 1861, no. 1, p. 3144-3153, 2017.

  • T. Di Meo, W. Ghattas, C. Herrero, C. Velours, P. Minard, J. - P. Mahy, R. Ricoux, and A. Urvoas, “αRep A3: A versatile artificial scaffold for metalloenzyme design”, Chemistry (Weinheim an Der Bergstrasse, Germany), 2017.
    Abstract: αRep is a new family of artificial proteins based on a thermostable alpha-helical repeated motif. One of its members, αRep A3, forms a stable homo-dimer with a wide cleft that is able to receive metal complexes and thus appears as suitable for generating new artificial biocatalysts. Based on the crystal structure of αRep A3, two positions (F119 and Y26) were chosen and changed independently into cysteine residues. A phenanthroline ligand was covalently attached to the unique cysteine of each protein variant and the corresponding biohybrids were purified and characterized. Once mutated and coupled to phenanthroline, the protein remained folded and dimeric. Copper(II) was bound specifically by the two biohybrids with two different binding modes and, in addition, the holo biohybrid A3F119NPH was found to be able to catalyze enantioselectively the Diels-Alder (D-A) cycloaddition with up to 62% ee. This study validates the choice of the αRep A3 dimer as a protein scaffold and provides a new promising route for the design and production of new enantioselective biohybrids based on entirely artificial proteins issued from a highly diverse library.
    Tags: artificial repeat proteins, B3S, Diels-Alder reaction, Enantioselective Catalysis, MIP, PF, PIM.

  • S. A. Díaz, G. Lasarte Aragonés, S. Buckhout-White, X. Qiu, E. Oh, K. Susumu, J. S. Melinger, A. L. Huston, N. Hildebrandt, and I. L. Medintz, “Bridging Lanthanide to Quantum Dot Energy Transfer with a Short-Lifetime Organic Dye”, The Journal of Physical Chemistry Letters, p. 2182-2188, 2017.
    Abstract: Semiconductor nanocrystals or quantum dots (QDs) should act as excellent Förster resonance energy transfer (FRET) acceptors due to their large absorption cross section, tunable emission, and high quantum yields. Engaging this type of FRET can be complicated due to direct excitation of the QD acceptor along with its longer excited-state lifetime. Many cases of QDs acting as energy transfer acceptors are within time-gated FRET from long-lifetime lanthanides, which allow the QDs to decay before observing FRET. Efficient QD sensitization requires the lanthanide to be in close proximity to the QD. To overcome the lifetime mismatch issues and limited transfer range, we utilized a Cy3 dye to bridge the energy transfer from an extremely long lived terbium emitter to the QD. We demonstrated that short-lifetime dyes can be used as energy transfer relays between extended lifetime components and in this way increased the distance of terbium-QD FRET to ∼14 nm.
    Tags: B3S, NANO.

  • G. Dimchev, A. Steffen, F. Kage, V. Dimchev, J. Pernier, M. - F. Carlier, and K. Rottner, “Efficiency of lamellipodia protrusion is determined by the extent of cytosolic actin assembly”, Molecular Biology of the Cell, p. mbc.E16-05-0334, Mar. 2017.

  • L. Ducassou, L. Dhers, G. Jonasson, N. Pietrancosta, J. - L. Boucher, D. Mansuy, and F. André, “Membrane-bound human orphan cytochrome P450 2U1: Sequence singularities, construction of a full 3D model, and substrate docking”, Biochimie, vol. 140, p. 166-175, 2017.
    Abstract: BACKGROUND: Human cytochrome P450 2U1 (CYP2U1) is an orphan CYP that exhibits several distinctive characteristics among the 57 human CYPs with a highly conserved sequence in almost all living organisms. METHODS: We compared its protein sequence with those of the 57 human CYPs and constructed a 3D structure of a full-length CYP2U1 model bound to a POPC membrane. We also performed docking experiments of arachidonic acid (AA) and N-arachidonoylserotonin (AS) in this model. RESULTS: The protein sequence of CYP2U1 displayed two unique characteristics when compared to those of the human CYPs, the presence of a longer N-terminal region upstream of the putative trans-membrane helix (TMH) containing 8 proline residues, and of an insert of about 20 amino acids containing 5 arginine residues between helices A' and A. Its N-terminal part upstream of TMH involved an additional short terminal helix, in a manner similar to what was reported in the crystal structure of Saccharomyces cerevisiae CYP51. Our model also showed a specific interaction between the charged residues of insert AA' and phosphate groups of lipid polar heads, suggesting a possible role of this insert in substrate recruitment. Docking of AA and AS in this model showed these substrates in channel 2ac, with the terminal alkyl chain of AA or the indole ring of AS close to the heme, in agreement with the reported CYP2U1-catalyzed AA and AS hydroxylation regioselectivities. MAJOR CONCLUSION AND GENERAL SIGNIFICANCE: This model should be useful to find new endogenous or exogenous CYP2U1 substrates and to interpret the regioselectivity of their hydroxylation.
    Tags: Access channels, Active site topology, Arachidonic acid, B3S, LSOD, Membrane interaction, molecular dynamics, N-arachidonoylserotonin.

