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Accueil > Départements > Biochimie, Biophysique et Biologie Structurale > Françoise OCHSENBEIN & Raphaël GUEROIS : Assemblage moléculaire et intégrité du génome

Publications de l’équipe

2018


  • 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 www.meet-u.org.
    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.

  • 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. 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.


  • 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.

  • 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.

  • 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.


  • A. A. Nadaradjane, R. Guerois, et J. Andreani, « Protein-Protein Docking Using Evolutionary Information », in Protein Complex Assembly, vol. 1764, J. A. Marsh, Éd. New York, NY: Springer New York, 2018, p. 429-447.

  • T. Q. Nguyen, M. Chenon, F. Vilela, C. Velours, M. Aumont-Nicaise, J. Andreani, P. F. Varela, P. Llinas, et J. Ménétrey, « Correction: Structural plasticity of the N-terminal capping helix of the TPR domain of kinesin light chain », PloS One, vol. 13, nᵒ 5, p. e0197193, 2018.
    Résumé : [This corrects the article DOI: 10.1371/journal.pone.0186354.].
    Mots-clés : AMIG, B3S, MIKICA, PF, PIM.

  • C. Quignot, J. Rey, J. Yu, P. Tufféry, R. Guerois, et J. Andreani, « InterEvDock2: an expanded server for protein docking using evolutionary and biological information from homology models and multimeric inputs », Nucleic Acids Research, mai 2018.
    Résumé : Computational protein docking is a powerful strategy to predict structures of protein-protein interactions and provides crucial insights for the functional characterization of macromolecular cross-talks. We previously developed InterEvDock, a server for ab initio protein docking based on rigid-body sampling followed by consensus scoring using physics-based and statistical potentials, including the InterEvScore function specifically developed to incorporate co-evolutionary information in docking. InterEvDock2 is a major evolution of InterEvDock which allows users to submit input sequences - not only structures - and multimeric inputs and to specify constraints for the pairwise docking process based on previous knowledge about the interaction. For this purpose, we added modules in InterEvDock2 for automatic template search and comparative modeling of the input proteins. The InterEvDock2 pipeline was benchmarked on 812 complexes for which unbound homology models of the two partners and co-evolutionary information are available in the PPI4DOCK database. InterEvDock2 identified a correct model among the top 10 consensus in 29% of these cases (compared to 15-24% for individual scoring functions) and at least one correct interface residue among 10 predicted in 91% of these cases. InterEvDock2 is thus a unique protein docking server, designed to be useful for the experimental biology community. The InterEvDock2 web interface is available at http://bioserv.rpbs.univ-paris-diderot.fr/services/InterEvDock2/.
    Mots-clés : AMIG, B3S.

  • S. P. Visweshwaran, P. A. Thomason, R. Guerois, S. Vacher, E. V. Denisov, L. A. Tashireva, M. E. Lomakina, C. Lazennec-Schurdevin, G. Lakisic, S. Lilla, N. Molinie, V. Henriot, Y. Mechulam, A. Y. Alexandrova, N. V. Cherdyntseva, I. Bièche, E. Schmitt, R. H. Insall, et A. Gautreau, « The trimeric coiled-coil HSBP1 protein promotes WASH complex assembly at centrosomes », The EMBO journal, mai 2018.
    Résumé : The Arp2/3 complex generates branched actin networks that exert pushing forces onto different cellular membranes. WASH complexes activate Arp2/3 complexes at the surface of endosomes and thereby fission transport intermediates containing endocytosed receptors, such as α5β1 integrins. How WASH complexes are assembled in the cell is unknown. Here, we identify the small coiled-coil protein HSBP1 as a factor that specifically promotes the assembly of a ternary complex composed of CCDC53, WASH, and FAM21 by dissociating the CCDC53 homotrimeric precursor. HSBP1 operates at the centrosome, which concentrates the building blocks. HSBP1 depletion in human cancer cell lines and in Dictyostelium amoebae phenocopies WASH depletion, suggesting a critical role of the ternary WASH complex for WASH functions. HSBP1 is required for the development of focal adhesions and of cell polarity. These defects impair the migration and invasion of tumor cells. Overexpression of HSBP1 in breast tumors is associated with increased levels of WASH complexes and with poor prognosis for patients.
    Mots-clés : actin cytoskeleton, AMIG, Arp2/3 complex, B3S, cell migration and invasion, centrosome, multiprotein complex assembly.

