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1. Prediction of protein assemblies, the next frontier: The CASP14-CAPRI experiment

Author: Xiaoqin Zou, Théo Mauri, Hang Shi, Shaowen Zhu, Justas Dapkūnas, Yuanfei Sun, Didier Barradas-Bautista, Raphael A. G. Chaleil, Ragul Gowthaman, Sohee Kwon, Xianjin Xu, Zuzana Jandova, Genki Terashi, Ryota Ashizawa, Petras J. Kundrotas, Shuang Zhang, Tunde Aderinwale, Jian Liu, Sandor Vajda, Paul A. Bates, Jianlin Cheng, Daisuke Kihara, Luis A. Rodríguez-Lumbreras, Carlos A. Del Carpio Muñoz, Liming Qiu, Guillaume Brysbaert, Jorge Roel-Touris, Česlovas Venclovas, Tereza Clarence, Rui Yin, Amar Singh, Patryk A. Wesołowski, Rafał Ślusarz, Adam Liwo, Guangbo Yang, Agnieszka S. Karczyńska, Yoshiki Harada, Sergei Kotelnikov, Yuya Hanazono, Charlotte W. van Noort, Marc F. Lensink, Jonghun Won, Adam K. Sieradzan, Israel Desta, Xufeng Lu, Charles Christoffer, Anna Antoniak, Taeyong Park, Sheng-You Huang, Tsukasa Nakamura, Brian G. Pierce, Usman Ghani, Yang Shen, Luigi Cavallo, Chaok Seok, Hao Li, Nurul Nadzirin, Ghazaleh Taherzadeh, Jacob Verburgt, Rodrigo V. Honorato, Artur Giełdoń, Jeffrey J. Gray, Dima Kozakov, Ming Liu, Shan Chang, Eiichiro Ichiishi, Manon Réau, Rui Duan, Francesco Ambrosetti, Johnathan D. Guest, Juan Fernández-Recio, Alexandre M. J. J. Bonvin, Ilya A. Vakser, Farhan Quadir, Yumeng Yan, Ren Kong, Sameer Velankar, Sergei Grudinin, Mateusz Kogut, Mikhail Ignatov, Yasuomi Kiyota, Hyeonuk Woo, Shoshana J. Wodak, Ameya Harmalkar, Shinpei Kobayashi, Panagiotis I. Koukos, Zhen Cao, Kliment Olechnovič, Cezary Czaplewski, Xiao Wang, Agnieszka G. Lipska, Kathryn A. Porter, Peicong Lin, Emilia A. Lubecka, Nasser Hashemi, Bin Liu, Mayuko Takeda-Shitaka, Karolina Zięba, Dzmitry Padhorny, Zhuyezi Sun, Daipayan Sarkar, Romina Oliva, Andrey Alekseenko, Siri Camee van Keulen, Mireia Rosell, Raj S. Roy, Brian Jiménez-García, Jinsol Yang, Martyna Maszota-Zieleniak, Cancer Research UK, Department of Energy and Climate Change (UK), European Commission, Institut National de Recherche en Informatique et en Automatique (France), Medical Research Council (UK), Japan Society for the Promotion of Science, Ministerio de Ciencia, Innovación y Universidades (España), Agencia Estatal de Investigación (España), National Institute of General Medical Sciences (US), National Institutes of Health (US), National Natural Science Foundation of China, National Science Foundation (US), Unité de Glycobiologie Structurale et Fonctionnelle (UGSF), Université de Lille-Centre National de la Recherche Scientifique (CNRS)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), European Bioinformatics Institute [Hinxton] (EMBL-EBI), EMBL Heidelberg, Biomolecular Modelling Laboratory [London], The Francis Crick Institute [London], Jiangsu University of Technology [Changzhou], Department of Electrical Engineering and Computer Science [Columbia] (EECS), University of Missouri [Columbia] (Mizzou), University of Missouri System-University of Missouri System, Institute for Data Science and Informatics [Columbia], University of Gdańsk (UG), Faculty of Electronics, Telecommunications and Informatics [GUT Gdańsk] (ETI), Gdańsk University of Technology (GUT), Medical University of Gdańsk, Graduate School of Medical Sciences [Nagoya], Nagoya City University [Nagoya, Japan], International University of Health and Welfare Hospital (IUHW Hospital), Department of Chemical and Biomolecular Engineering [Baltimore], Johns Hopkins University (JHU), Bijvoet Center of Biomolecular Research [Utrecht], Utrecht University [Utrecht], Stony Brook University [SUNY] (SBU), State University of New York (SUNY), Innopolis University, Boston University [Boston] (BU), Russian Academy of Sciences [Moscow] (RAS), Barcelona Supercomputing Center - Centro Nacional de Supercomputacion (BSC - CNS), Universidad de La Rioja (UR), Algorithms for Modeling and Simulation of Nanosystems (NANO-D), Inria Grenoble - Rhône-Alpes, Institut National de Recherche en Informatique et en Automatique (Inria)-Institut National de Recherche en Informatique et en Automatique (Inria)-Laboratoire Jean Kuntzmann (LJK), Institut National de Recherche en Informatique et en Automatique (Inria)-Centre National de la Recherche Scientifique (CNRS)-Université Grenoble Alpes (UGA)-Institut polytechnique de Grenoble - Grenoble Institute of Technology (Grenoble INP ), Université Grenoble Alpes (UGA)-Centre National de la Recherche Scientifique (CNRS)-Université Grenoble Alpes (UGA)-Institut polytechnique de Grenoble - Grenoble Institute of Technology (Grenoble INP ), Université Grenoble Alpes (UGA), Données, Apprentissage et Optimisation (DAO), Laboratoire Jean Kuntzmann (LJK), Université Grenoble Alpes (UGA)-Institut National de Recherche en Informatique et en Automatique (Inria)-Centre National de la Recherche Scientifique (CNRS)-Université Grenoble Alpes (UGA)-Institut polytechnique de Grenoble - Grenoble Institute of Technology (Grenoble INP ), Huazhong University of Science and Technology [Wuhan] (HUST), Indiana University - Purdue University Indianapolis (IUPUI), Indiana University System, Graduate School of Information Sciences [Sendaï], Tohoku University [Sendai], National Institutes for Quantum and Radiological Science and Technology (QST), University of Maryland [Baltimore], King Abdullah University of Science and Technology (KAUST), University of Naples Federico II, Texas A&M University [Galveston], Seoul National University [Seoul] (SNU), Kitasato University, University of Kansas [Lawrence] (KU), Vilnius University [Vilnius], University of Missouri System, VIB-VUB Center for Structural Biology [Bruxelles], VIB [Belgium], Sub NMR Spectroscopy, Sub Overig UiLOTS, Sub Mathematics Education, NMR Spectroscopy, Université de Lille, CNRS, Unité de Glycobiologie Structurale et Fonctionnelle (UGSF) - UMR 8576, European Bioinformatics Institute [Hinxton] [EMBL-EBI], Department of Electrical Engineering and Computer Science [Columbia] [EECS], Faculty of Chemistry [Univ Gdańsk], Faculty of Electronics, Telecommunications and Informatics [GUT Gdańsk] [ETI], International University of Health and Welfare Hospital [IUHW Hospital], Johns Hopkins University [JHU], Stony Brook University [SUNY] [SBU], Department of Biomedical Engineering [Boston], Instituto de Ciencias de la Vid y el Vino [ICVV], Huazhong University of Science and Technology [Wuhan] [HUST], Indiana University - Purdue University Indianapolis [IUPUI], National Institutes for Quantum and Radiological Science and Technology [QST], King Abdullah University of Science and Technology [KAUST], Università degli Studi di Napoli 'Parthenope' = University of Naples [PARTHENOPE], Seoul National University [Seoul] [SNU], University of Kansas [Lawrence] [KU], University of Missouri [Columbia] [Mizzou], Unité de Glycobiologie Structurale et Fonctionnelle - UMR 8576 (UGSF), Université de Lille-Centre National de la Recherche Scientifique (CNRS), University of Naples Federico II = Università degli studi di Napoli Federico II, European Project: 675728,H2020,H2020-EINFRA-2015-1,BioExcel(2015), European Project: 823830,H2020-EU.1.4.1.3. Development, deployment and operation of ICT-based e-infrastructures, H2020-EU.1.4. EXCELLENT SCIENCE - Research Infrastructures ,BioExcel-2(2019), European Project: 777536,H2020-EU.1.4.1.3. Development, deployment and operation of ICT-based e-infrastructures, and H2020-EU.1.4. EXCELLENT SCIENCE - Research Infrastructures,EOSC-hub(2018)
Subjects: Models, Molecular, blind prediction, CAPRI, CASP, docking, oligomeric state, protein assemblies, protein complexes, protein docking, protein–protein interaction, template-based modeling, Computer science, [SDV]Life Sciences [q-bio], Machine learning, computer.software_genre, Biochemistry, Article, protein-protein interaction, 03 medical and health sciences, Sequence Analysis, Protein, Structural Biology, Server, Protein Interaction Domains and Motifs, Molecular Biology, ComputingMilieux_MISCELLANEOUS, 030304 developmental biology, 0303 health sciences, Binding Sites, business.industry, 030302 biochemistry & molecular biology, Computational Biology, Proteins, 3. Good health, Molecular Docking Simulation, Artificial intelligence, business, computer, Software
Abstract: We present the results for CAPRI Round 50, the fourth joint CASP-CAPRI protein assembly prediction challenge. The Round comprised a total of twelve targets, including six dimers, three trimers, and three higher-order oligomers. Four of these were easy targets, for which good structural templates were available either for the full assembly, or for the main interfaces (of the higher-order oligomers). Eight were difficult targets for which only distantly related templates were found for the individual subunits. Twenty-five CAPRI groups including eight automatic servers submitted ~1250 models per target. Twenty groups including six servers participated in the CAPRI scoring challenge submitted ~190 models per target. The accuracy of the predicted models was evaluated using the classical CAPRI criteria. The prediction performance was measured by a weighted scoring scheme that takes into account the number of models of acceptable quality or higher submitted by each group as part of their five top-ranking models. Compared to the previous CASP-CAPRI challenge, top performing groups submitted such models for a larger fraction (70–75%) of the targets in this Round, but fewer of these models were of high accuracy. Scorer groups achieved stronger performance with more groups submitting correct models for 70–80% of the targets or achieving high accuracy predictions. Servers performed less well in general, except for the MDOCKPP and LZERD servers, who performed on par with human groups. In addition to these results, major advances in methodology are discussed, providing an informative overview of where the prediction of protein assemblies currently stands., Cancer Research UK, Grant/Award Number: FC001003; Changzhou Science and Technology Bureau, Grant/Award Number: CE20200503; Department of Energy and Climate Change, Grant/Award Numbers: DE-AR001213, DE-SC0020400, DE-SC0021303; H2020 European Institute of Innovation and Technology, Grant/Award Numbers: 675728, 777536, 823830; Institut national de recherche en informatique et en automatique (INRIA), Grant/Award Number: Cordi-S; Lietuvos Mokslo Taryba, Grant/Award Numbers: S-MIP-17-60, S-MIP-21-35; Medical Research Council, Grant/Award Number: FC001003; Japan Society for the Promotion of Science KAKENHI, Grant/Award Number: JP19J00950; Ministerio de Ciencia e Innovación, Grant/Award Number: PID2019-110167RB-I00; Narodowe Centrum Nauki, Grant/Award Numbers: UMO-2017/25/B/ST4/01026, UMO-2017/26/M/ST4/00044, UMO-2017/27/B/ST4/00926; National Institute of General Medical Sciences, Grant/Award Numbers: R21GM127952, R35GM118078, RM1135136, T32GM132024; National Institutes of Health, Grant/Award Numbers: R01GM074255, R01GM078221, R01GM093123, R01GM109980, R01GM133840, R01GN123055, R01HL142301, R35GM124952, R35GM136409; National Natural Science Foundation of China, Grant/Award Number: 81603152; National Science Foundation, Grant/Award Numbers: AF1645512, CCF1943008, CMMI1825941, DBI1759277, DBI1759934, DBI1917263, DBI20036350, IIS1763246, MCB1925643; NWO, Grant/Award Number: TOP-PUNT 718.015.001; Wellcome Trust, Grant/Award Number: FC001003
Published: 2021
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2. Nucleation of protein mesocrystals via oriented attachment

