2018

Publications 2018

288.     Zhan, Y., Marchand, C.H., Maes, A., Mauries, A., Sun, Y., Dhaliwal, J.S., Uniacke, J., Arragain, S., Jiang, H., Gold, N.D. et al. (2018) Pyrenoid functions revealed by proteomics in Chlamydomonas reinhardtii. PLoS One, 13, e0185039. http://www.ncbi.nlm.nih.gov/pubmed/29481573

287.     Wang, Y.J., Rico-Lastres, P., Lezamiz, A., Mora, M., Solsona, C., Stirnemann, G. and Garcia-Manyes, S. (2018) DNA Binding Induces a Nanomechanical Switch in the RRM1 Domain of TDP-43. J Phys Chem Lett, 9, 3800-3807. http://www.ncbi.nlm.nih.gov/pubmed/29924934

286.     Wang, X., Wisser, F.M., Canivet, J., Fontecave, M. and Mellot-Draznieks, C. (2018) Immobilization of a Full Photosystem in the Large-Pore MIL-101 Metal-Organic Framework for CO2 reduction. ChemSusChem. https://www.ncbi.nlm.nih.gov/pubmed/29978953

285.     Vakirlis, N., Hebert, A.S., Opulente, D.A., Achaz, G., Hittinger, C.T., Fischer, G., Coon, J.J. and Lafontaine, I. (2018) A Molecular Portrait of De Novo Genes in Yeasts. Mol Biol Evol, 35, 631-645. http://www.ncbi.nlm.nih.gov/pubmed/29220506

284.     Trellet, M., Ferey, N., Flotynski, J., Baaden, M. and Bourdot, P. (2018) Semantics for an Integrative and Immersive Pipeline Combining Visualization and Analysis of Molecular Data. J Integr Bioinform, 15. http://www.ncbi.nlm.nih.gov/pubmed/29982236

283.     Sutherland, G.A., Grayson, K.J., Adams, N.B.P., Mermans, D.M.J., Jones, A.S., Robertson, A.J., Auman, D.B., Brindley, A.A., Sterpone, F., Tuffery, P. et al. (2018) Probing the quality control mechanism of the Escherichia coli twin-arginine translocase with folding variants of a de novo-designed heme protein. J Biol Chem, 293, 6672-6681. http://www.ncbi.nlm.nih.gov/pubmed/29559557

282.     Sterpone, F., Doutreligne, S., Tran, T.T., Melchionna, S., Baaden, M., Nguyen, P.H. and Derreumaux, P. (2018) Multi-scale simulations of biological systems using the OPEP coarse-grained model. Biochem Biophys Res Commun, 498, 296-304. http://www.ncbi.nlm.nih.gov/pubmed/28917842

281.     Sterpone, F., Derreumaux, P. and Melchionna, S. (2018) Molecular Mechanism of Protein Unfolding under Shear: A Lattice Boltzmann Molecular Dynamics Study. J Phys Chem B, 122, 1573-1579. http://www.ncbi.nlm.nih.gov/pubmed/29328657

280.     Sommer, C., Rumpel, S., Roy, S., Fares, C., Artero, V., Fontecave, M., Reijerse, E. and Lubitz, W. (2018) Spectroscopic investigations of a semi-synthetic [FeFe] hydrogenase with propane di-selenol as bridging ligand in the binuclear subsite: comparison to the wild type and propane di-thiol variants. J Biol Inorg Chem. http://www.ncbi.nlm.nih.gov/pubmed/29627860

279.     Shai, N., Yifrach, E., van Roermund, C.W.T., Cohen, N., Bibi, C., Ijlst, L., Cavellini, L., Meurisse, J., Schuster, R., Zada, L. et al. (2018) Systematic mapping of contact sites reveals tethers and a function for the peroxisome-mitochondria contact. Nature Communications, In Press.

278.     Serra-Batiste, M., Tolchard, J., Giusti, F., Zoonens, M. and Carulla, N. (2018) Stabilization of a Membrane-Associated Amyloid-beta Oligomer for Its Validation in Alzheimer's Disease. Front Mol Biosci, 5, 38. http://www.ncbi.nlm.nih.gov/pubmed/29725595

277.     Sacquin-Mora, S. (2018) Mechanical variations in proteins with large-scale motions highlight the formation of structural locks. J Struct Biol. http://www.ncbi.nlm.nih.gov/pubmed/29852221