  • Y. Duroc, R. Kumar, L. Ranjha, C. Adam, R. Guérois, K. Md Muntaz, M. - C. Marsolier-Kergoat, F. Dingli, R. Laureau, D. Loew, B. Llorente, J. - B. Charbonnier, P. Cejka, and V. Borde, “Concerted action of the MutLβ heterodimer and Mer3 helicase regulates the global extent of meiotic gene conversion”, eLife, vol. 6, Jan. 2017.
    Tags: AMIG, B3S, biochemistry, Chromosomes, genes, INTGEN, Meiosis, mismatch repair, Recombination, S. cerevisiae.

  • N. El Bakkali-Tahéri, S. Tachon, M. Orio, S. Bertaina, M. Martinho, V. Robert, M. Réglier, T. Tron, P. Dorlet, and A. J. Simaan, “Characterization of Cu(II)-reconstituted ACC Oxidase using experimental and theoretical approaches”, Archives of Biochemistry and Biophysics, 2017.
    Abstract: 1-Aminocyclopropane-1-carboxylic acid oxidase (ACCO) is a non heme iron(II) containing enzyme that catalyzes the final step of the ethylene biosynthesis in plants. The iron(II) ion is bound in a facial triad composed of two histidines and one aspartate (H177, D179 and H234). Several active site variants were generated to provide alternate binding motifs and the enzymes were reconstituted with copper(II). Continuous wave (cw) and pulsed Electron Paramagnetic Resonance (EPR) spectroscopies as well as Density Functional Theory (DFT) calculations were performed and models for the copper(II) binding sites were deduced. In all investigated enzymes, the copper ion is equatorially coordinated by the two histidine residues (H177 and H234) and probably two water molecules. The copper-containing enzymes are inactive, even when hydrogen peroxide is used in peroxide shunt approach. EPR experiments and DFT calculations were undertaken to investigate substrate's (ACC) binding on the copper ion and the results were used to rationalize the lack of copper-mediated activity.
    Tags: ACC Oxidase, B3S, Copper, Density functional theory calculations, Electron paramagnetic resonance, Ethylene, LSOD.

  • E. Errasti-Murugarren, A. Rodríguez-Banqueri, and J. L. Vázquez-Ibar, “Split GFP Complementation as Reporter of Membrane Protein Expression and Stability in E. coli: A Tool to Engineer Stability in a LAT Transporter”, Methods in Molecular Biology (Clifton, N.J.), vol. 1586, p. 181-195, 2017.
    Abstract: Obtaining enough quantity of recombinant membrane transport proteins with optimal purity and stability for structural studies is a remarkable challenge. In this chapter, we describe a protocol to engineer SteT, the amino acid transporter of Bacillus subtilis, in order to improve its heterologous expression in Escherichia coli and its stability in detergent micelles. We built a library of 70 SteT mutants, combining a random mutagenesis protocol with a split GFP assay as reporter of protein folding and membrane insertion. Mutagenesis was restricted to residues situated in the transmembrane domains. Improved versions of SteT were successfully identified after analyzing the expression yield and monodispersity in detergent micelles of the library's members.
    Tags: B3S, FSEC, Heterologous expression, LAT, LPSM, Membrane Transport Proteins, Split GFP, SteT.

  • K. Feilke, G. Ajlani, and A. Krieger-Liszkay, “Overexpression of plastid terminal oxidase in Synechocystis sp. PCC 6803 alters cellular redox state”, Philosophical Transactions of the Royal Society of London. Series B, Biological Sciences, vol. 372, no. 1730, 2017.
    Abstract: Cyanobacteria are the most ancient organisms performing oxygenic photosynthesis, and they are the ancestors of plant plastids. All plastids contain the plastid terminal oxidase (PTOX), while only certain cyanobacteria contain PTOX. Many putative functions have been discussed for PTOX in higher plants including a photoprotective role during abiotic stresses like high light, salinity and extreme temperatures. Since PTOX oxidizes PQH2 and reduces oxygen to water, it is thought to protect against photo-oxidative damage by removing excess electrons from the plastoquinone (PQ) pool. To investigate the role of PTOX we overexpressed rice PTOX fused to the maltose-binding protein (MBP-OsPTOX) in Synechocystis sp. PCC 6803, a model cyanobacterium that does not encode PTOX. The fusion was highly expressed and OsPTOX was active, as shown by chlorophyll fluorescence and P700 absorption measurements. The presence of PTOX led to a highly oxidized state of the NAD(P)H/NAD(P)(+) pool, as detected by NAD(P)H fluorescence. Moreover, in the PTOX overexpressor the electron transport capacity of PSI relative to PSII was higher, indicating an alteration of the photosystem I (PSI) to photosystem II (PSII) stoichiometry. We suggest that PTOX controls the expression of responsive genes of the photosynthetic apparatus in a different way from the PQ/PQH2 ratio.This article is part of the themed issue 'Enhancing photosynthesis in crop plants: targets for improvement'.
    Tags: B3S, cellular redox state, chlorophyll fluorescence, LBMS, MROP, NAD(P)H fluorescence, P700 absorption, plastid terminal oxidase, Synechocystis sp. PCC 6803.