Author: Nani Van Gerven, Rick R. M. Joosten, Wai Li Ling, Alexander E. S. Van Driessche, Nico A. J. M. Sommerdijk, Mike Sleutel, Maria Bacia, Institut des Sciences de la Terre (ISTerre), Institut national des sciences de l'Univers (INSU - CNRS)-Institut de recherche pour le développement [IRD] : UR219-Université Savoie Mont Blanc (USMB [Université de Savoie] [Université de Chambéry])-Centre National de la Recherche Scientifique (CNRS)-Université Gustave Eiffel-Université Grenoble Alpes (UGA), VIB-VUB Center for Structural Biology [Bruxelles], VIB [Belgium], Department of Chemical Engineering and Chemistry [Eindhoven], Eindhoven University of Technology [Eindhoven] (TU/e), Institut de biologie structurale (IBS - UMR 5075), Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche Interdisciplinaire de Grenoble (IRIG), Direction de Recherche Fondamentale (CEA) (DRF (CEA)), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Direction de Recherche Fondamentale (CEA) (DRF (CEA)), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Grenoble Alpes (UGA), Department of Biochemistry, Department of Molecular Biology, Faculty of Science, Radboud University, Radboud Institute for Molecular Life Sciences (RIMLS), 6525GA Nijmegen, the Netherlands, Department of Molecular Biology, Radboud Institute for Molecular Life Sciences (RIMLS), Oncode Institute, Radboud University, Nijmegen, the Netherland, Structural Biology Brussels (SBB), Vrije Universiteit Brussel (VUB), ANR-10-INBS-0005,FRISBI,Infrastructure Française pour la Biologie Structurale Intégrée(2010), ANR-17-EURE-0003,CBH-EUR-GS,CBH-EUR-GS(2017), Centre National de la Recherche Scientifique (CNRS)-PRES Université de Grenoble-Université Joseph Fourier - Grenoble 1 (UJF)-Institut Français des Sciences et Technologies des Transports, de l'Aménagement et des Réseaux (IFSTTAR)-Institut national des sciences de l'Univers (INSU - CNRS)-Institut de recherche pour le développement [IRD] : UR219-Université Savoie Mont Blanc (USMB [Université de Savoie] [Université de Chambéry]), Institut national des sciences de l'Univers (INSU - CNRS)-Institut de recherche pour le développement [IRD] : UR219-Université Grenoble Alpes (UGA)-Université Gustave Eiffel-Centre National de la Recherche Scientifique (CNRS)-Université Savoie Mont Blanc (USMB [Université de Savoie] [Université de Chambéry]), Centre National de la Recherche Scientifique (CNRS)-Université Grenoble Alpes (UGA)-Institut de Recherche Interdisciplinaire de Grenoble (IRIG), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA), Institute for Complex Molecular Systems, Materials and Interface Chemistry, Physical Chemistry, Department of Bio-engineering Sciences, and Structural Biology Brussels
Subjects: 0301 basic medicine, Models, Molecular, Chemistry(all), Nucleation, General Physics and Astronomy, Nanoparticle, Crystallography, X-Ray, 01 natural sciences, law.invention, MESH: Recombinant Proteins, law, Crystallization, Aldose-Ketose Isomerases, MESH: Crystallization, Multidisciplinary, MESH: Kinetics, [SDV.BBM.BS]Life Sciences [q-bio]/Biochemistry, Molecular Biology/Structural Biology [q-bio.BM], Self-assembly, Nanocrystalline material, Recombinant Proteins, MESH: Cryoelectron Microscopy, Protein crystallization, MESH: Models, Molecular, Materials science, Science, Nanotechnology, Physics and Astronomy(all), 010402 general chemistry, Molecular resolution, General Biochemistry, Genetics and Molecular Biology, Article, 03 medical and health sciences, MESH: Nanostructures, Point Mutation, [CHIM]Chemical Sciences, MESH: Particle Size, Particle Size, MESH: Aldose-Ketose Isomerases, MESH: Point Mutation, Biochemistry, Genetics and Molecular Biology(all), Cryoelectron Microscopy, Proteins, General Chemistry, MESH: Crystallography, X-Ray, 0104 chemical sciences, Nanostructures, Kinetics, 030104 developmental biology, Phase transitions and critical phenomena, Nanocrystal, [SDU]Sciences of the Universe [physics], Nanomedicine Radboud Institute for Molecular Life Sciences [Radboudumc 19]
Abstract: Self-assembly of proteins holds great promise for the bottom-up design and production of synthetic biomaterials. In conventional approaches, designer proteins are pre-programmed with specific recognition sites that drive the association process towards a desired organized state. Although proven effective, this approach poses restrictions on the complexity and material properties of the end-state. An alternative, hierarchical approach that has found wide adoption for inorganic systems, relies on the production of crystalline nanoparticles that become the building blocks of a next-level assembly process driven by oriented attachment (OA). As it stands, OA has not yet been observed for protein systems. Here we employ cryo-transmission electron microscopy (cryoEM) in the high nucleation rate limit of protein crystals and map the self-assembly route at molecular resolution. We observe the initial formation of facetted nanocrystals that merge lattices by means of OA alignment well before contact is made, satisfying non-trivial symmetry rules in the process. As these nanocrystalline assemblies grow larger we witness imperfect docking events leading to oriented aggregation into mesocrystalline assemblies. These observations highlight the underappreciated role of the interaction between crystalline nuclei, and the impact of OA on the crystallization process of proteins., Past studies on protein nucleation have focused on the routes that molecules follow towards a crystalline cluster, while possible interactions that may occur between nuclei have not been investigated. Here, the authors show that in the high supersaturation limit such interactions dominate the nucleation process in the form of inter-nucleus docking driving by oriented attachment.
Published: 2021
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3. Megabodies expand the nanobody toolkit for protein structure determination by single-particle cryo-EM

Author: Alexandre Wohlkonig, Hugues Nury, Baptiste Fischer, Tomasz Uchański, Eleftherios Zarkadas, Philip N. Ward, Thomas Zögg, Wim F. Vranken, Uriel López-Sánchez, Han Remaut, Jan Steyaert, S. Masiulis, A. Radu Aricescu, Valentina Kalichuk, Els Pardon, Andrija Sente, Miriam Weckener, James H. Naismith, Department of Bio-engineering Sciences, Structural Biology Brussels, Basic (bio-) Medical Sciences, Chemistry, Informatics and Applied Informatics, VIB-VUB Center for Structural Biology [Bruxelles], and VIB [Belgium]
Subjects: Scaffold protein, Models, Molecular, Materials science, Cryo-electron microscopy, Protein Conformation, [SDV]Life Sciences [q-bio], Immunoglobulin domain, Yeast display, Biochemistry, Article, 03 medical and health sciences, Protein structure, Humans, Molecular Biology, ComputingMilieux_MISCELLANEOUS, 030304 developmental biology, 0303 health sciences, Molecular Structure, Resolution (electron density), Cryoelectron Microscopy, Cell Biology, Single-Domain Antibodies, Receptors, GABA-A, Lipids, Single Molecule Imaging, Structural biology, Membrane protein, Multiprotein Complexes, Biophysics, Single-Cell Analysis, Biotechnology
Abstract: Nanobodies are popular and versatile tools for structural biology. They have a compact single immunoglobulin domain organization, bind target proteins with high affinities while reducing their conformational heterogeneity and stabilize multi-protein complexes. Here we demonstrate that engineered nanobodies can also help overcome two major obstacles that limit the resolution of single-particle cryo-electron microscopy reconstructions: particle size and preferential orientation at the water-air interfaces. We have developed and characterized constructs, termed megabodies, by grafting nanobodies onto selected protein scaffolds to increase their molecular weight while retaining the full antigen-binding specificity and affinity. We show that the megabody design principles are applicable to different scaffold proteins and recognition domains of compatible geometries and are amenable for efficient selection from yeast display libraries. Moreover, we demonstrate that megabodies can be used to obtain three-dimensional reconstructions for membrane proteins that suffer from severe preferential orientation or are otherwise too small to allow accurate particle alignment.
Published: 2021
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4. Chemical shift assignments of the partially deuterated Fyn SH2–SH3 domain

Author: Peter Tompa, Karine Loth, Fabien Kieken, Nico A. J. van Nuland, Tom Lenaerts, Informatics and Applied Informatics, Structural Biology Brussels, Department of Bio-engineering Sciences, Structural Biology Brussels (SBB), Vrije Universiteit Brussel (VUB), VIB-VUB Center for Structural Biology [Bruxelles], VIB [Belgium], Centre de biophysique moléculaire (CBM), Université d'Orléans (UO)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)-Institut de Chimie du CNRS (INC), AI-lab, Vakgroep Computerwetenschappen, Université Libre de Bruxelles, Département d'informatique (MLG), Interuniversity Institute of Bioinformatics in Brussels (IB2), Université libre de Bruxelles (ULB)-Vrije Universiteit Brussel (VUB), Vrije Universiteit [Brussels] (VUB), Université d'Orléans (UO)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS), and Université Libre de Bruxelles - Institut de Bioinformatique de Bruxelles
Subjects: 0301 basic medicine, animal structures, Chemistry, Stereochemistry, Kinase, [SDV]Life Sciences [q-bio], Phosphatase, SH3–SH2, Biochemistry, NMR, SH3 domain, Homology (biology), Src family, 03 medical and health sciences, Fyn kinase, Tandem domains, 030104 developmental biology, FYN, Deuterium, Structural Biology, Tyrosine kinase, Proto-oncogene tyrosine-protein kinase Src
Abstract: Src Homology 2 and 3 (SH2 and SH3) are two key protein interaction modules involved in regulating the activity of many proteins such as tyrosine kinases and phosphatases by respective recognition of phosphotyrosine and proline-rich regions. In the Src family kinases, the inactive state of the protein is the direct result of the interaction of the SH2 and the SH3 domain with intra-molecular regions, leading to a closed structure incompetent with substrate modification. Here, we report the 1H, 15N and 13C backbone- and side-chain chemical shift assignments of the partially deuterated Fyn SH3-SH2 domain and structural differences between tandem and single domains. The BMRB accession number is 27165.
Published: 2017
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5. Reversion of antibiotic resistance in Mycobacterium tuberculosis by spiroisoxazoline SMARt-420

Author: Alexandre Wohlkonig, David Hot, Sebastien Gagneux, Marc Gitzinger, Julia Feldmann, Mireia Coscolla, Marion Flipo, Nicolas Willand, Martin Moune, Kamel Djaout, Mehdi Kiass, Priscille Brodin, Vincent Delorme, Vanessa Mathys, Rosangela Frita, Karine Soetaert, Benoit Deprez, Ludovic Huot, Nicolas Blondiaux, René Wintjens, Christian Kemmer, Alain R. Baulard, Vincent Trebosc, Camille Locht, Matthieu Desroses, Rudy Antoine, Willand, Nicolas, Appel à projets générique - Reprogrammation de la bioactivation des thioamides comme alternative antituberculeuse - - Tea-4-Two2014 - ANR-14-CE14-0027 - Appel à projets générique - VALID, Equipements d'excellence - Plateau de microscopie de criblage à haut débit et d'analyse à très haute résolution - - Imaginex BioMed2010 - ANR-10-EQPX-0004 - EQPX - VALID, EGID Diabetes Pole - - EGID2010 - ANR-10-LABX-0046 - LABX - VALID, Plate forme Lilloise de séquençage du génome humain pour une médecine personnalisée - - LIGAN PM2010 - ANR-10-EQPX-0007 - EQPX - VALID, A Chemical Genomics Approach of Intracellular Mycobacterium tuberculosis Towards Defining Specific Host Pathogen Interactions - INTRACELLTB - - EC:FP7:ERC2010-12-01 - 2015-11-30 - 260901 - VALID, Compensatory Evolution and Epistasis in Multidrug-resistant Mycobacterium tuberculosis - EVODRTB - - EC:FP7:ERC2013-04-01 - 2018-03-31 - 309540 - VALID, More Medicines for Tuberculosis - MM4TB - - EC:FP7:HEALTH2011-02-01 - 2016-01-31 - 260872 - VALID, Centre d’Infection et d’Immunité de Lille - INSERM U 1019 - UMR 9017 - UMR 8204 (CIIL), Institut Pasteur de Lille, Réseau International des Instituts Pasteur (RIIP)-Réseau International des Instituts Pasteur (RIIP)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Université de Lille-Centre Hospitalier Régional Universitaire [Lille] (CHRU Lille)-Centre National de la Recherche Scientifique (CNRS), Médicaments et molécules pour agir sur les Systèmes Vivants - U 1177 (M2SV), Réseau International des Instituts Pasteur (RIIP)-Réseau International des Instituts Pasteur (RIIP)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Université de Lille, Karolinska Institutet [Stockholm], Institut Scientifique de Santé Publique [Belgique] - Scientific Institute of Public Health [Belgium] (WIV-ISP), Réseau International des Instituts Pasteur (RIIP), Tuberculosis Lab [Korea], Institut Pasteur Korea - Institut Pasteur de Corée, Réseau International des Instituts Pasteur (RIIP)-Réseau International des Instituts Pasteur (RIIP), Bioversys AG [Basel], University of Basel (Unibas), Université libre de Bruxelles (ULB), VIB-VUB Center for Structural Biology [Bruxelles], VIB [Belgium], Vrije Universiteit Brussel [Bruxelles] (VUB), Swiss Tropical and Public Health Institute [Basel], This work was supported by l’Agence Nationale de la Recherche (ANR), France (Tea-4-Two, ANR-14-CE14-0027-01) (ANR-10-EQPX-04-01), by EU grants ERC-STG INTRACELLTB no 260901, the Feder (12001407 (D-AL), PRIM (NewBio4Tb), European Research Council (grant 309540-EVODRTB), SystemsX.ch, Institut National de la Santé et de la Recherche Médicale, Université de Lille, Institut Pasteur de Lille, Centre National de la Recherche Scientifique, the Région Hauts-de-France (convention no. 12000080), and Société d’Accélération du Transfert de Technologie Nord. R.W. is Research Associate at the National Fund for Scientific Research (FNRS-FRS) (Belgium). M.M. was supported by PRIM (NewBio4Tb), V.D. was supported by EU grant 260872, and V.T. was suppported by the Marie Curie Initial Training Network (ITN-2013-607694-Translocation). The authors also thank the Unité Mixte de Recherche UMR 8199, Lille Integrated Genomics Network for Advanced Personalized Medicine (LIGAN-PM) Genomics platform (Lille, France), which belongs to the Federation de Recherche 3508 Labex EGID (European Genomics Institute for Diabetes, ANR-10-LABX-46) and was supported by the Agence Nationale de la Recherche (ANR) Equipex 2010 session (ANR-10-EQPX-07-01, LIGAN-PM). The LIGAN-PM Genomics platform is supported by the Fonds Européen de Développement Régional and the Region Hauts-de-France., ANR-14-CE14-0027,Tea-4-Two,Reprogrammation de la bioactivation des thioamides comme alternative antituberculeuse(2014), ANR-10-EQPX-0004,Imaginex BioMed,Plateau de microscopie de criblage à haut débit et d'analyse à très haute résolution(2010), ANR-10-LABX-0046,EGID,EGID Diabetes Pole(2010), ANR-10-EQPX-0007,LIGAN PM,Plate forme Lilloise de séquençage du génome humain pour une médecine personnalisée(2010), European Project: 260901,EC:FP7:ERC,ERC-2010-StG_20091118,INTRACELLTB(2010), European Project: 309540,EC:FP7:ERC,ERC-2012-StG_20111109,EVODRTB(2013), European Project: 260872,EC:FP7:HEALTH,FP7-HEALTH-2010-single-stage,MM4TB(2011), and Centre National de la Recherche Scientifique (CNRS)-Centre Hospitalier Régional Universitaire [Lille] (CHRU Lille)-Université de Lille-Institut National de la Santé et de la Recherche Médicale (INSERM)-Institut Pasteur de Lille
Subjects: 0301 basic medicine, Tuberculosis, medicine.drug_class, [CHIM.THER] Chemical Sciences/Medicinal Chemistry, 030106 microbiology, Antibiotics, Reversion, [CHIM.THER]Chemical Sciences/Medicinal Chemistry, Microbiology, Mycobacterium tuberculosis, 03 medical and health sciences, Antibiotic resistance, [CHIM] Chemical Sciences, medicine, [CHIM]Chemical Sciences, chemistry.chemical_classification, Multidisciplinary, biology, medicine.disease, biology.organism_classification, 3. Good health, 030104 developmental biology, Enzyme, chemistry, Ethionamide, Bacteria, medicine.drug
Abstract: Countering TB prodrug resistance The arsenal of antibiotics for treating tuberculosis (TB) contains many prodrugs, such as ethionamide, which need activation by normal metabolism to release their toxic effects. Ethionamide is potentiated by small molecules. Blondiaux et al. screened for more potent analogs and identified a lead compound called SMARt-420. This small molecule inactivates a TetR-like repressor, EthR2, and boosts ethionamide activation. SMARt-420 successfully promoted clearance of multidrug-resistant strains of Mycobacterium tuberculosis from the lungs of mice. Science , this issue p. 1206
Published: 2017
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6. A community proposal to integrate structural bioinformatics activities in ELIXIR (3D-Bioinfo Community)