2017


  • C. Caillet-Saguy, A. Toto, R. Guerois, P. Maisonneuve, E. di Silvio, K. Sawyer, S. Gianni, et 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, août 2017.
    Résumé : 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.
    Mots-clés : AMIG, B3S.


  • L. Celma, C. Corbinais, J. Vercruyssen, X. Veaute, I. L. de la Sierra-Gallay, R. Guérois, D. Busso, A. Mathieu, S. Marsin, S. Quevillon-Cheruel, et J. P. Radicella, « Structural basis for the substrate selectivity of Helicobacter pylori NucT nuclease activity », PLOS ONE, vol. 12, nᵒ 12, p. e0189049, déc. 2017.


  • 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, et V. Borde, « Concerted action of the MutLβ heterodimer and Mer3 helicase regulates the global extent of meiotic gene conversion », eLife, vol. 6, janv. 2017.
    Mots-clés : AMIG, B3S, biochemistry, Chromosomes, genes, INTGEN, Meiosis, mismatch repair, Recombination, S. cerevisiae.

  • R. Grzela, J. Nusbaum, S. Fieulaine, F. Lavecchia, M. Desmadril, N. Nhiri, A. Van Dorsselaer, S. Cianferani, E. Jacquet, T. Meinnel, et C. Giglione, « Peptide deformylases from Vibrio parahaemolyticus phage and bacteria display similar deformylase activity and inhibitor binding clefts », Biochimica Et Biophysica Acta, oct. 2017.
    Résumé : Unexpected peptide deformylase (PDF) genes were recently retrieved in numerous marine phage genomes. While various hypotheses dealing with the occurrence of these intriguing sequences have been made, no further characterization and functional studies have been described thus far. In this study, we characterize the bacteriophage Vp16 PDF enzyme, as representative member of the newly identified C-terminally truncated viral PDFs. We show here that conditions classically used for bacterial PDFs lead to an enzyme exhibiting weak activity. Nonetheless, our integrated biophysical and biochemical approaches reveal specific effects of pH and metals on Vp16 PDF stability and activity. A novel purification protocol taking in account these data allowed strong improvement of Vp16 specific activity to values similar to those of bacterial PDFs. We next show that Vp16PDF is as sensitive to the natural inhibitor compound of PDFs, actinonin, as bacterial PDFs. Comparison of the 3D structures of Vp16 and E. coli PDFs bound to actinonin also reveals that both PDFs display identical substrate binding mode. We conclude that bacteriophage Vp16 PDF protein has functional peptide deformylase activity and we suggest that encoded phage PDFs might be important for viral fitness.
    Mots-clés : AMIG, B3S, BDG, DBG, Enzyme mechanism, IMAPP, MIP, N-terminal methionine excision, Peptide deformylase, PF, PIM, PROMTI, Structure, Virus.

  • A. Méneret, E. A. Franz, O. Trouillard, T. C. Oliver, Y. Zagar, S. P. Robertson, Q. Welniarz, R. J. M. K. Gardner, C. Gallea, M. Srour, C. Depienne, C. L. Jasoni, C. Dubacq, F. Riant, J. - C. Lamy, M. - P. Morel, R. Guérois, J. Andreani, C. Fouquet, M. Doulazmi, M. Vidailhet, G. A. Rouleau, A. Brice, A. Chédotal, I. Dusart, E. Roze, et D. Markie, « Mutations in the netrin-1 gene cause congenital mirror movements », The Journal of Clinical Investigation, sept. 2017.
    Résumé : Netrin-1 is a secreted protein that was first identified 20 years ago as an axon guidance molecule that regulates midline crossing in the CNS. It plays critical roles in various tissues throughout development and is implicated in tumorigenesis and inflammation in adulthood. Despite extensive studies, no inherited human disease has been directly associated with mutations in NTN1, the gene coding for netrin-1. Here, we have identified 3 mutations in exon 7 of NTN1 in 2 unrelated families and 1 sporadic case with isolated congenital mirror movements (CMM), a disorder characterized by involuntary movements of one hand that mirror intentional movements of the opposite hand. Given the diverse roles of netrin-1, the absence of manifestations other than CMM in NTN1 mutation carriers was unexpected. Using multimodal approaches, we discovered that the anatomy of the corticospinal tract (CST) is abnormal in patients with NTN1-mutant CMM. When expressed in HEK293 or stable HeLa cells, the 3 mutated netrin-1 proteins were almost exclusively detected in the intracellular compartment, contrary to WT netrin-1, which is detected in both intracellular and extracellular compartments. Since netrin-1 is a diffusible extracellular cue, the pathophysiology likely involves its loss of function and subsequent disruption of axon guidance, resulting in abnormal decussation of the CST.
    Mots-clés : AMIG, B3S.