  • S. Fieulaine, R. Alves de Sousa, L. Maigre, K. Hamiche, M. Alimi, J. - M. Bolla, A. Taleb, A. Denis, J. - M. Pagès, I. Artaud, T. Meinnel, and C. Giglione, “Corrigendum: A unique peptide deformylase platform to rationally design and challenge novel active compounds”, Scientific Reports, vol. 7, p. 39365, Jan. 2017.

  • V. R. Figliuolo, L. E. B. Savio, H. Safya, H. Nanini, C. Bernardazzi, A. Abalo, H. S. P. de Souza, J. Kanellopoulos, P. Bobé, C. M. L. M. Coutinho, and R. Coutinho-Silva, “P2X7 receptor promotes intestinal inflammation in chemically induced colitis and triggers death of mucosal regulatory T cells”, Biochimica Et Biophysica Acta, 2017.
    Abstract: P2X7 receptor activation contributes to inflammation development in different pathologies. We previously reported that the P2X7 receptor is over-expressed in the gut mucosa of patients with inflammatory bowel disease, and that P2X7 inhibition protects against chemically induced colitis. Here, we investigated in detail the role of the P2X7 receptor in inflammatory bowel disease development, by treating P2X7 knockout (KO) and WT mice with two different (and established) colitis inductors. P2X7 KO mice were protected against gut inflammation induced by 2,4,6-trinitrobenzenesulfonic acid or oxazolone, with no weight loss or gut histological alterations after treatment. P2X7 receptor knockout induced regulatory T cell accumulation in the colon, as evaluated by qRT-PCR for FoxP3 expression and immunostaining for CD90/CD45RB(low). Flow cytometry analysis of mesenteric lymph node cells showed that P2X7 activation (by ATP) triggered regulatory T cell death. In addition, such cells from P2X7 KO mice expressed more CD103, suggesting increased migration of regulatory T cells to the colon (relative to the WT). Our results show that the P2X7 has a key role during inflammation development in inflammatory bowel disease, by triggering the death and retention in the mesenteric lymph nodes of regulatory T cells that would otherwise promote immune system tolerance in the gut.
    Tags: ATP, B3S, colitis, MIP, P2X7 receptor, regulatory T cells.

  • G. Folpini, T. Siebert, M. Woerner, S. Abel, D. Laage, and T. Elsaesser, “Water Librations in the Hydration Shell of Phospholipids”, The Journal of Physical Chemistry Letters, p. 4492-4497, 2017.
    Abstract: The hydrophilic phosphate moiety in the headgroup of phospholipids forms strong hydrogen bonds with water molecules in the first hydration layer. Time-domain terahertz spectroscopy in a range from 100 to 1000 cm(-1) reveals the influence of such interactions on rotations of water molecules. We determine librational absorption spectra of water nanopools in phospholipid reverse micelles for a range from w0 = 2 to 16 waters per phospholipid molecule. A pronounced absorption feature with maximum at 830 cm(-1) is superimposed on a broad absorption band between 300 and 1000 cm(-1). Molecular dynamics simulations of water in the reverse micelles suggest that the feature at 830 cm(-1) arises from water molecules forming one or two strong hydrogen bonds with phosphate groups, while the broad component comes from bulk-like environments. This behavior is markedly different from water interacting with less polar surfaces.
    Tags: B3S, LBMS.

  • R. Grzela, J. Nusbaum, S. Fieulaine, F. Lavecchia, W. V. Bienvenut, C. Dian, T. Meinnel, and C. Giglione, “The C-terminal residue of phage Vp16 PDF, the smallest peptide deformylase, acts as an offset element locking the active conformation”, Scientific Reports, vol. 7, no. 1, p. 11041, 2017.
    Abstract: Prokaryotic proteins must be deformylated before the removal of their first methionine. Peptide deformylase (PDF) is indispensable and guarantees this mechanism. Recent metagenomics studies revealed new idiosyncratic PDF forms as the most abundant family of viral sequences. Little is known regarding these viral PDFs, including the capacity of the corresponding encoded proteins to ensure deformylase activity. We provide here the first evidence that viral PDFs, including the shortest PDF identified to date, Vp16 PDF, display deformylase activity in vivo, despite the absence of the key ribosome-interacting C-terminal region. Moreover, characterization of phage Vp16 PDF underscores unexpected structural and molecular features with the C-terminal Isoleucine residue significantly contributing to deformylase activity both in vitro and in vivo. This residue fully compensates for the absence of the usual long C-domain. Taken together, these data elucidate an unexpected mechanism of enzyme natural evolution and adaptation within viral sequences.
    Tags: B3S, DBG, IMAPP, PROMTI.