Author: Orengo, Christine, Velankar, Sameer, Wodak, Shoshana, Zoete, Vincent, Bonvin, Alexandre M.J.J., Elofsson, Arne, Feenstra, K. Anton, Gerloff, Dietland L., Hamelryck, Thomas, Hancock, John M., Helmer-Citterich, Manuela, Hospital, Adam, Orozco, Modesto, Perrakis, Anastassis, Rarey, Matthias, Soares, Claudio, Sussman, Joel L., Thornton, Janet M., Tuffery, Pierre, Tusnady, Gabor, Wierenga, Rikkert, Salminen, Tiina, Schneider, Bohdan, Sub NMR Spectroscopy, NMR Spectroscopy, University College of London [London] (UCL), European Bioinformatics Institute [Hinxton] (EMBL-EBI), EMBL Heidelberg, VIB-VUB Center for Structural Biology [Bruxelles], VIB [Belgium], Swiss Institute of Bioinformatics [Lausanne] (SIB), Université de Lausanne (UNIL), Utrecht University [Utrecht], Science for Life Laboratory [Solna], Royal Institute of Technology [Stockholm] (KTH ), Vrije Universiteit Amsterdam [Amsterdam] (VU), IBIVU, Department of Computer Science, Faculty of Sciences (IBIVU,), University of Amsterdam [Amsterdam] (UvA), Luxembourg Centre For Systems Biomedicine (LCSB), University of Luxembourg [Luxembourg], University of Copenhagen = Københavns Universitet (KU), Università degli Studi di Roma Tor Vergata [Roma], Barcelona Institute of Science and Technology (BIST), Netherlands Cancer Institute (NKI), Antoni van Leeuwenhoek Hospital, Universität Hamburg (UHH), Instituto de Tecnologia Química e Biológica António Xavier (ITQB), Universidade Nova de Lisboa = NOVA University Lisbon (NOVA), Weizmann Institute of Science [Rehovot, Israël], Ressource Parisienne en Bioinformatique Structurale, Institute of Enzymology [Budapest], Research Centre for Natural Sciences, Hungarian Academy of Sciences (MTA)-Hungarian Academy of Sciences (MTA), University of Oulu, Åbo Akademi University [Turku], Institute of Biotechnology of the Czech Academy of Sciences (IBT / CAS), Czech Academy of Sciences [Prague] (CAS), Bioinformatics, AIMMS, Integrative Bioinformatics, Sub NMR Spectroscopy, and NMR Spectroscopy
Subjects: 0301 basic medicine, Computer science, [SDV]Life Sciences [q-bio], Genomics, Biological Science Disciplines, ELIXIR, Instruct-ERIC, biomolecular structure, nucleic acids structure, protein structure, structural bioinformatics, General Biochemistry, Genetics and Molecular Biology, Field (computer science), 03 medical and health sciences, Structural bioinformatics, Data sequences, SDG 17 - Partnerships for the Goals, Humans, Settore BIO/10, General Pharmacology, Toxicology and Pharmaceutics, computer.programming_language, 030102 biochemistry & molecular biology, General Immunology and Microbiology, Computational Biology, Proteins, General Medicine, Articles, Opinion Article, Data science, Outreach, Europe, 030104 developmental biology, Elixir (programming language), Benchmark data, computer
Abstract: Structural bioinformatics provides the scientific methods and tools to analyse, archive, validate, and present the biomolecular structure data generated by the structural biology community. It also provides an important link with the genomics community, as structural bioinformaticians also use the extensive sequence data to predict protein structures and their functional sites. A very broad and active community of structural bioinformaticians exists across Europe, and 3D-Bioinfo will establish formal platforms to address their needs and better integrate their activities and initiatives. Our mission will be to strengthen the ties with the structural biology research communities in Europe covering life sciences, as well as chemistry and physics and to bridge the gap between these researchers in order to fully realize the potential of structural bioinformatics. Our Community will also undertake dedicated educational, training and outreach efforts to facilitate this, bringing new insights and thus facilitating the development of much needed innovative applications e.g. for human health, drug and protein design. Our combined efforts will be of critical importance to keep the European research efforts competitive in this respect. Here we highlight the major European contributions to the field of structural bioinformatics, the most pressing challenges remaining and how Europe-wide interactions, enabled by ELIXIR and its platforms, will help in addressing these challenges and in coordinating structural bioinformatics resources across Europe. In particular, we present recent activities and future plans to consolidate an ELIXIR 3D-Bioinfo Community in structural bioinformatics and propose means to develop better links across the community. These include building new consortia, organising workshops to establish data standards and seeking community agreement on benchmark data sets and strategies. We also highlight existing and planned collaborations with other ELIXIR Communities and other European infrastructures, such as the structural biology community supported by Instruct-ERIC, with whom we have synergies and overlapping common interests.
Published: 2020
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7. Hepatitis C virus sequence divergence preserves p7 viroporin structural and dynamic features

Author: Latifah Almanea, Juan H. Bolivar, Nicole Zitzmann, François Dehez, Nicole Holzmann, Chris Chipot, Jolyon K. Claridge, Jason R. Schnell, Benjamin P. Oestringer, Oxford Glycobiology Institute, University of Oxford [Oxford], Department of Biochemistry [Oxford], Immunocore Limited, Structural Biology Brussels (SBB), Vrije Universiteit Brussel (VUB), Structural Biology Research Center, VIB, 1050 Brussels, Belgium, VIB-VUB Center for Structural Biology [Bruxelles], VIB [Belgium]-VIB [Belgium], Laboratoire International Associé (LIA), University of Illinois at Urbana-Champaign [Urbana], University of Illinois System-University of Illinois System-Centre National de la Recherche Scientifique (CNRS), Department of Physics [Illinois at Urbana-Champaign, USA], University of Illinois System-University of Illinois System, Laboratoire de Physique et Chimie Théoriques (LPCT), and Institut de Chimie du CNRS (INC)-Université de Lorraine (UL)-Centre National de la Recherche Scientifique (CNRS)
Subjects: Genotype, Hepatitis C virus, lcsh:Medicine, Hepacivirus, Viral Nonstructural Proteins, medicine.disease_cause, Endoplasmic Reticulum, Ion Channels, Protein Structure, Secondary, Article, Viroporin Proteins, Viroporin, 03 medical and health sciences, Viral Proteins, medicine, Humans, Secretion, [SDV.BBM]Life Sciences [q-bio]/Biochemistry, Molecular Biology, Amino Acid Sequence, lcsh:Science, Protein secondary structure, Ion channel, ComputingMilieux_MISCELLANEOUS, 030304 developmental biology, Genetics, 0303 health sciences, Multidisciplinary, Chemistry, Endoplasmic reticulum, lcsh:R, 030302 biochemistry & molecular biology, Hepatitis C, 3. Good health, [SDV.BBM.BP]Life Sciences [q-bio]/Biochemistry, Molecular Biology/Biophysics, Transmembrane domain, lcsh:Q, Molecular modelling, Solution-state NMR
Abstract: The hepatitis C virus (HCV) viroporin p7 oligomerizes to form ion channels, which are required for the assembly and secretion of infectious viruses. The 63-amino acid p7 monomer has two putative transmembrane domains connected by a cytosolic loop, and has both N- and C- termini exposed to the endoplasmic reticulum (ER) lumen. NMR studies have indicated differences between p7 structures of distantly related HCV genotypes. A critical question is whether these differences arise from the high sequence variation between the different isolates and if so, how the divergent structures can support similar biological functions. Here, we present a side-by-side characterization of p7 derived from genotype 1b (isolate J4) in the detergent 6-cyclohexyl-1-hexylphosphocholine (Cyclofos-6) and p7 derived from genotype 5a (isolate EUH1480) in n-dodecylphosphocholine (DPC). The 5a isolate p7 in conditions previously associated with a disputed oligomeric form exhibits secondary structure, dynamics, and solvent accessibility broadly like those of the monomeric 1b isolate p7. The largest differences occur at the start of the second transmembrane domain, which is destabilized in the 5a isolate. The results show a broad consensus among the p7 variants that have been studied under a range of different conditions and indicate that distantly related HCVs preserve key features of structure and dynamics.
Published: 2019
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8. Allostery in Its Many Disguises: From Theory to Applications

Author: Yassmine Chebaro, Annick Dejaegere, Ruth Nussinov, Rebecca C. Wade, Simone Orioli, Jocelyne Vreede, Riccardo Ravasio, Paraskevi Gkeka, Jing Li, Gerhard Stock, Chung-Jung Tsai, Ivet Bahar, Emanuele Paci, Pietro Faccioli, Joanna Panecka-Hofman, John Karanicolas, Peter G. Bolhuis, Jean-Pierre Changeux, Shoshana J. Wodak, Masha Y. Niv, Antonella Di Pizio, Giulia Palermo, Roland H. Stote, Tom McLeish, Matthieu Wyart, Carolina Brito, Peter Hamm, J. Andrew McCammon, Vincent J. Hilser, Amnon Horovitz, Jerome Eberhardt, Ivan Rivalta, Nikolay V. Dokholyan, Igor N. Berezovsky, Marco Cecchini, Le Yan, Hyunbum Jang, Dima Kozakov, Dzmitry Padhorny, VIB-VUB Center for Structural Biology [Bruxelles], VIB [Belgium], Institut de Génétique et de Biologie Moléculaire et Cellulaire (IGBMC), Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)-Université de Strasbourg (UNISTRA), Institut de Chimie de Strasbourg, Université de Strasbourg (UNISTRA)-Centre National de la Recherche Scientifique (CNRS), Institut Pasteur [Paris], Collège de France (CdF), Physics Department and INFN, University of Trento [Trento], Universidade Federal do Rio Grande do Sul [Porto Alegre] (UFRGS), Ecole Polytechnique Fédérale de Lausanne (EPFL), Laboratoire de Chimie - UMR5182 (LC), École normale supérieure - Lyon (ENS Lyon)-Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Centre National de la Recherche Scientifique (CNRS), Molecular and Cellular Modeling Group, Heidelberg Institute for Theoretical Studies (HITS ), Department of Biomedical Engineering [Boston], Boston University [Boston] (BU), University of Leeds, University of North Carolina at Chapel Hill, University of North Carolina [Chapel Hill] (UNC), University of North Carolina System (UNC)-University of North Carolina System (UNC), National University of Singapore (NUS), Weizmann Institute of Science [Rehovot, Israël], Johns Hopkins University (JHU), University of Pittsburgh (PITT), Pennsylvania Commonwealth System of Higher Education (PCSHE), Université de Strasbourg (UNISTRA)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS), Centre National de la Recherche Scientifique (CNRS)-Université Louis Pasteur - Strasbourg I-Institut de Chimie du CNRS (INC), Collège de France (CdF (institution)), Institute of Condensed Matter Physics [Lausanne], University of California [Santa Barbara] (UCSB), University of California, Centre National de la Recherche Scientifique (CNRS)-Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-École normale supérieure - Lyon (ENS Lyon)-Institut de Chimie du CNRS (INC), Cancer and Inflammation Program, Leidos Biomedical Research Inc., Frederick National Laboratory, Frederick National Laboratory for Cancer Research (FNLCR), Stony Brook University [SUNY] (SBU), State University of New York (SUNY), University of York [York, UK], European Union's Horizon 2020 Research and Innovation Program under grant agreement no. 720270 (HBP SGA1)NIH grants R01GM114015, R01GM064803, and R01GM123247, grants P41GM103712 and P30DA035778Marie Curie Reintegration Grant (FP7-PEOPLE-2009-RG, no. 256533), European Project: 720270,H2020 Pilier Excellent Science,H2020-Adhoc-2014-20,HBP SGA1(2016), European Project: 256533,EC:FP7:PEOPLE,FP7-PEOPLE-2009-RG,COMPUT DRUG DESIGN(2010), Simulation of Biomolecular Systems (HIMS, FNWI), Wodak, Shoshana J, Paci, Emanuele, Dokholyan, Nikolay V, Berezovsky, Igor N, Horovitz, Amnon, Li, Jing, Hilser, Vincent J, Bahar, Ivet, Karanicolas, John, Stock, Gerhard, Hamm, Peter, Stote, Roland H, Eberhardt, Jerome, Chebaro, Yassmine, Dejaegere, Annick, Cecchini, Marco, Changeux, Jean-Pierre, Bolhuis, Peter G, Vreede, Jocelyne, Faccioli, Pietro, Orioli, Simone, Ravasio, Riccardo, Yan, Le, Brito, Carolina, Wyart, Matthieu, Gkeka, Paraskevi, Rivalta, Ivan, Palermo, Giulia, McCammon, J Andrew, Panecka-Hofman, Joanna, Wade, Rebecca C, Di Pizio, Antonella, Niv, Masha Y, Nussinov, Ruth, Tsai, Chung-Jung, Jang, Hyunbum, Padhorny, Dzmitry, Kozakov, Dima, McLeish, Tom, Wodak, S, Paci, E, Dokholyan, N, Berezovsky, I, Horovitz, A, Li, J, Hilser, V, Bahar, I, Karanicolas, J, Stock, G, Hamm, P, Stote, R, Eberhardt, J, Chebaro, Y, Dejaegere, A, Cecchini, M, Changeux, J, Bolhuis, P, Vreede, J, Faccioli, P, Orioli, S, Ravasio, R, Yan, L, Brito, C, Wyart, M, Gkeka, P, Rivalta, I, Palermo, G, Mccammon, J, Panecka-Hofman, J, Wade, R, Di Pizio, A, Niv, M, Nussinov, R, Tsai, C, Jang, H, Padhorny, D, Kozakov, D, Mcleish, T, and Centre National de la Recherche Scientifique (CNRS)-Université de Strasbourg (UNISTRA)
Subjects: Transcription, Genetic, Computer science, nuclear receptors, Biosensing Techniques, allosteric switche, Structural Biology, chemical rescue, Allostery, ComputingMilieux_MISCELLANEOUS, Cognitive science, mechanisms, 0303 health sciences, Protein function, ligand-binding, elastic network model, molecular dynamic, dynamic allostery, 030302 biochemistry & molecular biology, regulation, protein function, Biological Sciences, [SDV.BIBS]Life Sciences [q-bio]/Quantitative Methods [q-bio.QM], [CHIM.THEO]Chemical Sciences/Theoretical and/or physical chemistry, modulation, Generic Health Relevance, elastic network models, Thermodynamics, Transcription, Allosteric Site, Metabolic Networks and Pathways, signal transduction, Signal Transduction, 1.1 Normal biological development and functioning, Biophysics, allosteric drug, Molecular Dynamics Simulation, Article, 03 medical and health sciences, protein conformational changes, Genetic, Allosteric Regulation, Underpinning research, conformational-changes, Information and Computing Sciences, Animals, Humans, Molecular Biology, Elastic network models, allosteric material, 030304 developmental biology, pathway, energy landscape, Proteins, allosteric switches, molecular dynamics, protein conformational change, allosteric drugs, Conceptual framework, Gene Expression Regulation, Drug Design, network, Chemical Sciences, protein
Abstract: Allosteric regulation plays an important role in many biological processes, such as signal transduction, transcriptional regulation, and metabolism. Allostery is rooted in the fundamental physical properties of macromo-lecular systems, but its underlying mechanisms are still poorly understood. A collection of contributions to a recent interdisciplinary CECAM (Center Européen de Calcul Atomique et Moléculaire) workshop is used here to provide an overview of the progress and remaining limitations in the understanding of the mechanistic foundations of allostery gained from computational and experimental analyses of real protein systems and model systems. The main conceptual frameworks instrumental in driving the field are discussed. We illustrate the role of these frameworks in illuminating molecular mechanisms and explaining cellular processes, and describe some of their promising practical applications in engineering molecular sensors and informing drug design efforts.
Published: 2019
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9. A comprehensive analysis of the protein-ligand interactions in crystal structures of Mycobacterium tuberculosis EthR