  • T. Q. Nguyen, M. Chenon, F. Vilela, C. Velours, M. Aumont-Nicaise, J. Andreani, P. F. Varela, P. Llinas, et J. Ménétrey, « Structural plasticity of the N-terminal capping helix of the TPR domain of kinesin light chain », PloS One, vol. 12, nᵒ 10, p. e0186354, 2017.
    Résumé : Kinesin1 plays a major role in neuronal transport by recruiting many different cargos through its kinesin light chain (KLC). Various structurally unrelated cargos interact with the conserved tetratricopeptide repeat (TPR) domain of KLC. The N-terminal capping helix of the TPR domain exhibits an atypical sequence and structural features that may contribute to the versatility of the TPR domain to bind different cargos. We determined crystal structures of the TPR domain of both KLC1 and KLC2 encompassing the N-terminal capping helix and show that this helix exhibits two distinct and defined orientations relative to the rest of the TPR domain. Such a difference in orientation gives rise, at the N-terminal part of the groove, to the formation of one hydrophobic pocket, as well as to electrostatic variations at the groove surface. We present a comprehensive structural analysis of available KLC1/2-TPR domain structures that highlights that ligand binding into the groove can be specific of one or the other N-terminal capping helix orientations. Further, structural analysis reveals that the N-terminal capping helix is always involved in crystal packing contacts, especially in a TPR1:TPR1' contact which highlights its propensity to be a protein-protein interaction site. Together, these results underline that the structural plasticity of the N-terminal capping helix might represent a structural determinant for TPR domain structural versatility in cargo binding.
    Mots-clés : AMIG, Amino Acid Motifs, Amino Acid Sequence, Animals, B3S, Conserved Sequence, Humans, Ligands, Mice, Microtubule-Associated Proteins, MIKICA, Models, Molecular, PF, PIM, Protein Conformation, alpha-Helical, Protein Domains.


  • P. V. Sauer, J. Timm, D. Liu, D. Sitbon, E. Boeri-Erba, C. Velours, N. Mücke, J. Langowski, F. Ochsenbein, G. Almouzni, et D. Panne, « Insights into the molecular architecture and histone H3-H4 deposition mechanism of yeast Chromatin assembly factor 1 », eLife, vol. 6, mars 2017.
    Mots-clés : AMIG, B3S, PF, PIM.


  • J. Yu, J. Andreani, F. Ochsenbein, et R. Guerois, « Lessons from (co-)evolution in the docking of proteins and peptides for CAPRI Rounds 28-35: Coevolution in CAPRI Rounds 28-35 », Proteins: Structure, Function, and Bioinformatics, vol. 85, nᵒ 3, p. 378-390, 2017.

2016


  • M. Biondini, A. Sadou-Dubourgnoux, P. Paul-Gilloteaux, G. Zago, M. D. Arslanhan, F. Waharte, E. Formstecher, M. Hertzog, J. Yu, R. Guerois, A. Gautreau, G. Scita, J. Camonis, et M. C. Parrini, « Direct interaction between exocyst and Wave complexes promotes cell protrusions and motility », Journal of Cell Science, vol. 129, nᵒ 20, p. 3756-3769, oct. 2016.
    Résumé : Coordination between membrane trafficking and actin polymerization is fundamental in cell migration, but a dynamic view of the underlying molecular mechanisms is still missing. The Rac1 GTPase controls actin polymerization at protrusions by interacting with its effector, the Wave regulatory complex (WRC). The exocyst complex, which functions in polarized exocytosis, has been involved in the regulation of cell motility. Here, we show a physical and functional connection between exocyst and WRC. Purified components of exocyst and WRC directly associate in vitro, and interactions interfaces are identified. The exocyst-WRC interaction is confirmed in cells by co-immunoprecipitation and is shown to occur independently of the Arp2/3 complex. Disruption of the exocyst-WRC interaction leads to impaired migration. By using time-lapse microscopy coupled to image correlation analysis, we visualized the trafficking of the WRC towards the front of the cell in nascent protrusions. The exocyst is necessary for WRC recruitment at the leading edge and for resulting cell edge movements. This direct link between the exocyst and WRC provides a new mechanistic insight into the spatio-temporal regulation of cell migration.
    Mots-clés : AMIG, B3S, Exocyst, Motility, Ral, Wave.