  • N. Hildebrandt, C. M. Spillmann, W. R. Algar, T. Pons, M. H. Stewart, E. Oh, K. Susumu, S. A. Díaz, J. B. Delehanty, and I. L. Medintz, “Energy Transfer with Semiconductor Quantum Dot Bioconjugates: A Versatile Platform for Biosensing, Energy Harvesting, and Other Developing Applications”, Chemical Reviews, vol. 117, no. 2, p. 536-711, Jan. 2017.

  • J. Ho, E. Kish, D. D. Méndez-Hernández, K. WongCarter, S. Pillai, G. Kodis, J. Niklas, O. G. Poluektov, D. Gust, T. A. Moore, A. L. Moore, V. S. Batista, and B. Robert, “Triplet-triplet energy transfer in artificial and natural photosynthetic antennas”, Proceedings of the National Academy of Sciences of the United States of America, 2017.
    Abstract: In photosynthetic organisms, protection against photooxidative stress due to singlet oxygen is provided by carotenoid molecules, which quench chlorophyll triplet species before they can sensitize singlet oxygen formation. In anoxygenic photosynthetic organisms, in which exposure to oxygen is low, chlorophyll-to-carotenoid triplet-triplet energy transfer (T-TET) is slow, in the tens of nanoseconds range, whereas it is ultrafast in the oxygen-rich chloroplasts of oxygen-evolving photosynthetic organisms. To better understand the structural features and resulting electronic coupling that leads to T-TET dynamics adapted to ambient oxygen activity, we have carried out experimental and theoretical studies of two isomeric carotenoporphyrin molecular dyads having different conformations and therefore different interchromophore electronic interactions. This pair of dyads reproduces the characteristics of fast and slow T-TET, including a resonance Raman-based spectroscopic marker of strong electronic coupling and fast T-TET that has been observed in photosynthesis. As identified by density functional theory (DFT) calculations, the spectroscopic marker associated with fast T-TET is due primarily to a geometrical perturbation of the carotenoid backbone in the triplet state induced by the interchromophore interaction. This is also the case for the natural systems, as demonstrated by the hybrid quantum mechanics/molecular mechanics (QM/MM) simulations of light-harvesting proteins from oxygenic (LHCII) and anoxygenic organisms (LH2). Both DFT and electron paramagnetic resonance (EPR) analyses further indicate that, upon T-TET, the triplet wave function is localized on the carotenoid in both dyads.
    Tags: artificial photosynthesis, B3S, DFT calculations, LBMS, Photoprotection, Resonance Raman, triplet–triplet energy transfer.

  • F. Kage, M. Winterhoff, V. Dimchev, J. Mueller, T. Thalheim, A. Freise, S. Brühmann, J. Kollasser, J. Block, G. Dimchev, M. Geyer, H. - J. Schnittler, C. Brakebusch, T. E. B. Stradal, M. - F. Carlier, M. Sixt, J. Käs, J. Faix, and K. Rottner, “FMNL formins boost lamellipodial force generation”, Nature Communications, vol. 8, p. 14832, Mar. 2017.

  • E. Karakas, C. Taveneau, S. Bressanelli, M. Marchi, B. Robert, and S. Abel, “Derivation of original RESP atomic partial charges for MD simulations of the LDAO surfactant with AMBER: applications to a model of micelle and a fragment of the lipid kinase PI4KA”, Journal of Biomolecular Structure and Dynamics, vol. 35, no. 1, p. 159-181, Jan. 2017.
    Tags: Amber, B3S, Dimethylamines, fluorescence spectroscopy, IMAPP, LBMS, LDAO surfactant, lipid kinase PI4KA, Lipids, MD simulation, micelle, Micelles, Minor Histocompatibility Antigens, Molecular Conformation, Molecular Dynamics Simulation, molecular modeling, Phosphotransferases (Alcohol Group Acceptor), Protein Binding, Proteins, Static Electricity, Surface-Active Agents.