Author: Baptiste Villemagne, Hélène Perée, Alain R. Baulard, René Wintjens, Alexandre Wohlkonig, Sameh H. Soror, Hugues Prevet, Benoit Deprez, Martin Moune, Franck Meyer, Marion Flipo, Abdalkarim Tanina, Nicolas Willand, Faculté de Pharmacie [Bruxelles] (ULB), Université libre de Bruxelles (ULB), VIB-VUB Center for Structural Biology [Bruxelles], VIB [Belgium], Helwan University [Caire], Médicaments et molécules pour agir sur les Systèmes Vivants - U 1177 (M2SV), Institut Pasteur de Lille, Réseau International des Instituts Pasteur (RIIP)-Réseau International des Instituts Pasteur (RIIP)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Université de Lille, Centre d’Infection et d’Immunité de Lille - INSERM U 1019 - UMR 9017 - UMR 8204 (CIIL), Réseau International des Instituts Pasteur (RIIP)-Réseau International des Instituts Pasteur (RIIP)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Université de Lille-Centre Hospitalier Régional Universitaire [Lille] (CHRU Lille)-Centre National de la Recherche Scientifique (CNRS), We are grateful to the institutions that support our laboratory (Inserm), University of Lille, Institut Pasteur de Lille, CNRS, EU, Région Hauts de France and Pôle de Recherche Interdisciplinaire du Médicament (PRIM). AT thanks to the association ‘les Amis de l'Institut Pasteur à Bruxelles’ for the PhD fellowship. SS thanks the STDF for the support of HSBR (5590). RW is Research Associate at the National Fund for Scientific Research FNRS-FRS (Belgium)., ANR-14-CE14-0027,Tea-4-Two,Reprogrammation de la bioactivation des thioamides comme alternative antituberculeuse(2014), Centre National de la Recherche Scientifique (CNRS)-Centre Hospitalier Régional Universitaire [Lille] (CHRU Lille)-Université de Lille-Institut National de la Santé et de la Recherche Médicale (INSERM)-Institut Pasteur de Lille, Réseau International des Instituts Pasteur (RIIP)-Réseau International des Instituts Pasteur (RIIP), Willand, Nicolas, Appel à projets générique - Reprogrammation de la bioactivation des thioamides comme alternative antituberculeuse - - Tea-4-Two2014 - ANR-14-CE14-0027 - Appel à projets générique - VALID, Department of Bio-engineering Sciences, and Structural Biology Brussels
Subjects: Protein Folding, Stereochemistry, Protein Conformation, Biochimie, Chimie analytique, Biophysics, Repressor, Biophysique, Ligands, 01 natural sciences, Biochemistry, DNA-binding protein, Drug design, Analytical Chemistry, Mycobacterium tuberculosis, 03 medical and health sciences, chemistry.chemical_compound, Binding interaction, [CHIM.CRIS]Chemical Sciences/Cristallography, Molecule, Tuberculosis, TetR, [CHIM.CRIS] Chemical Sciences/Cristallography, Ethionamide, Molecular Biology, 030304 developmental biology, X-ray crystallography, 0303 health sciences, biology, 010405 organic chemistry, Chemistry, Hydrogen bond, Biologie moléculaire, biology.organism_classification, Small molecule, 0104 chemical sciences, 3. Good health, Repressor Proteins, Protein Multimerization, Protein ligand
Abstract: The Mycobacterium tuberculosis EthR is a member of the TetR family of repressors, controlling the expression of EthA, a mono-oxygenase responsible for the bioactivation of the prodrug ethionamide. This protein was established as a promising therapeutic target against tuberculosis, allowing, when inhibited by a drug-like molecule, to boost the action of ethionamide. Dozens of EthR crystal structures have been solved in complex with ligands. Herein, we disclose EthR structures in complex with 18 different small molecules and then performed in-depth analysis on the complete set of EthR structures that provides insights on EthR-ligand interactions. The 81 molecules solved in complex with EthR show a large diversity of chemical structures that were split up into several chemical clusters. Two of the most striking common points of EthR-ligand interactions are the quasi-omnipresence of a hydrogen bond bridging compounds with Asn179 and the high occurrence of π-π interactions involving Phe110. A systematic analysis of the protein-ligand contacts identified eight hot spot residues that defined the basic structural features governing the binding mode of small molecules to EthR. Implications for the design of new potent inhibitors are discussed., SCOPUS: ar.j, info:eu-repo/semantics/published
Published: 2018
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10. Neutrophils enhance early Trypanosoma brucei infection onset

Author: Marie Malissen, Guy Caljon, Carl De Trez, Fabienne Tacchini-Cottier, Stefan Magez, Jo A. Van Ginderachter, Dorien Mabille, Benoit Stijlemans, Patrick De Baetselier, Massimiliano Mazzone, Jan Van Den Abbeele, Cellular and Molecular Immunology (VIB), Vrije Universiteit Brussel (VUB), Laboratory of Myeloid Cell Immunology, Flanders Interuniversity Institute for Biotechnology (VIB), Vlaams Interuniversitair Instituut voor Biotechnologie, Department of Biochemistry, Université de Lausanne (UNIL)-WHO Collaborating Center for Research and Training in Immunology, Centre d'Immunologie de Marseille - Luminy (CIML), Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)-Aix Marseille Université (AMU), Structural Biology Research Center, VIB, 1050 Brussels, Belgium, VIB-VUB Center for Structural Biology [Bruxelles], VIB [Belgium]-VIB [Belgium], Vrije Universiteit Brussel - Myeloid Cell immunology Laboratory, Laboratory of cellular & Molecular Immunology [Vrije Universiteit Brussel], Cellular and Molecular Immunology, Department of Bio-engineering Sciences, Vriendenkring VUB, Université de Lausanne = University of Lausanne (UNIL)-WHO Collaborating Center for Research and Training in Immunology, and Aix Marseille Université (AMU)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)
Subjects: 0301 basic medicine, Chemokine CXCL5, Chemokine, GLOSSINA-MORSITANS, HOST, Neutrophils, Chemokine CXCL1, Interleukin-1beta, CATTLE, lcsh:Medicine, Parasitemia, Mice, Medicine and Health Sciences, SAND FLIES, lcsh:Science, AFRICAN TRYPANOSOMES, CONGOLENSE, Multidisciplinary, biology, FLIES, Dermis, Interleukin-10, 3. Good health, Multidisciplinary Sciences, CXCL1, Science & Technology - Other Topics, [SDV.IMM]Life Sciences [q-bio]/Immunology, Engineering sciences. Technology, Tsetse Flies, Trypanosoma brucei brucei, TSETSE-FLY, Trypanosoma brucei, Neutropenia, DENDRITIC CELLS, Article, Microbiology, Proinflammatory cytokine, 03 medical and health sciences, Animals, Gene Expression Regulation, Insect Bites and Stings, Insect Vectors, Interleukin-6, Luminescent Measurements, Trypanosomiasis, African, Trypanosomiasis, parasitic diseases, medicine, LOCAL SKIN REACTIONS, Biology, Science & Technology, lcsh:R, African, Biology and Life Sciences, medicine.disease, Leishmania, biology.organism_classification, 030104 developmental biology, SHEEP, general, biology.protein, lcsh:Q, LEISHMANIASIS
Abstract: In this study, Trypanosoma brucei was naturally transmitted to mice through the bites of infected Glossina morsitans tsetse flies. Neutrophils were recruited rapidly to the bite site, whereas monocytes were attracted more gradually. Expression of inflammatory cytokines (il1b, il6), il10 and neutrophil chemokines (cxcl1, cxcl5) was transiently up-regulated at the site of parasite inoculation. Then, a second influx of neutrophils occurred that coincided with the previously described parasite retention and expansion in the ear dermis. Congenital and experimental neutropenia models, combined with bioluminescent imaging, indicate that neutrophils do not significantly contribute to dermal parasite control and elicit higher systemic parasitemia levels during the infection onset. Engulfment of parasites by neutrophils in the skin was rarely observed and was restricted to parasites with reduced motility/viability, whereas live parasites escaped phagocytosis. To our knowledge, this study represents the first description of a trypanosome infection promoting role of early innate immunological reactions following an infective tsetse fly bite. Our data indicate that the trypanosome is not hindered in its early development and benefits from the host innate responses with the neutrophils being important regulators of the early infection, as already demonstrated for the sand fly transmitted Leishmania parasite.
Published: 2018
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11. Rational Design of Nanobody80 Loop Peptidomimetics

Author: Cecilia Betti, Els Pardon, Daniel Sejer Pedersen, May C. Morris, Samuel L. C. Moors, Krisztina Fehér, Jesper Mosolff Mathiesen, Jan Steyaert, Mia Danielsen, Frank De Proft, Cecilia Fabris, Nick Devoogdt, Marion Peyressatre, Vicky Caveliers, Charlotte Martin, Steven Ballet, José C. Martins, Chemistry, WE Academic Unit, Department of Bio-engineering Sciences, Faculty of Sciences and Bioengineering Sciences, Structural Biology Brussels, Translational Imaging Research Alliance, Medical Imaging, Supporting clinical sciences, General Chemistry, Vrije Universiteit Brussel (VUB), University of Copenhagen = Københavns Universitet (KU), Department of Drug Design and Pharmacology [Copenhagen] (ILF), Faculty of Health and Medical Sciences, University of Copenhagen = Københavns Universitet (KU)-University of Copenhagen = Københavns Universitet (KU), VIB-VUB Center for Structural Biology [Bruxelles], VIB [Belgium], Institut des Biomolécules Max Mousseron [Pôle Chimie Balard] (IBMM), Centre National de la Recherche Scientifique (CNRS)-Institut de Chimie du CNRS (INC)-Université de Montpellier (UM)-Ecole Nationale Supérieure de Chimie de Montpellier (ENSCM), Department of Organic and Macromolecular Chemistry, Universiteit Gent = Ghent University [Belgium] (UGENT), NMR and Structure Analysis Unit, In vivo Cellular and Molecular Imaging Laboratory, and Eenheid Algemene Chemie
Subjects: 0301 basic medicine, Protein-protein interactions, Stereochemistry, G protein, Peptidomimetic, receptors, Plasma protein binding, protein–protein interactions, 01 natural sciences, Catalysis, Protein–protein interaction, 03 medical and health sciences, MESH: Receptors, Adrenergic, Beta-2 / metabolism, Protein structure, [SDV.BBM]Life Sciences [q-bio]/Biochemistry, Molecular Biology, Binding site, G protein-coupled receptor, MESH: Optical Imaging, MESH: Peptidomimetics / chemical synthesis, 010405 organic chemistry, Chemistry, Organic Chemistry, Rational design, MESH: Single-Domain Antibodies / chemistry, General Chemistry, nanobodies, 0104 chemical sciences, 030104 developmental biology, MESH: HEK293 Cells, peptidomimetics, protein structures, [SDV.IB]Life Sciences [q-bio]/Bioengineering
Abstract: International audience; G protein-coupled receptors (GPCRs) play an important role in many cellular responses; as such, their mechanism of action is of utmost interest. To gain insight into the active conformation of GPCRs, the X-ray crystal structures of nanobody (Nb)-stabilized β2 -adrenergic receptor (β2 AR) have been reported. Nb80, in particular, is able to bind the intracellular G protein binding site of β2 AR and stabilize the receptor in an active conformation. Within Nb80, the complementarity-determining region 3 (CDR3) is responsible for most of the binding interactions. Hence, we hypothesized that peptidomimetics of the CDR3 loop might be sufficient for binding to the receptor, inhibiting the interaction of β2 AR with intracellular GPCR interacting proteins (e.g., G proteins). Based on previous crystallographic data, a set of peptidomimetics were synthesized that, similar to the Nb80 CDR3 loop, adopt a β-hairpin conformation. Syntheses, conformational analysis, binding and functional in vitro assays, as well as internalization experiments, were performed. We demonstrate that peptidomimetics can structurally mimic the CDR3 loop of a nanobody and its function by inhibiting G protein coupling as measured by partial inhibition of cAMP production.
Published: 2017
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12. Modeling protein-protein and protein-peptide complexes: CAPRI 6th edition

Author: Lensink, Marc, Velankar, Sameer, Wodak, Shoshana J., Unité de Glycobiologie Structurale et Fonctionnelle UMR 8576 (UGSF), Université de Lille-Institut National de la Recherche Agronomique (INRA)-Centre National de la Recherche Scientifique (CNRS), European Bioinformatics Institute [Hinxton] (EMBL-EBI), EMBL Heidelberg, VIB-VUB Center for Structural Biology [Bruxelles], VIB [Belgium], and Université de Lille-Centre National de la Recherche Scientifique (CNRS)
Subjects: Binding Sites, Protein Conformation, protein-peptide interation, Proteins, Computational Biology, Water, Capri, water modeling, protein docking, Nucleosomes, Molecular Docking Simulation, [CHIM.THEO]Chemical Sciences/Theoretical and/or physical chemistry, Benchmarking, Research Design, Multiprotein Complexes, Protein Interaction Mapping, Humans, Blind prediction, Peptides, Algorithms, Software, Protein Binding
Abstract: International audience; We present the sixth report evaluating the performance of methods for predicting the atomic resolution structures of protein complexes offered as targets to the community-wide initiative on the Critical Assessment of Predicted Interactions (CAPRI). The evaluation is based on a total of 20,670 predicted models for 8 protein-peptide complexes, a novel category of targets in CAPRI, and 12 protein-protein targets in CAPRI prediction Rounds held during the years 2013-2016. For two of the protein-protein targets, the focus was on the prediction of side-chain conformation and positions of interfacial water molecules. Seven of the protein-protein targets were particularly challenging owing to their multicomponent nature, to conformational changes at the binding site, or to a combination of both. Encouragingly, the very large multiprotein complex with the nucleosome was correctly predicted, and correct models were submitted for the protein-peptide targets, but not for some of the challenging protein-protein targets. Models of acceptable quality or better were obtained for 14 of the 20 targets, including medium quality models for 13 targets and high quality models for 8 targets, indicating tangible progress of present-day computational methods in modeling protein complexes with increased accuracy. Our evaluation suggests that the progress stems from better integration of different modeling tools with docking procedures, as well as the use of more sophisticated evolutionary information to score models. Nonetheless, adequate modeling of conformational flexibility in interacting proteins remains an important area with a crucial need for improvement. Proteins 2017; 85:359-377. © 2016 Wiley Periodicals, Inc.
Published: 2017
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13. Helicobacter pylori Adapts to Chronic Infection and Gastric Disease via pH-Responsive BabA-Mediated Adherence