276.     Roper, J.C., Mitrossilis, D., Stirnemann, G., Waharte, F., Brito, I., Fernandez-Sanchez, M.E., Baaden, M., Salamero, J. and Farge, E. (2018) The major beta-catenin/E-cadherin junctional binding site is a primary molecular mechano-transductor of differentiation in vivo. Elife, 7. https://www.ncbi.nlm.nih.gov/pubmed/30024850

275.     Perales-Calvo, J., Giganti, D., Stirnemann, G. and Garcia-Manyes, S. (2018) The force-dependent mechanism of DnaK-mediated mechanical folding. Sci Adv, 4, eaaq0243. http://www.ncbi.nlm.nih.gov/pubmed/29487911

274.     Nguyen, P.H., Del Castillo-Frias, M.P., Berthoumieux, O., Faller, P., Doig, A.J. and Derreumaux, P. (2018) Amyloid-beta/Drug Interactions from Computer Simulations and Cell-Based Assays. J Alzheimers Dis, 64, S659-S672. https://www.ncbi.nlm.nih.gov/pubmed/29562512

273.     Murail, S., Vasiliu, T., Neamtu, A., Barboiu, M., Sterpone, F. and Baaden, M. (2018) Water permeation across artificial I-quartet membrane channels: from structure to disorder. Faraday Discuss. https://www.ncbi.nlm.nih.gov/pubmed/29974103

272.     Mouhand, A., Belfetmi, A., Catala, M., Larue, V., Zargarian, L., Brachet, F., Gorelick, R.J., Van Heijenoort, C., Mirambeau, G., Barraud, P. et al. (2018) Modulation of the HIV nucleocapsid dynamics finely tunes its RNA-binding properties during virion genesis. Nucleic Acids Res. http://www.ncbi.nlm.nih.gov/pubmed/29986076

271.     Maikova, A., Peltier, J., Boudry, P., Hajnsdorf, E., Kint, N., Monot, M., Poquet, I., Martin-Verstraete, I., Dupuy, B. and Soutourina, O. (2018) Discovery of new type I toxin-antitoxin systems adjacent to CRISPR arrays in Clostridium difficile. Nucleic Acids Res. http://www.ncbi.nlm.nih.gov/pubmed/29529286

270.     Maes, A., Martinez, X., Druart, K., Laurent, B., Guegan, S., Marchand, C.H., Lemaire, S.D. and Baaden, M. (2018) MinOmics, an Integrative and Immersive Tool for Multi-Omics Analysis. J Integr Bioinform, 15. http://www.ncbi.nlm.nih.gov/pubmed/29927748

269.     Longatte, G., Sayegh, A., Delacotte, J., Rappaport, F., Wollman, F.-A., Guille Collignon, M. and Lemaître, F. (2018) Investigation of Photocurrents Resulting from Living Unicellular Algae Suspension with Quinones over Time. Chemical Science. http://dx.doi.org/10.1039/C8SC03058H

268.     Liponska, A., Jamalli, A., Kuras, R., Suay, L., Garbe, E., Wollman, F.A., Laalami, S. and Putzer, H. (2018) Tracking the elusive 5' exonuclease activity of Chlamydomonas reinhardtii RNase J. Plant Mol Biol, 96, 641-653. http://www.ncbi.nlm.nih.gov/pubmed/29600502

267.     Le Bon, C., Marconnet, A., Masscheleyn, S., Popot, J.L. and Zoonens, M. (2018) Folding and stabilizing membrane proteins in amphipol A8-35. Methods. http://www.ncbi.nlm.nih.gov/pubmed/29678587

266.     Lagarde, N., Carbone, A. and Sacquin-Mora, S. (2018) Hidden partners: Using cross-docking calculations to predict binding sites for proteins with multiple interactions. Proteins, 86, 723-737. http://www.ncbi.nlm.nih.gov/pubmed/29664226

265.     Kocsis, I., Sorci, M., Vanselous, H., Murail, S., Sanders, S.E., Licsandru, E., Legrand, Y.M., van der Lee, A., Baaden, M., Petersen, P.B. et al. (2018) Oriented chiral water wires in artificial transmembrane channels. Sci Adv, 4, eaao5603. http://www.ncbi.nlm.nih.gov/pubmed/29582016

264.     Kim, R., Kanamaru, S., Mikawa, T., Prévost, C., Ishii, K., Ito, K., Uchiyama, S., Oda, M., Iwasaki, H., Kim, S.K. et al. (2018) RecA requires two molecules of Mg2+ ions for its optimal strand exchange activity in vitro. Nucleic Acids Research, 46, 2548-2559. https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5861410/pdf/gky048.pdf