  • J. Keirsse-Haquin, T. Picaud, L. Bordes, A. G. de Gracia, and A. Desbois, “Modulation of the flavin-protein interactions in NADH peroxidase and mercuric ion reductase: a resonance Raman study”, European biophysics journal: EBJ, 2017.
    Abstract: NADH peroxidase (Npx) and mercuric ion reductase (MerA) are flavoproteins belonging to the pyridine nucleotide:disulfide oxidoreductases (PNDO) and catalyzing the reduction of toxic substrates, i.e., hydrogen peroxide and mercuric ion, respectively. To determine the role of the flavin adenine dinucleotide (FAD) in the detoxification mechanism, the resonance Raman (RR) spectra of these enzymes under various redox and ligation states have been investigated using blue and/or near-UV excitation(s). These data were compared to those previously obtained for glutathione reductase (GR), another enzyme of the PNDO family, but catalyzing the reduction of oxidized glutathione. Spectral differences have been detected for the marker bands of the isoalloxazine ring of Npx, MerA, and GR. They provide evidence for different catalytic mechanisms in these flavoproteins. The RR modes of the oxidized and two-electron reduced (EH2) forms of Npx are related to very tight flavin-protein interactions maintaining a nearly planar conformation of the isoalloxazine tricycle, a low level of H-bonding at the N1/N5 and O2/O4 sites, and a strong H-bond at N3H. They also indicate minimal changes in FAD structure and environment upon either NAD(H) binding or reduction of the sulfinic redox center. All these spectroscopic data support an enzyme functioning centered on the Cys-SO(-)/Cys-S(-) redox moiety and a neighbouring His residue. On the contrary, the RR data on various functional forms of MerA are indicative of a modulation of both ring II distortion and H-bonding states of the N5 site and ring III. The Cd(II) binding to the EH2-NADP(H) complexes, biomimetic intermediates in the reaction of Hg(II) reduction, provokes important spectral changes. They are interpreted in terms of flattening of the isoalloxazine ring and large decreases in H-bonding at the N5 site and ring III. The large flexibility of the FAD structure and environment in MerA is in agreement with proposed mechanisms involving C4a(flavin) adducts.
    Tags: B3S, Detoxification mechanism, Flavin–protein interactions, Isoalloxazine modes, LBMS, Resonance Raman.

  • M. Kopečná, A. Vigouroux, J. Vilím, R. Končitíková, P. Briozzo, E. Hájková, L. Jašková, K. von Schwartzenberg, M. Šebela, S. Moréra, and D. Kopečný, “The ALDH21 gene found in lower plants and some vascular plants codes for a NADP(+) -dependent succinic semialdehyde dehydrogenase”, The Plant Journal: For Cell and Molecular Biology, 2017.
    Abstract: Lower plant species including some green algae, non-vascular plants (bryophytes) as well as the oldest vascular plants (lycopods) and ferns (monilophytes) possess a unique aldehyde dehydrogenase (ALDH) gene named ALDH21, which is upregulated during dehydration. However, the gene is absent in flowering plants. Here, we show that ALDH21 from the moss Physcomitrella patens codes for a tetrameric NADP(+) -dependent succinic semialdehyde dehydrogenase (SSALDH), which converts succinic semialdehyde, an intermediate of the γ-aminobutyrate (GABA) shunt pathway, into succinate in the cytosol. NAD(+) is a very poor coenzyme for ALDH21 unlike for mitochondrial SSALDHs (ALDH5), which are the closest related ALDH members. Structural comparison between the apoform and the coenzyme complex reveal that NADP(+) binding induces a conformational change of the loop carrying Arg-228, which seals the NADP(+) in the coenzyme cavity via its 2'-phosphate and α-phosphate groups. The crystal structure with the bound product succinate shows that its carboxylate group establishes salt bridges with both Arg-121 and Arg-457 and a hydrogen bond with Tyr-296. While both arginine residues are pre-formed for substrate/product binding, Tyr-296 moves by more than 1 Å. Both R121A and R457A variants are almost inactive demonstrating a key role of each arginine in catalysis. Our study implies that bryophytes but presumably also some green algae, lycopods and ferns, which carry both ALDH21 and ALDH5 genes, can oxidize SSAL to succinate in both cytosol and mitochondria indicating more diverse GABA shunt pathway compared with higher plants carrying only the mitochondrial ALDH5. This article is protected by copyright. All rights reserved.
    Tags: aldehyde dehydrogenase, ALDH21, ALDH5, B3S, GABA, MESB3S, Physcomitrella patens, site-directed mutagenesis, structure-function, succinic semialdehyde, x-ray crystallography.

  • P. V. Krasteva and H. Sondermann, “Versatile modes of cellular regulation via cyclic dinucleotides”, Nature Chemical Biology, vol. 13, no. 4, p. 350-359, Mar. 2017.

  • J. Lang, A. Vigouroux, A. El Sahili, A. Kwasiborski, M. Aumont-Nicaise, Y. Dessaux, J. A. Shykoff, S. Moréra, and D. Faure, “Fitness costs restrict niche expansion by generalist niche-constructing pathogens”, The ISME Journal, vol. 11, no. 2, p. 374-385, 2017.