  • H. Delattre, O. Souiai, K. Fagoonee, R. Guerois, et M. - A. Petit, « Phagonaute: A web-based interface for phage synteny browsing and protein function prediction », Virology, vol. 496, p. 42-50, 2016.


  • M. F. Lensink, S. Velankar, A. Kryshtafovych, S. - Y. Huang, D. Schneidman-Duhovny, A. Sali, J. Segura, N. Fernandez-Fuentes, S. Viswanath, R. Elber, S. Grudinin, P. Popov, E. Neveu, H. Lee, M. Baek, S. Park, L. Heo, G. Rie Lee, C. Seok, S. Qin, H. - X. Zhou, D. W. Ritchie, B. Maigret, M. - D. Devignes, A. Ghoorah, M. Torchala, R. A. G. Chaleil, P. A. Bates, E. Ben-Zeev, M. Eisenstein, S. S. Negi, Z. Weng, T. Vreven, B. G. Pierce, T. M. Borrman, J. Yu, F. Ochsenbein, R. Guerois, A. Vangone, J. P. G. L. M. Rodrigues, G. van Zundert, M. Nellen, L. Xue, E. Karaca, A. S. J. Melquiond, K. Visscher, P. L. Kastritis, A. M. J. J. Bonvin, X. Xu, L. Qiu, C. Yan, J. Li, Z. Ma, J. Cheng, X. Zou, Y. Shen, L. X. Peterson, H. - R. Kim, A. Roy, X. Han, J. Esquivel-Rodriguez, D. Kihara, X. Yu, N. J. Bruce, J. C. Fuller, R. C. Wade, I. Anishchenko, P. J. Kundrotas, I. A. Vakser, K. Imai, K. Yamada, T. Oda, T. Nakamura, K. Tomii, C. Pallara, M. Romero-Durana, B. Jiménez-García, I. H. Moal, J. Férnandez-Recio, J. Y. Joung, J. Y. Kim, K. Joo, J. Lee, D. Kozakov, S. Vajda, S. Mottarella, D. R. Hall, D. Beglov, A. Mamonov, B. Xia, T. Bohnuud, C. A. Del Carpio, E. Ichiishi, N. Marze, D. Kuroda, S. S. Roy Burman, J. J. Gray, E. Chermak, L. Cavallo, R. Oliva, A. Tovchigrechko, et S. J. Wodak, « Prediction of homoprotein and heteroprotein complexes by protein docking and template-based modeling: A CASP-CAPRI experiment: Prediction of Homo and Heteroprotein Complexes by Protein Docking and Modeling », Proteins: Structure, Function, and Bioinformatics, vol. 84, p. 323-348, 2016.


  • P. Llinas, M. Chenon, T. Q. Nguyen, C. Moreira, A. de Régibus, A. Coquard, M. J. Ramos, R. Guérois, P. A. Fernandes, et J. Ménétrey, « Structure of a truncated form of leucine zipper II of JIP3 reveals an unexpected antiparallel coiled-coil arrangement », Acta Crystallographica Section F Structural Biology Communications, vol. 72, nᵒ 3, p. 198-206, mars 2016.