Author: Verena Königer, D. Scott Merrell, Roman Andriiovych Moskalenko, Rainer Haas, Thomas Borén, Sara Henriksson, Jafar Mahdavi, Abhijit Chowdhury, Johan Ögren, Anders Hofer, Jay V. Solnick, Dan Danielsson, Sara K. Lindén, Dag Ilver, Konstantinos S. Papadakos, Susanne Vikström, Jörgen Ådén, Jan Holgersson, Gerhard Gröbner, Alexej Schmidt, Jeanna Bugaytsova, Oscar Björnham, Göran O. Bylund, Rolf Sjöström, Stefan Oscarson, Dionyssios N. Sgouras, Lori M. Hansen, Yevgen A Chernov, Anders Esberg, Kristof Moonens, Christopher Aisenbrey, Charles Kelly, Ludmilla A. Morozova-Roche, Jeannette M. Whitmire, Beatriz Martinez-Gonzalez, Asish K. Mukhopadhyay, Angela Eldridge, Nicklas Strömberg, Robert H. Gilman, Andre Dubois, Lars Engstrand, Staffan Schedin, Brett A. Chromy, Justine Younson, Matthew Goldman, Anna Shevtsova, Macarena P. Quintana-Hayashi, Hui Liu, Magnus Unemo, Lena Rakhimova, Anna Åberg, Sebastian Suerbaum, Anna Arnqvist, Pär Gideonsson, Maréne Landström, Douglas E. Berg, Kristoffer Brännström, Anders Olofsson, Melissa Mendez, G. Balakrish Nair, Han Remaut, Umeå University, School of Life Sciences, University of Nottingham, UK (UON), Sahlgrenska Academy at University of Gothenburg [Göteborg], Université libre de Bruxelles (ULB), VIB-VUB Center for Structural Biology [Bruxelles], VIB [Belgium], Sumy State University, Max Von Pettenkofer Institute (MVP), Ludwig-Maximilians-Universität München (LMU), Uniformed Services University of the Health Sciences (USUHS), King‘s College London, Johns Hopkins Bloomberg School of Public Health [Baltimore], Johns Hopkins University (JHU), School of Digestive and Liver Diseases [Kolkata] (SDLD), National Institute of Cholera and Enteric Diseases, Translational Health Science and Technology Institute [Faridabad] (THSTI), Institut Pasteur Hellénique, Réseau International des Instituts Pasteur (RIIP), Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Karolinska Institutet [Stockholm], Örebro University Hospital [Örebro, Sweden], Hannover Medical School [Hannover] (MHH), German Center for Infection Research - partner site Hannover-Braunschweig (DZIF), School of Chemistry and Chemical Biology (UCD), University College Dublin [Dublin] (UCD), University of California [Davis] (UC Davis), University of California, German Center for Infection Research, Partnersite Munich (DZIF), Département d'Informatique [Bruxelles] (ULB), Faculté des Sciences [Bruxelles] (ULB), Université libre de Bruxelles (ULB)-Université libre de Bruxelles (ULB), University of California [San Diego] (UC San Diego), This work was supported by grants from Vetenskapsrådet (VR/M) to T.B. and S.K.L., Cancerfonden to T.B. and A.A., VR/NT to A.A. and S. Schedin, Formas to S.K.L., the J.C. Kempe and Seth M. Kempe Memorial Foundation, the Knut and Alice Wallenberg Foundation (2012.0090) to T.B. and M.L., European Union Seventh Framework Program GastricGlycoExplorer ITN grant number 316929 to T.B. and Y.A.C., Magn. Bergvall’s Foundation to S. Schedin, DFG (SFB 900/A1) to S. Suerbaum, DFG (HA2697/16-1) to R.H., FP6 ANR-06-PATHO-00701 ERA-NET and Actions Concertées Inter-Pasteuriennes (ACIP) (2006) to D.N.S., NIH R01DK063041 to D.E.B., NIH CA082312 to D.S.M., NIH AI070803 and AI081037 to J.V.S., CSIR project, India (No. 37(1640)/14/EMR –II) to A.K.M., and VIB and FWO (grants: G033717N and 12H8416N) to K.M. and H.R., This paper is dedicated to the memory of our friend, collaborator, and co-author Dr. Andre Dubois, a great scientist who contributed importantly both intellectually and materially to this project. We thank S. Michopoulos and G. Mantzaris for H. pylori clinical isolates and Ö. Furberg (NoPolo.se), N. Ulander (softplanbangkok.com), S. Lindström, and M. Borén for the digital movie, tech, art, and figure work, respectively., Vrije Universiteit Brussel, Basic (bio-) Medical Sciences, Structural Biology Brussels, and Department of Bio-engineering Sciences
Subjects: 0301 basic medicine, MESH: Hydrogen-Ion Concentration, Gastric acidity, MESH: Helicobacter Infections/pathology, MESH: Helicobacter pylori/physiology, Disease, adaptation, Bacterial Adhesion, polymorphism, acid responsiveness, MESH: Bacterial Adhesion, Bacterial, Hydrogen-Ion Concentration, gastric acidity, Adhesins, 3. Good health, Cell and molecular biology, medicine.anatomical_structure, Infectious Diseases, MESH: Gastric Mucosa/microbiology, Medical Microbiology, 030106 microbiology, Immunology, Digestive Diseases - (Peptic Ulcer), Biology, blood group antigen-binding adhesion, Microbiology, Helicobacter Infections, diversity, Vaccine Related, 03 medical and health sciences, Virology, ABO blood group system, Biodefense, Gastric mucosa, medicine, MESH: Helicobacter Infections/microbiology, multimerization, Adhesins, Bacterial, subpopulations, Helicobacter pylori, Prevention, gastric cancer, MESH: Adhesins, Bacterial/metabolism, biology.organism_classification, [SDV.MP.BAC]Life Sciences [q-bio]/Microbiology and Parasitology/Bacteriology, MESH: Gastric Mucosa/pathology, Bacterial adhesin, Chronic infection, 030104 developmental biology, Emerging Infectious Diseases, Gastric Mucosa, Parasitology, Digestive Diseases
Abstract: The BabA adhesin mediates high-affinity binding of Helicobacter pylori to the ABO blood group antigen-glycosylated gastric mucosa. Here we show that BabA is acid responsive-binding is reduced at low pH and restored by acid neutralization. Acid responsiveness differs among strains; often correlates with different intragastric regions and evolves during chronic infection and disease progression; and depends on pH sensor sequences in BabA and on pH reversible formation of high-affinity binding BabA multimers. We propose that BabA's extraordinary reversible acid responsiveness enables tight mucosal bacterial adherence while also allowing an effective escape from epithelial cells and mucus that are shed into the acidic bactericidal lumen andthat bio-selection and changes in BabA bindingproperties through mutation and recombination with babA-related genes are selected by differencesamong individuals and by changes in gastric acidity over time. These processes generate diverse H.pylori subpopulations, in which BabA's adaptive evolution contributes to H.pylori persistence and overt gastric disease.
Published: 2017
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14. Structural basis of GM-CSF and IL-2 sequestration by the viral decoy receptor GIF

Author: Felix, Jan, Kandiah, Eaazhisai, De Munck, Steven, Bloch, Yehudi, Van Zundert, Gydo C P, Pauwels, Kris, Dansercoer, Ann, Novanska, Katka, Read, Randy J., Bonvin, Alexandre M J J, Vergauwen, Bjorn, Verstraete, Kenneth, Gutsche, Irina, Savvides, Savvas N., Sub NMR Spectroscopy, NMR Spectroscopy, Sub NMR Spectroscopy, NMR Spectroscopy, Laboratory for Protein Biochemistry and Biomolecular Engineering, Department of Biochemistry, Physiology and Microbiology, Universiteit Gent = Ghent University (UGENT), Institut de biologie structurale (IBS - UMR 5075 ), Centre National de la Recherche Scientifique (CNRS)-Université Grenoble Alpes [2016-2019] (UGA [2016-2019])-Institut de Recherche Interdisciplinaire de Grenoble (IRIG), Direction de Recherche Fondamentale (CEA) (DRF (CEA)), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Direction de Recherche Fondamentale (CEA) (DRF (CEA)), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA), Bijvoet Center for Biomolecular Research [Utrecht], Utrecht University [Utrecht], Structural Biology Research Center, VIB, 1050 Brussels, Belgium, VIB-VUB Center for Structural Biology [Bruxelles], VIB [Belgium]-VIB [Belgium], Masaryk University [Brno] (MUNI), Department of Haematology, University of Cambridge [UK] (CAM), beamlines P14 and P12 of the EMBL at PETRA3-DESY (Hamburg, Germany), Proxima 2 and SWING at SOLEIL French National Synchrotron (Gif-sur-Yvette, France), research fellowships from Research Foundation Flanders (FWO, Belgium), pre-doctoral research fellows of the Flemish Agency for Innovation and Entrepreneurship (VLAIO), FWO research grants G0597.10, G0643.07N, and G0B7912N, infrastructure grant AUGE-11-029 from the Hercules Foundation (Belgium), and the Flanders Institute for Biotechnology (VIB), Grenoble Instruct center (ISBG, UMS 3518 CNRS-CEA-UJF-EMBL), ANR-10-INBS-0005,FRISBI,Infrastructure Française pour la Biologie Structurale Intégrée(2010), ANR-10-LABX-0049,GRAL,Grenoble Alliance for Integrated Structural Cell Biology(2010), Universiteit Gent = Ghent University [Belgium] (UGENT), Université Grenoble Alpes [2016-2019] (UGA [2016-2019])-Institut de Recherche Interdisciplinaire de Grenoble (IRIG), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Centre National de la Recherche Scientifique (CNRS), Read, Randy J [0000-0001-8273-0047], Apollo - University of Cambridge Repository, Department of Bio-engineering Sciences, and Faculty of Sciences and Bioengineering Sciences
Subjects: Models, Molecular, 0301 basic medicine, Chemistry(all), viruses, medicine.medical_treatment, General Physics and Astronomy, CHEMOKINE-BINDING-PROTEIN, Poxviridae Infections, Plasma protein binding, Crystallography, X-Ray, medicine.disease_cause, Biochemistry, Medicine and Health Sciences, CRYSTAL-STRUCTURE, skin and connective tissue diseases, Receptor, INTERLEUKIN-2, Parapoxvirus, Multidisciplinary, [SDV.BBM.BS]Life Sciences [q-bio]/Biochemistry, Molecular Biology/Structural Biology [q-bio.BM], INHIBITOR, Orf virus, COLONY-STIMULATING FACTOR, VACCINIA VIRUS, 3. Good health, Cell biology, Molecular mimicry, Cytokine, Host-Pathogen Interactions, Mammalia, Cytokines, ddc:500, Decoy, Protein Binding, Viral protein, Science, chemical and pharmacologic phenomena, Biology, Physics and Astronomy(all), Article, General Biochemistry, Genetics and Molecular Biology, Viral Proteins, 03 medical and health sciences, Immune system, medicine, Humans, X-ray crystallography, COMPLEX, COWPOX VIRUS, Biochemistry, Genetics and Molecular Biology(all), Poxviridae, HEK 293 cells, Granulocyte-Macrophage Colony-Stimulating Factor, General Chemistry, biochemical phenomena, metabolism, and nutrition, Virology, biological factors, HEK293 Cells, 030104 developmental biology, kinetics, Multiprotein Complexes, Interleukin-2, SYSTEM, Genetics and Molecular Biology(all)
Abstract: Subversion of the host immune system by viruses is often mediated by molecular decoys that sequester host proteins pivotal to mounting effective immune responses. The widespread mammalian pathogen parapox Orf virus deploys GIF, a member of the poxvirus immune evasion superfamily, to antagonize GM-CSF (granulocyte macrophage colony-stimulating factor) and IL-2 (interleukin-2), two pleiotropic cytokines of the mammalian immune system. However, structural and mechanistic insights into the unprecedented functional duality of GIF have remained elusive. Here we reveal that GIF employs a dimeric binding platform that sequesters two copies of its target cytokines with high affinity and slow dissociation kinetics to yield distinct complexes featuring mutually exclusive interaction footprints. We illustrate how GIF serves as a competitive decoy receptor by leveraging binding hotspots underlying the cognate receptor interactions of GM-CSF and IL-2, without sharing any structural similarity with the cytokine receptors. Our findings contribute to the tracing of novel molecular mimicry mechanisms employed by pathogenic viruses., Viruses often subvert the host immune system using molecular decoys to prevent an effective immune response. Here, the authors examine the structural details of the viral decoy receptor GIF and its antagnosim of GM-CSF and IL-2.
Published: 2016
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15. Prediction of homo- and hetero-protein complexes by protein docking and template-based modeling: a CASP-CAPRI experiment