  • A. Le Dur, T. L. Laï, M. - G. Stinnakre, A. Laisné, N. Chenais, S. Rakotobe, B. Passet, F. Reine, S. Soulier, L. Herzog, G. Tilly, H. Rézaei, V. Béringue, J. - L. Vilotte, and H. Laude, “Divergent prion strain evolution driven by PrP(C) expression level in transgenic mice”, Nature Communications, vol. 8, p. 14170, 2017.
    Abstract: Prions induce a fatal neurodegenerative disease in infected host brain based on the refolding and aggregation of the host-encoded prion protein PrP(C) into PrP(Sc). Structurally distinct PrP(Sc) conformers can give rise to multiple prion strains. Constrained interactions between PrP(C) and different PrP(Sc) strains can in turn lead to certain PrP(Sc) (sub)populations being selected for cross-species transmission, or even produce mutation-like events. By contrast, prion strains are generally conserved when transmitted within the same species, or to transgenic mice expressing homologous PrP(C). Here, we compare the strain properties of a representative sheep scrapie isolate transmitted to a panel of transgenic mouse lines expressing varying levels of homologous PrP(C). While breeding true in mice expressing PrP(C) at near physiological levels, scrapie prions evolve consistently towards different strain components in mice beyond a certain threshold of PrP(C) overexpression. Our results support the view that PrP(C) gene dosage can influence prion evolution on homotypic transmission.
    Tags: ACTIN, B3S.

  • M. J. Llansola-Portoles, R. Litvin, C. Ilioaia, A. A. Pascal, D. Bina, and B. Robert, “Pigment structure in the violaxanthin-chlorophyll-a-binding protein VCP”, Photosynthesis Research, 2017.
    Abstract: Resonance Raman spectroscopy was used to evaluate pigment-binding site properties in the violaxanthin-chlorophyll-a-binding protein (VCP) from Nannochloropsis oceanica. The pigments bound to this antenna protein are chlorophyll-a, violaxanthin, and vaucheriaxanthin. The molecular structures of bound Chl-a molecules are discussed with respect to those of the plant antenna proteins LHCII and CP29, the crystal structures of which are known. We show that three populations of carotenoid molecules are bound by VCP, each of which is in an all-trans configuration. We assign the lower-energy absorption transition of each of these as follows. One violaxanthin population absorbs at 485 nm, while the second population is red-shifted and absorbs at 503 nm. The vaucheriaxanthin population absorbs at 525 nm, a position red-shifted by 2138 cm(-1) as compared to isolated vaucheriaxanthin in n-hexane. The red-shifted violaxanthin is slightly less planar than the blue-absorbing one, as observed for the two central luteins in LHCII, and we suggest that these violaxanthins occupy the two equivalent binding sites in VCP at the centre of the cross-brace. The presence of a highly red-shifted vaucheriaxanthin in VCP is reminiscent of the situation of FCP, in which (even more) highly red-shifted populations of fucoxanthin are present. Tuning carotenoids to absorb in the green-yellow region of the visible spectrum appears to be a common evolutionary response to competition with other photosynthetic species in the aquatic environment.
    Tags: B3S, Carotenoids, LBMS, Light-harvesting complex, Nannochloropsis oceanica, Resonance Raman, VCP.

  • M. J. Llansola-Portoles, R. Sobotka, E. Kish, M. K. Shukla, A. A. Pascal, T. Polívka, and B. Robert, “Twisting a β-Carotene, an Adaptive Trick from Nature for Dissipating Energy during Photoprotection”, Journal of Biological Chemistry, vol. 292, no. 4, p. 1396-1403, Jan. 2017.
    Tags: B3S, carotenoid, Chlorophyll, Cyanobacteria, LBMS, light-harvesting complex (antenna complex), photosynthesis.

  • M. Loussouarn, A. Krieger-Liszkay, L. Svilar, A. Bily, S. Birtic, and M. Havaux, “Carnosic acid and carnosol, two major antioxidants of rosemary, act through different mechanisms”, Plant Physiology, 2017.
    Abstract: Carnosic acid, a phenolic diterpene specific of the Lamiaceae family, is highly abundant in rosemary species. Despite numerous industrial and medicinal/pharmaceutical applications of its antioxidative features, this compound in planta and its antioxidant mechanism have received little attention, except a few studies of rosemary plants under natural conditions. In vitro analyses, using HPLC-UV and luminescence imaging, revealed that carnosic acid and its major oxidized derivative, carnosol, protect lipids from oxidation. Both compounds preserved linolenic acid and monogalactosyldiacylglycerol from singlet oxygen and from hydroxyl radical. When applied exogenously, they were both able to protect thylakoid membranes prepared from Arabidopsis leaves against lipid peroxidation. Different levels of carnosic acid and carnosol in two contrasted rosemary varieties correlated with tolerance to lipid peroxidation. Upon ROS oxidation of lipids, carnosic acid was consumed and oxidized into various derivatives, including into carnosol, while carnosol resisted, suggesting that carnosic acid is a chemical quencher of ROS. The antioxidative function of carnosol relies on another mechanism, occurring directly in lipid oxidation process. Under oxidative conditions that did not involve ROS generation, carnosol inhibited lipid peroxidation, contrary to carnosic acid. Using spin probes and EPR detection, we confirmed that carnosic acid, rather than carnosol, is a ROS quencher. Various oxidized derivatives of carnosic acid were detected in rosemary leaves in low light, indicating chronic oxidation of this compound, and accumulated in plants exposed to stress conditions, in parallel with a loss of carnosic acid, confirming that chemical quenching of ROS by carnosic acid takes place in planta.
    Tags: B3S, MROP.