263.     Joseph, T.T. and Henin, J. (2018) Molecular Mechanics Parameterization of Anesthetic Molecules. Methods Enzymol, 602, 61-76. http://www.ncbi.nlm.nih.gov/pubmed/29588041

262.     Hitaishi, V., Clement, R., Bourassin, N., Baaden, M., de Poulpiquet, A., Sacquin-Mora, S., Ciaccafava, A. and Lojou, E. (2018) Controlling Redox Enzyme Orientation at Planar Electrodes. Catalysts, 8, 192. http://www.mdpi.com/2073-4344/8/5/192

261.     Harigua-Souiai, E., Abdelkrim, Y.Z., Bassoumi-Jamoussi, I., Zakraoui, O., Bouvier, G., Essafi-Benkhadir, K., Banroques, J., Desdouits, N., Munier-Lehmann, H., Barhoumi, M. et al. (2018) Identification of novel leishmanicidal molecules by virtual and biochemical screenings targeting Leishmania eukaryotic translation initiation factor 4A. PLoS Negl Trop Dis, 12, e0006160. http://www.ncbi.nlm.nih.gov/pubmed/29346371

260.     Fogeron, T., Todorova, T.K., Porcher, J.-P., Gomez-Mingot, M., Chamoreau, L.-M., Mellot-Draznieks, C., Li, Y. and Fontecave, M. (2018) A Bioinspired Nickel(bis-dithiolene) Complex as a Homogeneous Catalyst for Carbon Dioxide Electroreduction. ACS Catalysis, 8, 2030-2038. https://pubs.acs.org/doi/10.1021/acscatal.7b03383

259.     Elbahnsi, A., Retureau, R., Baaden, M., Hartmann, B. and Oguey, C. (2018) Holding the Nucleosome Together: A Quantitative Description of the DNA-Histone Interface in Solution. J Chem Theory Comput, 14, 1045-1058. http://www.ncbi.nlm.nih.gov/pubmed/29262675

258.     El Mishri, E.S., Boutant, E., Mouhand, A., Larue, V., Thomas, A., Richert, L., Vivet-Boudout, V., Mély, Y., Tisné, C., Muriaux, D. et al. (2018) The NC domain and the p6 PTAP motif of HIV-1 Gag both contribute to the interaction of Gag with the cellular TSG101-UEV domain. Biochem Biophys Acta, In press.

257.     Durand, S. and Condon, C. (2018) RNases and Helicases in Gram-Positive Bacteria. Microbiol Spectr, 6. http://www.ncbi.nlm.nih.gov/pubmed/29651979

256.     Dumas, L., Zito, F., Auroy, P., Johnson, X., Peltier, G. and Alric, J. (2018) Structure-Function Analysis of Chloroplast Proteins via Random Mutagenesis Using Error-Prone PCR. Plant Physiol, 177, 465-475. http://www.ncbi.nlm.nih.gov/pubmed/29703866

255.     Dilworth, M.V., Piel, M.S., Bettaney, K.E., Ma, P., Luo, J., Sharples, D., Poyner, D.R., Gross, S.R., Moncoq, K., Henderson, P.J.F. et al. (2018) Microbial expression systems for membrane proteins. Methods. http://www.ncbi.nlm.nih.gov/pubmed/29656078

254.     Dalier, F., Dubacheva, G.V., Coniel, M., Zanchi, D., Galtayries, A., Piel, M., Marie, E. and Tribet, C. (2018) Mixed Copolymer Adlayers Allowing Reversible Thermal Control of Single Cell Aspect Ratio. ACS Appl Mater Interfaces, 10, 2253-2258. http://www.ncbi.nlm.nih.gov/pubmed/29314825

253.     Crozet, P., Navarro, F.J., Willmund, F., Mehrshahi, P., Bakowski, K., Lauersen, K.J., Perez-Perez, M.E., Auroy, P., Gorchs Rovira, A., Sauret-Gueto, S. et al. (2018) Birth of a photosynthetic chassis: a MoClo toolkit enabling synthetic biology in the microalga Chlamydomonas reinhardtii. ACS Synth Biol. https://www.ncbi.nlm.nih.gov/pubmed/30165733

252.     Corey, R.A., Pyle, E., Allen, W.J., Watkins, D.W., Casiraghi, M., Miroux, B., Arechaga, I., Politis, A. and Collinson, I. (2018) Specific cardiolipin-SecY interactions are required for proton-motive force stimulation of protein secretion. Proc Natl Acad Sci U S A, 115, 7967-7972. https://www.ncbi.nlm.nih.gov/pubmed/30012626