Author: Eichiro Ichiishi, Dmitri Beglov, Bernard Maigret, Gyu Rie Lee, Artem B. Mamonov, Shoshana J. Wodak, Jonathan C. Fuller, Dima Kozakov, Jong Young Joung, Petr Popov, Xiaofeng Yu, Keehyoung Joo, João P. G. L. M. Rodrigues, Anna Vangone, Koen M. Visscher, Xiaoqin Zou, Paul A. Bates, Andriy Kryshtafovych, Shourya S. Roy Burman, Daisuke Kihara, Romina Oliva, Efrat Ben-Zeev, Jeffrey J. Gray, Yang Shen, Li C. Xue, Sameer Velankar, Emilie Neveu, Shruthi Viswanath, Dina Schneidman-Duhovny, Juan Esquivel-Rodríguez, Mieczyslaw Torchala, Amit Roy, Alexandre M. J. J. Bonvin, David R. Hall, Tanggis Bohnuud, Xusi Han, David W. Ritchie, Ron Elber, Daisuke Kuroda, Zhiwei Ma, Joan Segura, Carlos A. Del Carpio, Nicholas A. Marze, Jong Yun Kim, Andrej Sali, Petras J. Kundrotas, Ezgi Karaca, Neil J. Bruce, Chaok Seok, Panagiotis L. Kastritis, Shen You Huang, Ilya A. Vakser, Lim Heo, Sanbo Qin, Raphael A. G. Chaleil, Adrien S. J. Melquiond, Miguel Romero-Durana, Anisah W. Ghoorah, Surendra S. Negi, Andrey Tovchigrechko, Françoise Ochsenbein, Narcis Fernandez-Fuentes, Liming Qiu, Miriam Eisenstein, Mehdi Nellen, Marie-Dominique Devignes, Lenna X. Peterson, Jinchao Yu, Minkyung Baek, Brian G. Pierce, Hasup Lee, Toshiyuki Oda, Rebecca C. Wade, Raphael Guerois, Juan Fernández-Recio, Iain H. Moal, Edrisse Chermak, Sergei Grudinin, Sangwoo Park, Ivan Anishchenko, Chengfei Yan, Thom Vreven, Kentaro Tomii, Bing Xia, Hyung Rae Kim, Chiara Pallara, Jooyoung Lee, Kazunori D. Yamada, Xianjin Xu, Kenichiro Imai, Zhiping Weng, Luigi Cavallo, Tyler M. Borrman, Jianlin Cheng, Marc F. Lensink, Huan-Xiang Zhou, Jilong Li, Gydo C. P. van Zundert, Brian Jiménez-García, Tsukasa Nakamura, Scott E. Mottarella, Sandor Vajda, Institut de Recherche Interdisciplinaire [Villeneuve d'Ascq] ( IRI ), Université de Lille, Sciences et Technologies-Université de Lille, Droit et Santé-Centre National de la Recherche Scientifique ( CNRS ), European Molecular Biology Laboratory, European Bioinformatics Institute, Genome Center [UC Davis], University of California at Davis, Research Support Computing [Columbia], University of Missouri-Columbia, Bioinformatics Consortium and Department of Computer Science [Columbia], Department of Bioengineering and Therapeutic Sciences, University of California [San Francisco] ( UCSF ), Department of Pharmaceutical Chemistry, Department of Bioengineering and Therapeutic Sciences, Department of Pharmaceutical Chemistry, University of California [San Francisco] ( UCSF ) -California Institute for Quantitative Biosciences, GN7 of the National Institute for Bioinformatics (INB) and Biocomputing Unit, Centro Nacional de Biotecnología (CSIC), Institute of Biological, Environmental and Rural Sciences ( IBERS ), Institute for Computational Engineering and Sciences [Austin] ( ICES ), University of Texas at Austin [Austin], Department of Computer Science, Department of Chemistry, Algorithms for Modeling and Simulation of Nanosystems ( NANO-D ), Inria Grenoble - Rhône-Alpes, Institut National de Recherche en Informatique et en Automatique ( Inria ) -Institut National de Recherche en Informatique et en Automatique ( Inria ) -Laboratoire Jean Kuntzmann ( LJK ), Université Pierre Mendès France - Grenoble 2 ( UPMF ) -Université Joseph Fourier - Grenoble 1 ( UJF ) -Institut Polytechnique de Grenoble - Grenoble Institute of Technology-Centre National de la Recherche Scientifique ( CNRS ) -Université Grenoble Alpes ( UGA ) -Université Pierre Mendès France - Grenoble 2 ( UPMF ) -Université Joseph Fourier - Grenoble 1 ( UJF ) -Institut Polytechnique de Grenoble - Grenoble Institute of Technology-Centre National de la Recherche Scientifique ( CNRS ) -Université Grenoble Alpes ( UGA ) -Institut National Polytechnique de Grenoble ( INPG ), Moscow Institute of Physics and Technology [Moscow] ( MIPT ), Seoul National University [Seoul], Florida State University [Tallahassee] ( FSU ), Computational Algorithms for Protein Structures and Interactions ( CAPSID ), Inria Nancy - Grand Est, Institut National de Recherche en Informatique et en Automatique ( Inria ) -Institut National de Recherche en Informatique et en Automatique ( Inria ) -Department of Complex Systems, Artificial Intelligence & Robotics ( LORIA - AIS ), Laboratoire Lorrain de Recherche en Informatique et ses Applications ( LORIA ), Institut National de Recherche en Informatique et en Automatique ( Inria ) -Université de Lorraine ( UL ) -Centre National de la Recherche Scientifique ( CNRS ) -Institut National de Recherche en Informatique et en Automatique ( Inria ) -Université de Lorraine ( UL ) -Centre National de la Recherche Scientifique ( CNRS ) -Laboratoire Lorrain de Recherche en Informatique et ses Applications ( LORIA ), Institut National de Recherche en Informatique et en Automatique ( Inria ) -Université de Lorraine ( UL ) -Centre National de la Recherche Scientifique ( CNRS ) -Université de Lorraine ( UL ) -Centre National de la Recherche Scientifique ( CNRS ), University of Mauritius, Biomolecular Modelling Laboratory, The Francis Crick Institute, Lincoln's Inn Fields Laboratory, G-INCPM, Weizmann Institute of Science, Chemical Research Support [Rehovot], Sealy Center for Structural Biology and Molecular Biophysics, The University of Texas Medical Branch ( UTMB ), Program in Bioinformatics and Integrative Biology [Worcester], University of Massachusetts Medical School [Worcester] ( UMASS ), Institut de Biologie Intégrative de la Cellule ( I2BC ), Université Paris-Saclay-Centre National de la Recherche Scientifique ( CNRS ) -Commissariat à l'énergie atomique et aux énergies alternatives ( CEA ) -Université Paris-Sud - Paris 11 ( UP11 ), Bijvoet Center for Biomolecular Research [Utrecht], Utrecht University [Utrecht], Dalton Cardiovascular Research Center [Columbia], Department of Computer Science [Columbia], Informatics Intitute, Department of Biochemistry, University of Missouri, UNIVERSITY OF MISSOURI, Toyota Technological Institute at Chicago [Chicago] ( TTIC ), Department of Biological Sciences, Purdue University, Purdue University [West Lafayette], Department of Computer Science [Purdue], Bioinformatics and Computational Biosciences Branch, Rocky Mountain Laboratories, Molecular and Cellular Modeling Group, Heidelberg Institute of Theoretical Studies, Center for Molecular Biology ( ZMBH ), Universität Heidelberg [Heidelberg], Interdisciplinary Center for Scientiﬁc Computing ( IWR ), Department of Molecular Biosciences [Lawrence], University of Kansas [Lawrence] ( KU ), Computational Biology Research Center ( CBRC ), National Institute of Advanced Industrial Science and Technology ( AIST ), Graduate School of Frontier Sciences, The University of Tokyo, Joint BSC-CRG-IRB Research Program in Computational Biology, Barcelona Supercomputing Center - Centro Nacional de Supercomputacion ( BSC - CNS ), Center for In-Silico Protein Science, Korea Institute for Advanced Study ( KIAS ), Center for Advanced Computation, Department of Biomedical Engineering [Boston], Boston University [Boston] ( BU ), Institute of Biological Diversity, International Pacific Institute of Indiana, Drosophila Genetic Resource Center, Kyoto Institute of Technology, International University of Health and Welfare Hospital ( IUHW Hospital ), International University of Health and Welfare Hospital, Department of Chemical and Biomolecular Engineering [Baltimore], Johns Hopkins University ( JHU ), Program in Molecular Biophysics [Baltimore], King Abdullah University of Science and Technology ( KAUST ), University of Naples, J Craig Venter Institute, Structural Biology Research Center, VIB, 1050 Brussels, Belgium, Institut de Recherche Interdisciplinaire [Villeneuve d'Ascq] (IRI), Université de Lille, Sciences et Technologies-Université de Lille, Droit et Santé-Centre National de la Recherche Scientifique (CNRS), European Bioinformatics Institute [Hinxton] (EMBL-EBI), EMBL Heidelberg, University of California [Davis] (UC Davis), University of California (UC)-University of California (UC), University of Missouri [Columbia] (Mizzou), University of Missouri System, University of California [San Francisco] (UC San Francisco), Centro Nacional de Biotecnología [Madrid] (CNB-CSIC), Consejo Superior de Investigaciones Científicas [Madrid] (CSIC)-Consejo Superior de Investigaciones Científicas [Madrid] (CSIC), Institute of Biological, Environmental and Rural Sciences (IBERS), Institute for Computational Engineering and Sciences [Austin] (ICES), Algorithms for Modeling and Simulation of Nanosystems (NANO-D), Institut National de Recherche en Informatique et en Automatique (Inria)-Institut National de Recherche en Informatique et en Automatique (Inria)-Institut polytechnique de Grenoble - Grenoble Institute of Technology (Grenoble INP )-Laboratoire Jean Kuntzmann (LJK ), Institut polytechnique de Grenoble - Grenoble Institute of Technology (Grenoble INP )-Institut National de Recherche en Informatique et en Automatique (Inria)-Centre National de la Recherche Scientifique (CNRS)-Université Grenoble Alpes [2016-2019] (UGA [2016-2019])-Centre National de la Recherche Scientifique (CNRS)-Université Grenoble Alpes [2016-2019] (UGA [2016-2019]), Moscow Institute of Physics and Technology [Moscow] (MIPT), Seoul National University [Seoul] (SNU), Florida State University [Tallahassee] (FSU), Computational Algorithms for Protein Structures and Interactions (CAPSID), Institut National de Recherche en Informatique et en Automatique (Inria)-Institut National de Recherche en Informatique et en Automatique (Inria)-Department of Complex Systems, Artificial Intelligence & Robotics (LORIA - AIS), Laboratoire Lorrain de Recherche en Informatique et ses Applications (LORIA), Institut National de Recherche en Informatique et en Automatique (Inria)-Université de Lorraine (UL)-Centre National de la Recherche Scientifique (CNRS)-Institut National de Recherche en Informatique et en Automatique (Inria)-Université de Lorraine (UL)-Centre National de la Recherche Scientifique (CNRS)-Laboratoire Lorrain de Recherche en Informatique et ses Applications (LORIA), Institut National de Recherche en Informatique et en Automatique (Inria)-Université de Lorraine (UL)-Centre National de la Recherche Scientifique (CNRS)-Université de Lorraine (UL)-Centre National de la Recherche Scientifique (CNRS), Biomolecular Modelling Laboratory [London], The Francis Crick Institute [London], Weizmann Institute of Science [Rehovot, Israël], The University of Texas Medical Branch (UTMB), University of Massachusetts Medical School [Worcester] (UMASS), University of Massachusetts System (UMASS)-University of Massachusetts System (UMASS), Institut de Biologie Intégrative de la Cellule (I2BC), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS), Assemblage moléculaire et intégrité du génome (AMIG), Département Biochimie, Biophysique et Biologie Structurale (B3S), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS)-Institut de Biologie Intégrative de la Cellule (I2BC), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS), University of Missouri System-University of Missouri System, Toyota Technological Institute at Chicago [Chicago] (TTIC), Department of Biological Sciences [Lafayette IN], Heidelberg Institute for Theoretical Studies (HITS ), Center for Molecular Biology (ZMBH), Universität Heidelberg [Heidelberg] = Heidelberg University, Interdisciplinary Center for Scientiﬁc Computing (IWR), University of Kansas [Lawrence] (KU), Computational Biology Research Center (CBRC), National Institute of Advanced Industrial Science and Technology (AIST), The University of Tokyo (UTokyo), Barcelona Supercomputing Center - Centro Nacional de Supercomputacion (BSC - CNS), Korea Institute for Advanced Study (KIAS), Boston University [Boston] (BU), International University of Health and Welfare Hospital (IUHW Hospital), Johns Hopkins University (JHU), King Abdullah University of Science and Technology (KAUST), University of Naples Federico II = Università degli studi di Napoli Federico II, J. Craig Venter Institute, VIB-VUB Center for Structural Biology [Bruxelles], VIB [Belgium], Centre National de la Recherche Scientifique (CNRS)-Université de Lille, Droit et Santé-Université de Lille, Sciences et Technologies, University of California-University of California, University of California [San Francisco] (UCSF), Centre National de la Recherche Scientifique (CNRS)-Université de Lorraine (UL)-Institut National de Recherche en Informatique et en Automatique (Inria)-Centre National de la Recherche Scientifique (CNRS)-Université de Lorraine (UL)-Institut National de Recherche en Informatique et en Automatique (Inria)-Laboratoire Lorrain de Recherche en Informatique et ses Applications (LORIA), Centre National de la Recherche Scientifique (CNRS)-Université de Lorraine (UL)-Institut National de Recherche en Informatique et en Automatique (Inria)-Centre National de la Recherche Scientifique (CNRS)-Université de Lorraine (UL), University of Naples Federico II, Barcelona Supercomputing Center, NMR Spectroscopy, and Sub NMR Spectroscopy
Subjects: 0301 basic medicine, Protein Conformation, alpha-Helical, Protein Folding, Computer science, International Cooperation, Amino Acid Motifs, Oligomer state, Homoprotein, DATA-BANK, computer.software_genre, Molecular Docking Simulation, Biochemistry, CAPRI Round 30, DESIGN, Structural Biology, ALIGN, Blind prediction, AFFINITY, Protein interaction, Enginyeria biomèdica [Àrees temàtiques de la UPC], ZDOCK, Oligomer State, computer.file_format, Articles, Protein structure prediction, Proteïnes--Investigació, 3. Good health, WEB SERVER, CASP, Thermodynamics, Data mining, CAPRI, Protein docking, Molecular Biology, Algorithms, INTERFACES, Protein Binding, [ INFO.INFO-MO ] Computer Science [cs]/Modeling and Simulation, Bioinformatics, STRUCTURAL BIOLOGY, Computational biology, Molecular Dynamics Simulation, Article, 03 medical and health sciences, [ INFO.INFO-BI ] Computer Science [cs]/Bioinformatics [q-bio.QM], Heteroprotein, Humans, Protein binding, Macromolecular docking, Protein Interaction Domains and Motifs, Homology modeling, ALGORITHM, Protein-protein docking, Internet, Binding Sites, Models, Statistical, 030102 biochemistry & molecular biology, Bacteria, Sequence Homology, Amino Acid, Computational Biology, Proteins, Protein Data Bank, [INFO.INFO-MO]Computer Science [cs]/Modeling and Simulation, Protein Structure, Tertiary, 030104 developmental biology, Structural biology, Docking (molecular), Protein structure, Protein Conformation, beta-Strand, Protein Multimerization, oligomer state, blind prediction, protein interaction, protein docking, [INFO.INFO-BI]Computer Science [cs]/Bioinformatics [q-bio.QM], computer, Software
Abstract: We present the results for CAPRI Round 30, the first joint CASP-CAPRI experiment, which brought together experts from the protein structure prediction and protein–protein docking communities. The Round comprised 25 targets from amongst those submitted for the CASP11 prediction experiment of 2014. The targets included mostly homodimers, a few homotetramers, and two heterodimers, and comprised protein chains that could readily be modeled using templates from the Protein Data Bank. On average 24 CAPRI groups and 7 CASP groups submitted docking predictions for each target, and 12 CAPRI groups per target participated in the CAPRI scoring experiment. In total more than 9500 models were assessed against the 3D structures of the corresponding target complexes. Results show that the prediction of homodimer assemblies by homology modeling techniques and docking calculations is quite successful for targets featuring large enough subunit interfaces to represent stable associations. Targets with ambiguous or inaccurate oligomeric state assignments, often featuring crystal contact-sized interfaces, represented a confounding factor. For those, a much poorer prediction performance was achieved, while nonetheless often providing helpful clues on the correct oligomeric state of the protein. The prediction performance was very poor for genuine tetrameric targets, where the inaccuracy of the homology-built subunit models and the smaller pair-wise interfaces severely limited the ability to derive the correct assembly mode. Our analysis also shows that docking procedures tend to perform better than standard homology modeling techniques and that highly accurate models of the protein components are not always required to identify their association modes with acceptable accuracy. We are most grateful to the PDBe at the European Bioinformatics Institute in Hinxton, UK, for hosting the CAPRI website. Our deepest thanks go to all the structural biologists and to the following structural genomics initiatives: Northeast Structural Genomics Consortium, Joint Center for Structural Genomics, NatPro PSI:Biology, New York Structural Genomics Research Center, Midwest Center for Structural Genomics, Structural Genomics Consortium, for contributing the targets for this joint CASP-CAPRI experiment. MFL acknowledges support from the FRABio FR3688 Research Federation “Structural & Functional Biochemistry of Biomolecular Assemblies.”
Published: 2016
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16. DisProt 7.0 : a major update of the database of disordered proteins