  • F. Ma, L. - J. Yu, M. J. Llansola-Portoles, B. Robert, Z. - Y. Wang-Otomo, and R. van Grondelle, “Metal Cations Induced αβ-BChl a Heterogeneity in LH1 as Revealed by Temperature-Dependent Fluorescence Splitting”, Chemphyschem: A European Journal of Chemical Physics and Physical Chemistry, 2017.
    Abstract: Two spectral forms of the core light-harvesting complex (LH1) of the purple bacterium Thermochromatium (Tch.) tepidum, the native Ca(2+) -binding and the Ba(2+) -substituted one, exhibit different fluorescence (FL) emission spectra at low temperature (T). While Ca-LH1 exhibits one emission band, an unusual splitting of the fluorescence is observed for Ba-LH1. These two sub-bands display the same spectral-width dependence according to T, but their intensity evolves differently with T. Based on the crystal structures, we propose that the FL splitting originates from a large αβ-BChl a transition energy heterogeneity, ≈600 cm(-1) , which is much larger compared with other LH1 and LH2 complexes (80-200 cm(-1) ). This large heterogeneity is induced by the inhomogeneous Coulomb (and possibly hydrogen-bonding) interactions exerted by Ba(2+) . The energy levels of the two LH1s were compared using exciton calculations in combination with Redfield theory. To simulate the FL splitting, an electronic transition containing two resonant bands was considered. This work shows how metal cations incorporated into the polypeptide modulate the electronic properties of BChl a aggregates.
    Tags: B3S, core light-harvesting complex, fluorescence spectroscopy, LBMS, Redfield theory, transition energy, αβ-BChl a heterogeneity.

  • M. Ma, I. Li de La Sierra Gallay, N. Lazar, O. Pellegrini, J. Lepault, C. Condon, D. Durand, and H. van Tilbeurgh, “Trz1, the long form RNase Z from yeast, forms a stable heterohexamer with endonuclease Nuc1 and mutarotase”, The Biochemical Journal, 2017.
    Abstract: Proteomic studies haves established that Trz1, Nuc1 and mutarotase form a complex in yeast. Trz1 is a b-lactamase type RNase composed of two b-lactamase type domains connected by a long linker that is responsible for the endonucleolytic cleavage at the 3'-end of tRNAs during the maturation process (RNase Z activity); Nuc1 is a dimeric mitochondrial nuclease involved in apoptosis, while mutarotase (encoded by YMR099C) catalyzes the conversion between the a- and b-configuration of glucose-6-phosphate. Using gel-filtration, SAXS and electron microscopy we demonstrated that Trz1, Nuc1 and mutarotase form a very stable heterohexamer, composed of two copies of each of the three subunits. A Nuc1 homodimer is at the centre of the complex, creating a two-fold symmetry and interacting with both Trz1 and mutarotase. Enzymatic characterization of the ternary complex revealed that the activities of Trz1 and mutarotase are not affected by complex formation, but that the Nuc1 activity is completely inhibited by mutarotase and partially by Trz1. This suggests that mutarotase and Trz1 might be regulators of the Nuc1 apoptotic nuclease activity.
    Tags: B3S, complex, CRYOEM, endoglucanase, FAAM, mutarotase, PF, RNASeZ, structure.

  • M. Ma, I. Li de la Sierra-Gallay, N. Lazar, O. Pellegrini, D. Durand, A. Marchfelder, C. Condon, and H. van Tilbeurgh, “The crystal structure of Trz1, the long form RNase Z from yeast”, Nucleic Acids Research, Apr. 2017.

  • P. K. Mandal, D. Shukla, V. Govind, Y. Boulard, and L. Ersland, “Glutathione Conformations and Its Implications for in vivo Magnetic Resonance Spectroscopy”, Journal of Alzheimer's disease: JAD, 2017.
    Abstract: Glutathione (GSH) is a major antioxidant in humans that is involved in the detoxification of reactive radicals and peroxides. The molecular structural conformations of GSH depend on the surrounding micro-environment, and it has been experimentally evaluated using NMR and Raman spectroscopic techniques as well as by molecular dynamics simulation studies. The converging report indicates that GSH exists mainly in two major conformations, i.e., "extended" and "folded". The NMR-derived information on the GSH conformers is essential to obtain optimal acquisition parameters in in vivo MRS experiments targeted for GSH detection. To further investigate the implications of GSH conformers in in vivo MRS studies and their relative proportions in healthy and pathological conditions, a multi-center clinical research study is necessary with a common protocol for GSH detection and quantification.
    Tags: Antioxidant, B3S, Brain, conformation, Glutathione, IMAPP, Magnetic Resonance Spectroscopy, molecular dynamics, nuclear magnetic resonance.

  • W. Mao, P. Daligaux, N. Lazar, T. Ha-Duong, C. Cavé, H. van Tilbeurgh, P. M. Loiseau, and S. Pomel, “Biochemical analysis of leishmanial and human GDP-Mannose Pyrophosphorylases and selection of inhibitors as new leads”, Scientific Reports, vol. 7, no. 1, 2017.