251.     Condon, C., Piton, J. and Braun, F. (2018) Distribution of the ribosome associated endonuclease Rae1 and the potential role of conserved amino acids in codon recognition. RNA Biol, 1-13. http://www.ncbi.nlm.nih.gov/pubmed/29557713

250.     Chipot, C., Dehez, F., Schnell, J.R., Zitzmann, N., Pebay-Peyroula, E., Catoire, L.J., Miroux, B., Kunji, E.R.S., Veglia, G., Cross, T.A. et al. (2018) Perturbations of Native Membrane Protein Structure in Alkyl Phosphocholine Detergents: A Critical Assessment of NMR and Biophysical Studies. Chem Rev, 118, 3559-3607. http://www.ncbi.nlm.nih.gov/pubmed/29488756

249.     Casiraghi, M., Damian, M., Lescop, E., Baneres, J.L. and Catoire, L.J. (2018) Illuminating the Energy Landscape of GPCRs: The Key Contribution of Solution-State NMR Associated with Escherichia coli as an Expression Host. Biochemistry, 57, 2297-2307. http://www.ncbi.nlm.nih.gov/pubmed/29607648

248.     Caserta, G., Papini, C., Adamska-Venkatesh, A., Pecqueur, L., Sommer, C., Reijerse, E., Lubitz, W., Gauquelin, C., Meynial-Salles, I., Pramanik, D. et al. (2018) Engineering an [FeFe]-Hydrogenase: Do Accessory Clusters Influence O2 Resistance and Catalytic Bias? J Am Chem Soc, 140, 5516-5526. http://www.ncbi.nlm.nih.gov/pubmed/29595965

247.     Brosse, A. and Guillier, M. (2018) Bacterial small RNAs in mixed regulatory networks. Microbiol. Spectrum In Press.

246.     Bou-Nader, C., Bregeon, D., Pecqueur, L., Fontecave, M. and Hamdane, D. (2018) Electrostatic Potential in the tRNA Binding Evolution of Dihydrouridine Synthases. Biochemistry. https://www.ncbi.nlm.nih.gov/pubmed/30149704

245.     Bou-Nader, C., Barraud, P., Pecqueur, L., Sacquin-Mora, S., Pérez, J., Velours, C., Fontecave, M., Tisné, C. and Hamdane, D. (2018) Molecular basis for transfer RNA substrate recognition by human dihydrouridine synthase. Nucleic Acids Res, In press.

244.     Boniello, G., Tribet, C., Marie, E., Croquette, V. and Zanchi, D. (2018) Rolling and Ageing in T-Ramp Soft Adhesion. Phys Rev. E 97, 012609.

243.     Berkovich, R., Fernandez, V.I., Stirnemann, G., Valle-Orero, J. and Fernandez, J.M. (2018) Segmentation and the Entropic Elasticity of Modular Proteins. J Phys Chem Lett, 9, 4707-4713. https://www.ncbi.nlm.nih.gov/pubmed/30058807

242.     Beedle, A.E.M., Mora, M., Davis, C.T., Snijders, A.P., Stirnemann, G. and Garcia-Manyes, S. (2018) Forcing the reversibility of a mechanochemical reaction. Nat Commun, 9, 3155. https://www.ncbi.nlm.nih.gov/pubmed/30089863

241.     Baumgardt, K., Gilet, L., Figaro, S. and Condon, C. (2018) The essential nature of YqfG, a YbeY homologue required for 3' maturation of Bacillus subtilis 16S ribosomal RNA is suppressed by deletion of RNase R. Nucleic Acids Res. http://www.ncbi.nlm.nih.gov/pubmed/29873764

240.     Barroso da Silva, F.L., Derreumaux, P. and Pasquali, S. (2018) Protein-RNA complexation driven by the charge regulation mechanism. Biochem Biophys Res Commun, 498, 264-273. http://www.ncbi.nlm.nih.gov/pubmed/28709871

239.     Baaden, M., Delalande, O., Ferey, N., Pasquali, S., Waldispuhl, J. and Taly, A. (2018) Ten simple rules to create a serious game, illustrated with examples from structural biology. PLoS Comput Biol, 14, e1005955. http://www.ncbi.nlm.nih.gov/pubmed/29518072

238.     Angius, F., Ilioaia, O., Amrani, A., Suisse, A., Rosset, L., Legrand, A., Abou-Hamdan, A., Uzan, M., Zito, F. and Miroux, B. (2018) A novel regulation mechanism of the T7 RNA polymerase based expression system improves overproduction and folding of membrane proteins. Sci Rep, 8, 8572. http://www.ncbi.nlm.nih.gov/pubmed/29872064

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