Author: Edoardo Salladini, Eva Schad, Antoine Schramm, Fiorella Tonello, Francesco Tabaro, A. Keith Dunker, Mauricio Macossay-Castillo, Sandra Macedo-Ribeiro, Per Warholm, Norman E. Davey, Maria Cristina Aspromonte, Jordi Pujols, Emanuela Leonardi, Beáta Szabó, Marco Necci, Konstantinos D. Tsirigos, Ivan Mičetić, Salvador Ventura, Wim F. Vranken, Giovanni Minervini, Radoslav Davidovic, Federica Quaglia, Attila Meszaros, Vladimir N. Uversky, Agnes Tantos, Lajos Kalmar, Nikoletta Murvai, Nevena Veljkovic, Peter Tompa, Tamas Lazar, Sonia Longhi, Arne Elofsson, Alessandra Gasparini, Damiano Piovesan, Silvio C. E. Tosatto, Daniel B. Roche, Zsuzsanna Dosztányi, Andrey V. Kajava, András Hatos, Christopher J. Oldfield, Università degli Studi di Padova = University of Padua (Unipd), Institute of Medical Technology and Tampere University Hospital, University of Tampere [Finland], Indiana University School of Medicine, Indiana University System, Conway Institute of Biomolecular & Biomedical Research, University College Dublin [Dublin] (UCD), Vinča Institute of Nuclear Sciences, University of Belgrade [Belgrade], Biophysics Research Group [Budapest] (ELTE-MTA 'Lendület'), Hungarian Academy of Sciences (MTA), Stockholm University, Centre de recherche en Biologie cellulaire de Montpellier (CRBM), Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS), Institut de Biologie Computationnelle (IBC), Institut National de la Recherche Agronomique (INRA)-Institut National de Recherche en Informatique et en Automatique (Inria)-Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS), ITMO University [Russia], University of Cambridge [UK] (CAM), Structural Biology Brussels (SBB), Vrije Universiteit Brussel (VUB), Structural Biology Research Center, VIB, 1050 Brussels, Belgium, VIB-VUB Center for Structural Biology [Bruxelles], VIB [Belgium]-VIB [Belgium], Instituto de Biologia Molecular e Celular (IBMC), Institut de Biotecnologia i Biomedicina, Universitat Autònoma de Barcelona (UAB), Architecture et fonction des macromolécules biologiques (AFMB), Institut National de la Recherche Agronomique (INRA)-Aix Marseille Université (AMU)-Centre National de la Recherche Scientifique (CNRS), Interuniversity Institute of Bioinformatics in Brussels (IB2), Université libre de Bruxelles (ULB)-Vrije Universiteit Brussel (VUB), Institute of Cytology of the Russian Academy of Science (St. Petersburg), Morsani College of Medicine, Department of Pediatrics, University of South Florida [Tampa] (USF), COST Action BM1405 NGP-net, ELIXIR-IIB (elixir-italy.org), ‘Lend ̈ulet’ Grant from the Hungarian Academyof Sciences [LP2014-16 to Z.D.], Hungarian Scientific Re-search Fund [OTKA K 108798 to Z.D.], AIRC ResearchFellowship (to D.P.), Spanish Ministerio de Educaci ́on Cul-tura i Deporte PhD Fellowship (to J.P.), Mexican Na-tional Council for Science and Technology (CONACYT)PhD Fellowship [215503 to M.M.-C.], Grant PortoNeu-roDRIve@i3S funded by Norte Portugal Regional Opera-tional Programme (NORTE 2020), under the PORTUGAL2020 Partnership Agreement, through the European Re-gional Development Fund (ERDF) (to S.M.-R.), DirectionG ́en ́erale des Arm ́ees and Aix-Marseille University PhDFellowship (to E.Sa.), OTKA Grant [PD-OTKA 108772 toE.Sc.], French Ministry of National Education, Researchand Technology PhD Fellowship (to A.S.), Ministry of Ed-ucation, Science and Technological Development of the Re-public of Serbia [173001, 173049 to N.V., R.D.], ICREA-Academia Award (to S.V.), Odysseus Grant from ResearchFoundation Flanders (FWO) [G.0029.12 to P.T.], AIRC IGGrant [17753 to S.T., in part], Italian Ministry of Health[GR-2011-02347754 to E.L., S.T., GR-2011-02346845 toS.T.], Swedish Research Council Grant [VR-NT 2012-5046to A.E.]. Computational resources were provided by theSwedish National Infrastructure for Computing (SNIC)at NSC. Funding for open access charge: COST ActionBM1405 NGP-net, Universita degli Studi di Padova, University of Padova and INFN Padova, Centre de recherche en Biologie Cellulaire (CRBM), Université Montpellier 1 (UM1)-Université Montpellier 2 - Sciences et Techniques (UM2)-Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS), Department of Veterinary Medicine, University of Cambridge, Cambridge, UK, Vrije Universiteit [Brussels] (VUB), Universitat Autònoma de Barcelona [Barcelona] (UAB), CNR Institute of Neuroscience, University of Padova, Interuniversity Institute of Bioinformatics in Brussels [ULB], Université Libre de Bruxelles [Bruxelles] (ULB), University of South Florida (USF), Université Montpellier 2 - Sciences et Techniques (UM2)-Centre National de la Recherche Scientifique (CNRS)-Université de Montpellier (UM)-Université Montpellier 1 (UM1), Université de Montpellier (UM)-Institut National de la Recherche Agronomique (INRA)-Institut National de Recherche en Informatique et en Automatique (Inria)-Centre National de la Recherche Scientifique (CNRS), and Centre National de la Recherche Scientifique (CNRS)-Aix Marseille Université (AMU)-Institut National de la Recherche Agronomique (INRA)
Subjects: 0301 basic medicine, Protein Conformation, Classification scheme, [SDV.BC]Life Sciences [q-bio]/Cellular Biology, Computational biology, Biology, Intrinsically disordered proteins, computer.software_genre, Crystallography, X-Ray, 03 medical and health sciences, Text mining, Protein structure, Research community, Fluorescence Resonance Energy Transfer, Genetics, Database Issue, Animals, Humans, Databases, Protein, Biological sciences, Nuclear Magnetic Resonance, Biomolecular, ComputingMilieux_MISCELLANEOUS, 030102 biochemistry & molecular biology, Database, business.industry, Généralités, Intrinsically Disordered Proteins, 030104 developmental biology, Förster resonance energy transfer, Forms and Records Control, Erratum, business, computer, Forecasting
Abstract: The Database of Protein Disorder (DisProt, URL: www.disprot.org) has been significantly updated and upgraded since its last major renewal in 2007. The current release holds information on more than 800 entries of IDPs/IDRs, i.e. intrinsically disordered proteins or regions that exist and function without a well-defined three-dimensional structure. We have re-curated previous entries to purge DisProt from conflicting cases, and also upgraded the functional classification scheme to reflect continuous advance in the field in the past 10 years or so. We define IDPs as proteins that are disordered along their entire sequence, i.e. entirely lack structural elements, and IDRs as regions that are at least five consecutive residues without well-defined structure. We base our assessment of disorder strictly on experimental evidence, such as X-ray crystallography and nuclear magnetic resonance (primary techniques) and a broad range of other experimental approaches (secondary techniques). Confident and ambiguous annotations are highlighted separately. DisProt 7.0 presents classified knowledge regarding the experimental characterization and functional annotations of IDPs/IDRs, and is intended to provide an invaluable resource for the research community for a better understanding structural disorder and for developing better computational tools for studying disordered proteins., SCOPUS: ar.j, info:eu-repo/semantics/published
Published: 2016
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17. Generation of a Nanobody Targeting the Paraflagellar Rod Protein of Trypanosomes

Author: Serge Muldermans, Bart Devreese, Stefan Magez, Philippe Bastin, Emmanuel Obishakin, Isabel Vandenberghe, Benoit Stijlemans, Julien Santi-Rocca, Cellular and Molecular Immunology (VIB), Vrije Universiteit Brussel (VUB), Structural Biology Research Center, VIB, 1050 Brussels, Belgium, VIB-VUB Center for Structural Biology [Bruxelles], VIB [Belgium]-VIB [Belgium], Laboratory of Myeloid Cell Immunology, Flanders Interuniversity Institute for Biotechnology (VIB), Biologie Cellulaire des Trypanosomes, Institut Pasteur [Paris]-Centre National de la Recherche Scientifique (CNRS), Department of Biochemistry and Microbiology, Universiteit Gent = Ghent University [Belgium] (UGENT), This work was supported by the European Union/FP7 Nanotryp (FP7-HEALTH 2007-2.3.4-1) and the Fund for Scientific Research Flanders (FWO). Work at the Institut Pasteur was funded by a French Government Investissement d'Avenir program, Laboratoire d'Excellence 'Integrative Biology of Emerging Infectious Diseases' (ANR-10-LABX-62- IBEID), the Institut Carnot Maladies Infectieuses and the Fondation pour la Recherche Médicale. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript., ANR-10-LABX-0062,IBEID,Integrative Biology of Emerging Infectious Diseases(2010), European Project: 223048,EC:FP7:HEALTH,FP7-HEALTH-2007-B,NANOTRYP(2009), Cellular and Molecular Immunology, Institut Pasteur [Paris] (IP)-Centre National de la Recherche Scientifique (CNRS), and Universiteit Gent = Ghent University (UGENT)
Subjects: Phage display, Protozoan Proteins, Antigen Processing and Recognition, Epitope, Zoonoses, Trypanosomes, Medicine and Health Sciences, Bio-panning techniques, RNA, Small Interfering, VIVAX, CONGOLENSE, Multidisciplinary, biology, DOMAIN ANTIBODY FRAGMENTS, DETECTION ENZYME IMMUNOASSAYS, Vaccination and Immunization, Trypanocidal Agents, Recombinant Proteins, nanobodies, 3. Good health, Infectious Diseases, [SDV.MP]Life Sciences [q-bio]/Microbiology and Parasitology, Veterinary Diseases, Flagella, INFECTIONS, Trypanosome-specific antigen, Medicine, RNA Interference, phage display, Immunoglobulin Heavy Chains, Camelids, New World, Research Article, Biotechnology, Trypanosoma, Infectious Disease Control, medicine.drug_class, Science, Immunology, Molecular Sequence Data, Biophysics, Bioengineering, Antigens, Protozoan, TSETSE-FLY, Monoclonal antibody, Antigen, Trypanosomiasis, medicine, Animals, FLAGELLUM, Amino Acid Sequence, Immunodiagnostics, Paraflagellar rod protein (PFR1), Biology and Life Sciences, BRUCEI, Trypanosoma evansi, Veterinary Parasitology, biology.organism_classification, Virology, Vector-Borne Diseases, Bionanotechnology, RNA, Parasitology, Veterinary Science, Sequence Alignment, Single-Chain Antibodies, AFRICAN TRYPANOSOMIASIS
Abstract: International audience; Trypanosomes are protozoan parasites that cause diseases in humans and livestock for which no vaccines are available. Disease eradication requires sensitive diagnostic tools and efficient treatment strategies. Immunodiagnostics based on antigen detection are preferable to antibody detection because the latter cannot differentiate between active infection and cure. Classical monoclonal antibodies are inaccessible to cryptic epitopes (based on their size-150 kDa), costly to produce and require cold chain maintenance, a condition that is difficult to achieve in trypanosomiasis endemic regions, which are mostly rural. Nanobodies are recombinant, heat-stable, small-sized (15 kDa), antigen-specific, single-domain, variable fragments derived from heavy chain-only antibodies in camelids. Because of numerous advantages over classical antibodies, we investigated the use of nanobodies for the targeting of trypanosome-specific antigens and diagnostic potential. An alpaca was immunized using lysates of Trypanosoma evansi. Using phage display and bio-panning techniques, a cross-reactive nanobody (Nb392) targeting all trypanosome species and isolates tested was selected. Imunoblotting, immunofluorescence microscopy, immunoprecipitation and mass spectrometry assays were combined to identify the target recognized. Nb392 targets paraflagellar rod protein (PFR1) of T. evansi, T. brucei, T. congolense and T. vivax. Two different RNAi mutants with defective PFR assembly (PFR2(RNAi) and KIF9B(RNAi)) were used to confirm its specificity. In conclusion, using a complex protein mixture for alpaca immunization, we generated a highly specific nanobody (Nb392) that targets a conserved trypanosome protein, i.e., PFR1 in the flagella of trypanosomes. Nb392 is an excellent marker for the PFR and can be useful in the diagnosis of trypanosomiasis. In addition, as demonstrated, Nb392 can be a useful research or PFR protein isolation tool.
Published: 2014
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18. Structural and mechanistic insights into the bacterial amyloid secretion channel CsgG