  • R. Martin, F. Lacombat, A. Espagne, N. Dozova, P. Plaza, J. Yamamoto, P. Müller, K. Brettel, and A. de la Lande, “Ultrafast flavin photoreduction in an oxidized animal (6-4) photolyase through an unconventional tryptophan tetrad”, Physical chemistry chemical physics: PCCP, 2017.
    Abstract: Photolyases are flavoenzymes repairing UV-induced lesions in DNA, which may be activated by a photoreduction of their FAD cofactor. In most photolyases, this photoreduction proceeds by electron transfer along a chain of three tryptophan (Trp) residues, connecting the flavin to the protein surface. Much less studied, animal (6-4) photolyases (repairing pyrimidine-pyrimidone (6-4) photoproducts) are particularly interesting as they were recently shown to have a longer electron transfer chain, counting four Trp residues. Using femtosecond polarized transient absorption spectroscopy, we performed a detailed analysis of the photoactivation reaction in the (6-4) photolyase of Xenopus laevis with oxidized FAD. We showed that the excited flavin is very quickly reduced (∼0.5 ps) by a nearby tryptophan residue, yielding FAD˙(-) and WH˙(+) radicals. Subsequent kinetic steps in the picosecond regime were assigned to the migration of the positive charge along the Trp tetrad, in competition with charge recombination. We propose that the positive charge is actually delocalized over various Trp residues during most of the dynamics and that charge recombination essentially occurs through the proximal tryptophanyl radical. Oxidation of the fourth tryptophan is thought to be reached about as fast as that of the third one (∼40 ps), based on a comparison with a mutant protein lacking the distal Trp, implying ultrafast electron transfer between these two residues. This unusual mechanism sheds light on the rich diversity of electron transfer pathways found in various photolyases, and evolution-related cryptochromes alike.
    Tags: B3S, LPB.

  • B. Y. Matsuyama, P. V. Krasteva, and M. V. A. S. Navarro, “Isothermal Titration Calorimetry to Determine Apparent Dissociation Constants (K d) and Stoichiometry of Interaction (n) of C-di-GMP Binding Proteins”, Methods in Molecular Biology (Clifton, N.J.), vol. 1657, p. 403-416, 2017.
    Abstract: Isothermal titration calorimetry (ITC) is a commonly used biophysical technique that enables the quantitative characterization of intermolecular interactions in solution. Based on enthalpy changes (ΔH) upon titration of the binding partner (e.g., a small-molecule ligand such as c-di-GMP) to the molecule of interest (e.g., a receptor protein), the resulting binding isotherms provide information on the equilibrium association/dissociation constants (K a, K d) and stoichiometry of binding (n), as well as on changes in the Gibbs free energy (ΔG) and entropy (ΔS) along the interaction. Here we present ITC experiments used for the characterization of c-di-GMP binding proteins and discuss advantages and potential caveats in the interpretation of results.
    Tags: B3S, Binding stoichiometry, c-di-GMP, C-di-GMP sensor proteins, Dissociation constant (K d), Intermolecular interactions, isothermal titration calorimetry (ITC), Receptor–ligand interactions, SBB.

  • A. Mezzetti and W. Leibl, “Time-resolved infrared spectroscopy in the study of photosynthetic systems”, Photosynthesis Research, vol. 131, no. 2, p. 121-144, 2017.
    Abstract: Time-resolved (TR) infrared (IR) spectroscopy in the nanosecond to second timescale has been extensively used, in the last 30 years, in the study of photosynthetic systems. Interesting results have also been obtained at lower time resolution (minutes or even hours). In this review, we first describe the used techniques-dispersive IR, laser diode IR, rapid-scan Fourier transform (FT)IR, step-scan FTIR-underlying the advantages and disadvantages of each of them. Then, the main TR-IR results obtained so far in the investigation of photosynthetic reactions (in reaction centers, in light-harvesting systems, but also in entire membranes or even in living organisms) are presented. Finally, after the general conclusions, the perspectives in the field of TR-IR applied to photosynthesis are described.
    Tags: B3S, Bacterial reaction centers, Carotenoids, Chlorophyll, Electron transfer, FTIR difference spectroscopy, Infrared, Kinetics, Light-harvesting systems, LPB, photosynthesis, Photosynthetic Reaction Center Complex Proteins, Photosystem I, Photosystem II, Proton transfer, Rapid-scan FTIR, Reaction centers, Rhodobacter sphaeroides, Spectroscopy, Fourier Transform Infrared, Step-scan FTIR, Thylakoids, Ubiquinone, Vibrational spectroscopy.

  • C. Mignée, R. Mutoh, A. Krieger-Liszkay, G. Kurisu, and P. Sétif, “Gallium ferredoxin as a tool to study the effects of ferredoxin binding to photosystem I without ferredoxin reduction”, Photosynthesis Research, Feb. 2017.

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