  • J. Yu et R. Guerois, « PPI4DOCK: large scale assessment of the use of homology models in free docking over more than 1000 realistic targets », Bioinformatics (Oxford, England), vol. 32, nᵒ 24, p. 3760-3767, déc. 2016.
    Résumé : MOTIVATION: Protein-protein docking methods are of great importance for understanding interactomes at the structural level. It has become increasingly appealing to use not only experimental structures but also homology models of unbound subunits as input for docking simulations. So far we are missing a large scale assessment of the success of rigid-body free docking methods on homology models. RESULTS: We explored how we could benefit from comparative modelling of unbound subunits to expand docking benchmark datasets. Starting from a collection of 3157 non-redundant, high X-ray resolution heterodimers, we developed the PPI4DOCK benchmark containing 1417 docking targets based on unbound homology models. Rigid-body docking by Zdock showed that for 1208 cases (85.2%), at least one correct decoy was generated, emphasizing the efficiency of rigid-body docking in generating correct assemblies. Overall, the PPI4DOCK benchmark contains a large set of realistic cases and provides new ground for assessing docking and scoring methodologies. AVAILABILITY AND IMPLEMENTATION: Benchmark sets can be downloaded from http://biodev.cea.fr/interevol/ppi4dock/ CONTACT: guerois@cea.frSupplementary information: Supplementary data are available at Bioinformatics online.
    Mots-clés : AMIG, B3S.


  • J. Yu, M. Vavrusa, J. Andreani, J. Rey, P. Tufféry, et R. Guerois, « InterEvDock: a docking server to predict the structure of protein–protein interactions using evolutionary information », Nucleic Acids Research, vol. 44, nᵒ W1, p. W542-W549, juill. 2016.

2015

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Publications majeures avant 2015

1. Richet N, Liu D, Legrand P, Velours C, Corpet A, Gaubert A, Bakail M, Moal-Raisin G, Guerois R, Compper C, Besle A, Guichard B, Almouzni G, Ochsenbein F (2015) Structural insight into how the human helicase subunit MCM2 may act as a histone chaperone together with ASF1 at the replication fork. Nucleic Acids Res. In press.

1. Lisboa J, Andreani J, Sanchez D, Boudes M, Collinet B, Liger D, van Tilbeurgh H, Guerois R*, Cheruel S* (2014) Molecular determinants of the DprA/RecA interaction for nucleation on ssDNA. Nucleic Acids Res 42(11):7395-408. (* co-last authors)

2. Pietrobon V, Fréon K, Hardy J, Costes A, Iraqui I, Ochsenbein F, Lambert SA (2014) The chromatin assembly factor 1 promotes Rad51-dependent template switches at replication forks by counteracting D-loop disassembly by the RecQ-type helicase Rqh1. PLoS Biol 12(10):e1001968.

3. Meurisse J, Bacquin A, Richet N, Charbonnier JB, Ochsenbein F, Peyroche A (2014) Hug1 is an intrinsically disordered protein that inhibits ribonucleotide reductase activity by directly binding Rnr2 subunit. Nucleic Acids Res. 42(21):13174-85.

4. Andreani J, Faure G, Guerois R (2013) InterEvScore : a novel coarse-grained interface scoring function using a multi-body statistical potential coupled to evolution. Bioinformatics 29 : 1742-1749.

5. Jiao Y*, Seeger K*, Lautrette A, Gaubert A, Mousson F, Guerois R, Mann C, Ochsenbein F (2012) Surprising complexity of the Asf1 histone chaperone-Rad53 kinase interaction. Proc Natl Acad Sci U S A 109 : 2866-2871

6. Barrault MB, Richet N, Godard C, Murciano B, Le Tallec B, Rousseau E, Legrand P, Charbonnier JB, Le Du MH, Guerois R, Ochsenbein F*, Peyroche A* (2012) Dual functions of the Hsm3 protein in chaperoning and scaffolding regulatory particle subunits during the proteasome assembly. Proc Natl Acad Sci U S A 109 : E1001-1010 (* co-last authors)

7. Faure G, Andreani J, Guerois R (2012) InterEvol database : exploring the structure and evolution of protein complex interfaces. Nucleic Acids Res 40 : D847-856

8. Lopes A, Amarir-Bouhram J, Faure G, Petit MA, Guerois R (2010) Detection of novel recombinases in bacteriophage genomes unveils Rad52, Rad51 and Gp2.5 remote homologs. Nucleic Acids Res 38 : 3952-3962

9. Madaoui H, Guerois R (2008) Coevolution at protein complex interfaces can be detected by the complementarity trace with important impact for predictive docking. Proc Natl Acad Sci U S A 105 : 7708-7713

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