Author: Jerome S. Pinkner, Rémi Fronzes, Francesca Gubellini, Parveen Goyal, Petya V. Krasteva, Han Remaut, Imke Van den Broeck, Gérard Pehau-Arnaudet, Matthew George Chapman, Scott J. Hultgren, Anastassia Troupiotis-Tsaïlaki, Wim Jonckheere, Nani Van Gerven, Stefan Howorka, VIB-VUB Center for Structural Biology [Bruxelles], VIB [Belgium], Vrije Universiteit Brussel (VUB), Biologie Structurale de la Sécrétion Bactérienne, Institut Pasteur [Paris] (IP)-Centre National de la Recherche Scientifique (CNRS), Université libre de Bruxelles (ULB), Washington University School of Medicine in St. Louis, Washington University in Saint Louis (WUSTL), University of Michigan [Ann Arbor], University of Michigan System, University College of London [London] (UCL), This research was supported by VIB through project grant PRJ9 (P.G., N.V.G. and H.R.), by Hercules Foundation through equipment grant UABR/09/005, by National Institutes of Health RO1 grants AI099099 and AI048689 (J.P. and S.J.H.) and A1073847 (M.R.C.), and by Institut Pasteur and Centre national de la recherche scientifique (F.G., G.P.A. and R.F.). S.H. is funded by the Engineering and Physical Sciences Research Council (Institutional Sponsorship Award), the National Physical Laboratory and University College London Chemistry. F.G. is the recipient of a ‘Bourse Roux’ from Institut Pasteur. P.V.K. was supported by the European Research Council (ERC)., Institut Pasteur [Paris]-Centre National de la Recherche Scientifique (CNRS), Faculty of Sciences and Bioengineering Sciences, Structural Biology Brussels, and Department of Bio-engineering Sciences
Subjects: Models, Molecular, Protein Conformation, Entropy, transmembrane signalling, MESH: Escherichia coli Proteins, 02 engineering and technology, curli, Crystallography, X-Ray, MESH: Membrane Transport Proteins, Cell membrane, Diffusion, Protein structure, MESH: Protein Conformation, HasR, Serratia marcescens, 0303 health sciences, Multidisciplinary, [SDV.BBM.BS]Life Sciences [q-bio]/Biochemistry, Molecular Biology/Structural Biology [q-bio.BM], Membrane transport protein, MESH: Escherichia coli, Escherichia coli Proteins, MESH: Periplasm, MESH: Diffusion, 021001 nanoscience & nanotechnology, MESH: Lipoproteins, MESH: Entropy, Transmembrane protein, Transport protein, Protein Transport, medicine.anatomical_structure, Biochemistry, Periplasm, 0210 nano-technology, Bacterial outer membrane, MESH: Models, Molecular, Amyloid, MESH: Protein Transport, Lipoproteins, [PHYS.PHYS.PHYS-BIO-PH]Physics [physics]/Physics [physics]/Biological Physics [physics.bio-ph], MESH: Biofilms, [SDV.BC]Life Sciences [q-bio]/Cellular Biology, Biology, Models, Biological, Article, 03 medical and health sciences, bacterial nutrient transporter, medicine, Escherichia coli, [CHIM.CRIS]Chemical Sciences/Cristallography, Secretion, [SDV.BBM]Life Sciences [q-bio]/Biochemistry, Molecular Biology, 030304 developmental biology, MESH: Amyloid, Cell Membrane, MESH: Models, Biological, Membrane Transport Proteins, haem, Periplasmic space, MESH: Crystallography, X-Ray, Biofilms, Biophysics, biology.protein, [INFO.INFO-BI]Computer Science [cs]/Bioinformatics [q-bio.QM], integrative approach, MESH: Cell Membrane
Abstract: International audience; Curli are functional amyloid fibres that constitute the major protein component of the extracellular matrix in pellicle biofilms formed by Bacteroidetes and Proteobacteria (predominantly of the α and γ classes). They provide a fitness advantage in pathogenic strains and induce a strong pro-inflammatory response during bacteraemia. Curli formation requires a dedicated protein secretion machinery comprising the outer membrane lipoprotein CsgG and two soluble accessory proteins, CsgE and CsgF. Here we report the X-ray structure of Escherichia coli CsgG in a non-lipidated, soluble form as well as in its native membrane-extracted conformation. CsgG forms an oligomeric transport complex composed of nine anticodon-binding-domain-like units that give rise to a 36-stranded β-barrel that traverses the bilayer and is connected to a cage-like vestibule in the periplasm. The transmembrane and periplasmic domains are separated by a 0.9-nm channel constriction composed of three stacked concentric phenylalanine, asparagine and tyrosine rings that may guide the extended polypeptide substrate through the secretion pore. The specificity factor CsgE forms a nonameric adaptor that binds and closes off the periplasmic face of the secretion channel, creating a 24,000 Å(3) pre-constriction chamber. Our structural, functional and electrophysiological analyses imply that CsgG is an ungated, non-selective protein secretion channel that is expected to employ a diffusion-based, entropy-driven transport mechanism.
Published: 2014
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19. Wheat germ in vitro translation to produce one of the most toxic sodium channel specific toxins

Author: Wael Gad, Khadija Wahni, Rahma Ben-Abderrazek, Joris Messens, Serge Muyldermans, Didier Vertommen, Balkiss Bouhaouala-Zahar, Department of Bio-engineering Sciences, Structural Biology Brussels, Cellular and Molecular Immunology, Ultrastructure, Brussels Center for Redox Biology, 1050 Brussels, Belgium, Brussels Center for Redox Biology, Structural Biology Research Center, VIB, 1050 Brussels, Belgium, VIB-VUB Center for Structural Biology [Bruxelles], VIB [Belgium]-VIB [Belgium], Structural Biology Brussels (SBB), Vrije Universiteit Brussel (VUB), Laboratoire des Venins et Biomolécules Thérapeutiques - Laboratory of Venoms and Therapeutic Biomolecules (LR11IPT08), Institut Pasteur de Tunis, Réseau International des Instituts Pasteur (RIIP)-Réseau International des Instituts Pasteur (RIIP), de Duve Institute, Université Catholique de Louvain = Catholic University of Louvain (UCL), Cellular and Molecular Immunology, Vrije Universiteit Brussel, 1050 Brussels, Belgium, Université de Tunis El Manar (UTM), This work was made possible by financial support from Vlaams Instituute Voor Biotechnologie (VIB) and the Flanders Hercules Foundation [grant number HERC16]. J.M. and S.M. are group leaders at the VIB.W.G. is supported by the European Student ExchangeProgramme ‘Erasmus Mundus ECW II’ [grant number 141085-EM-12008-BE-ERA Mundus – ECW]. D.V. is ‘collaborateur logistique of the FNRS-FRS Belgium’ R.B.A. is a Post-Doc in the group of B.B.Z. B.B.Z. is ‘scorpion venoms and antivenoms’ group leader at the IPT, and UCL - SSS/DDUV - Institut de Duve
Subjects: Male, [SDV]Life Sciences [q-bio], lcsh:Life, lcsh:QR1-502, QSOX, Quiescin sulfhydryl oxidase, Scorpion Venoms, Venom, medicine.disease_cause, hQSOX1b, human quiescin-sulphhydryl oxidase, Biochemistry, Median lethal dose, lcsh:Microbiology, GST, glutathione S-transferase, Sodium Channels, law.invention, Mice, law, WGE, wheat germ embryo, wheat germ extract, Triticum, Glutathione Transferase, PDI, protein disulphide isomerase, Scorpion toxin, biology, Research Support, Non-U.S. Gov't, [SDV.BA]Life Sciences [q-bio]/Animal biology, [SDV.BV.BOT]Life Sciences [q-bio]/Vegetal Biology/Botanics, LD50, median lethal dose, 3. Good health, IMAC, immobilized metal-ion-affinity chromatography, i.c.v., intracerebroventricular, [SDV.TOX]Life Sciences [q-bio]/Toxicology, Recombinant DNA, NbAahII10, Androctonus australis hector nanobody 10, Androctonus australis, Molecular Sequence Data, Biophysics, In Vitro Techniques, S2, TEV, tobacco etch virus, Scorpions, dromedary, Journal Article, medicine, Animals, Amino Acid Sequence, Molecular Biology, Escherichia coli, single-domain antibody, Original Paper, Toxin, Aah, Androctonus australis hector, Cell Biology, biology.organism_classification, rAahII, recombinant AahII, AahII, lcsh:QH501-531, CBB, Coomassie Brilliant Blue, Peptides, anti-venom, CDR1, complementary-determining region 1, recombinant protein
Abstract: Envenoming following scorpion sting is a common emergency in many parts of the world. During scorpion envenoming, highly toxic small polypeptides of the venom diffuse rapidly within the victim causing serious medical problems. The exploration of toxin structure-function relationship would benefit from the generation of soluble recombinant scorpion toxins in Escherichia coli. We developed an in vitro wheat germ translation system for the expression of the highly toxic Aah (Androctonus australis hector)II protein that requires the proper formation of four disulphide bonds. Soluble, recombinant N-terminal GST (glutathione S-transferase)-tagged AahII toxin is obtained in this in vitro translation system. After proteolytic removal of the GST-tag, purified rAahII (recombinant AahII) toxin, which contains two extra amino acids at its N terminal relative to the native AahII, is highly toxic after i.c.v. (intracerebroventricular) injection in Swiss mice. An LD50 (median lethal dose)-value of 10 ng (or 1.33 pmol), close to that of the native toxin (LD50 of 3 ng) indicates that the wheat germ in vitro translation system produces properly folded and biological active rAahII. In addition, NbAahII10 (Androctonus australis hector nanobody 10), a camel single domain antibody fragment, raised against the native AahII toxin, recognizes its cognate conformational epitope on the recombinant toxin and neutralizes the toxicity of purified rAahII upon injection in mice., A wheat germ embryo derived cell-free translation system expresses a biologically active, highly toxic scorpion venom protein that is fully neutralized by a camel single domain antibody fragment raised against the native scorpion toxin.
Published: 2014
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20. Prion Fibrillization Is Mediated by a Native Structural Element That Comprises Helices H2 and H3

Author: Human Rezaei, A. Pastore, Céline Chapuis, Kris Pauwels, Zhou Xu, Stéphanie Prigent, Cesira de Chiara, Miquel Adrover, Structural Biology Research Center, VIB, 1050 Brussels, Belgium, VIB-VUB Center for Structural Biology [Bruxelles], VIB [Belgium]-VIB [Belgium], Unité de recherche Virologie et Immunologie Moléculaires (VIM), Institut National de la Recherche Agronomique (INRA), Biologie Computationnelle et Quantitative = Laboratory of Computational and Quantitative Biology (LCQB), Institut de Biologie Paris Seine (IBPS), Institut National de la Santé et de la Recherche Médicale (INSERM)-Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-Centre National de la Recherche Scientifique (CNRS), Molecular Structure, The National Institute for Medical Research, Unité de recherche Virologie et Immunologie Moléculaires (VIM (UR 0892)), Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-Institut de Biologie Paris Seine (IBPS), and Sorbonne Université (SU)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)
Subjects: Circular dichroism, Amyloid, Protein Denaturation, Protein Folding, Magnetic Resonance Spectroscopy, Prions, Protein Conformation, [SDV]Life Sciences [q-bio], Sequence (biology), Biology, Biochemistry, 03 medical and health sciences, 0302 clinical medicine, Protein structure, Escherichia coli, Animals, Humans, Prion protein, [SDV.BBM.BC]Life Sciences [q-bio]/Biochemistry, Molecular Biology/Biochemistry [q-bio.BM], Molecular Biology, ComputingMilieux_MISCELLANEOUS, 030304 developmental biology, 0303 health sciences, Sheep, [SDV.BBM.BS]Life Sciences [q-bio]/Biochemistry, Molecular Biology/Structural Biology [q-bio.BM], Circular Dichroism, Genetic Variation, Neurodegenerative Diseases, Cell Biology, Protein tertiary structure, [SDV.BBM.BC]Life Sciences [q-bio]/Biochemistry, Molecular Biology/Biomolecules [q-bio.BM], [SDV.BBM.BP]Life Sciences [q-bio]/Biochemistry, Molecular Biology/Biophysics, Kinetics, Microscopy, Electron, [SDV.BBM.BS]Life Sciences [q-bio]/Biochemistry, Molecular Biology/Biomolecules [q-bio.BM], Membrane protein, Biophysics, Chromatography, Gel, Thermodynamics, Protein folding, [SDV.NEU]Life Sciences [q-bio]/Neurons and Cognition [q-bio.NC], 030217 neurology & neurosurgery, Molecular Biophysics
Abstract: Aggregation and misfolding of the prion protein (PrP) are thought to be the cause of a family of lethal neurodegenerative diseases affecting humans and other animals. Although the structures of PrP from several species have been solved, still little is known about the mechanisms that lead to the misfolded species. Here, we show that the region of PrP comprising the hairpin formed by the helices H2 and H3 is a stable independently folded unit able to retain its secondary and tertiary structure also in the absence of the rest of the sequence. We also prove that the isolated H2H3 is highly fibrillogenic and forms amyloid fibers morphologically similar to those obtained for the full-length protein. Fibrillization of H2H3 but not of full-length PrP is concomitant with formation of aggregates. These observations suggest a "banana-peeling" mechanism for misfolding of PrP in which H2H3 is the aggregation seed that needs to be first exposed to promote conversion from a helical to a beta-rich structure.
Published: 2010
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20 results on '"VIB-VUB Center for Structural Biology [Bruxelles]"'

1. Prediction of protein assemblies, the next frontier: The CASP14-CAPRI experiment

2. Nucleation of protein mesocrystals via oriented attachment

3. Megabodies expand the nanobody toolkit for protein structure determination by single-particle cryo-EM

4. Chemical shift assignments of the partially deuterated Fyn SH2–SH3 domain

5. Reversion of antibiotic resistance in Mycobacterium tuberculosis by spiroisoxazoline SMARt-420

6. A community proposal to integrate structural bioinformatics activities in ELIXIR (3D-Bioinfo Community)

7. Hepatitis C virus sequence divergence preserves p7 viroporin structural and dynamic features

8. Allostery in Its Many Disguises: From Theory to Applications

9. A comprehensive analysis of the protein-ligand interactions in crystal structures of Mycobacterium tuberculosis EthR

10. Neutrophils enhance early Trypanosoma brucei infection onset

11. Rational Design of Nanobody80 Loop Peptidomimetics

12. Modeling protein-protein and protein-peptide complexes: CAPRI 6th edition

13. Helicobacter pylori Adapts to Chronic Infection and Gastric Disease via pH-Responsive BabA-Mediated Adherence

14. Structural basis of GM-CSF and IL-2 sequestration by the viral decoy receptor GIF

15. Prediction of homo- and hetero-protein complexes by protein docking and template-based modeling: a CASP-CAPRI experiment

16. DisProt 7.0 : a major update of the database of disordered proteins

17. Generation of a Nanobody Targeting the Paraflagellar Rod Protein of Trypanosomes

18. Structural and mechanistic insights into the bacterial amyloid secretion channel CsgG

19. Wheat germ in vitro translation to produce one of the most toxic sodium channel specific toxins

20. Prion Fibrillization Is Mediated by a Native Structural Element That Comprises Helices H2 and H3

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