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1. Direct Comparison of Many-Body Methods for Realistic Electronic Hamiltonians

Author

Mark van Schilfgaarde, Andrew J. Millis, George H. Booth, Li Chen, Jia Li, Bastien Mussard, Lan Nguyen Tran, Kiel T. Williams, Cyrus Umrigar, Yuan Yao, Hao Shi, Garnet Kin-Lic Chan, Junhao Li, Sheng Guo, Mario Motta, Robert J. Anderson, Lucas K. Wagner, Shiwei Zhang, Sandeep Sharma, Dominika Zgid, Fabien Bruneval, Chun-Yao Niu, Ushnish Ray, Chia-Nan Yeh, Emanuel Gull, Department of Physics [Illinois at Urbana-Champaign, USA], University of Illinois at Urbana-Champaign [Urbana], University of Illinois System-University of Illinois System, Laboratory of Atomic and Solid State Physics [Ithaca] (LASSP), Cornell University [New York], Department of Physics [Ann Arbor], University of Michigan [Ann Arbor], University of Michigan System-University of Michigan System, Flatiron Institute, Simons Foundation, College of William and Mary [Williamsburg] (WM), IBM Almaden Research Center [San Jose], IBM, Zhengzhou University, California Institute of Technology (CALTECH), King‘s College London, Department of Chemistry [Ann Arbor], Department of Chemistry and Biochemistry [Boulder], University of Colorado [Boulder], Service de recherches de métallurgie physique (SRMP), Département des Matériaux pour le Nucléaire (DMN), CEA-Direction des Energies (ex-Direction de l'Energie Nucléaire) (CEA-DES (ex-DEN)), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Paris-Saclay-CEA-Direction des Energies (ex-Direction de l'Energie Nucléaire) (CEA-DES (ex-DEN)), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Paris-Saclay, and Columbia University [New York]

Subjects
Condensed Matter - Materials Science, Strongly Correlated Electrons (cond-mat.str-el), 010304 chemical physics, Computer science, Physics, QC1-999, Materials Science (cond-mat.mtrl-sci), FOS: Physical sciences, General Physics and Astronomy, 7. Clean energy, 01 natural sciences, Many body, Condensed Matter - Strongly Correlated Electrons, Classical mechanics, 0103 physical sciences, [PHYS.COND.CM-SCE]Physics [physics]/Condensed Matter [cond-mat]/Strongly Correlated Electrons [cond-mat.str-el], 010306 general physics
Abstract

A large collaboration carefully benchmarks 20 first principles many-body electronic structure methods on a test set of 7 transition metal atoms, and their ions and monoxides. Good agreement is attained between the 3 systematically converged methods, resulting in experiment-free reference values. These reference values are used to assess the accuracy of modern emerging and scalable approaches to the many-electron problem. The most accurate methods obtain energies indistinguishable from experimental results, with the agreement mainly limited by the experimental uncertainties. Comparison between methods enables a unique perspective on calculations of many-body systems of electrons., Simons collaboration on the many-electron problem

Published
2020
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2. 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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3. Structural Basis for Broad HIV-1 Neutralization by the MPER-Specific Human Broadly Neutralizing Antibody LN01

Author

Christophe Chipot, Timothée Bruel, Georgia D. Tomaras, Antonio Lanzavecchia, Dora Pinto, David C. Montefiori, Giuseppe Pantaleo, Winfried Weissenhorn, Sonia Barbieri, Agostino Riva, Craig Fenwick, Davide Corti, Maciej Tarkowski, Christophe Caillat, Olivier Schwartz, David Jarrossay, Andrea Minola, Michael S. Seaman, Jérémy Dufloo, Chiara Silacci, François Dehez, Serafima Guseva, Xiaoying Shen, Institute for Research in Biomedicine [Ticono, Suisse], Université de Lausanne = University of Lausanne (UNIL), 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), Laboratoire de Physique et Chimie Théoriques (LPCT), Institut de Chimie du CNRS (INC)-Université de Lorraine (UL)-Centre National de la Recherche Scientifique (CNRS), Department of Physics [Illinois at Urbana-Champaign, USA], University of Illinois at Urbana-Champaign [Urbana], University of Illinois System-University of Illinois System, Institute for Biomedicine [Bolzano, Italy] (Eurac Research), Affiliated Institute of the University of Lübeck, Humabs BioMed SA, Duke Human Vaccine Institute [Durham, North Carolina, USA], Université Paris Diderot - Paris 7 (UPD7), Luigi Sacco University Hospital [Milan], Rheumatology Unit, Milano (ASST Fatebenefratelli-Sacco), Virus et Immunité - Virus and immunity, Institut Pasteur [Paris]-Centre National de la Recherche Scientifique (CNRS), Vaccine Research Institute (VRI), Université Paris-Est Créteil Val-de-Marne - Paris 12 (UPEC UP12), Université Sorbonne Paris Cité (USPC), Beth Israel Deaconess Medical Center, Beth Israel Deaconess Medical Center [Boston] (BIDMC), Harvard Medical School [Boston] (HMS)-Harvard Medical School [Boston] (HMS), Duke University Medical Center, Institute for Research in Biomedicine, ANR-10-INBS-0005,FRISBI,Infrastructure Française pour la Biologie Structurale Intégrée(2010), ANR-17-EURE-0003,CBH-EUR-GS,CBH-EUR-GS(2017), European Project: 681137,H2020,H2020-PHC-2015-single-stage_RTD,EAVI2020(2015), Université de Lausanne (UNIL), 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), Duke Human Vaccine Institute, and Duke School of Medicine

Subjects
Env, education, Mice, Transgenic, HIV Antibodies, Gp41, Microbiology, Neutralization, Epitope, Article, Cell Line, broadly neutralizing antibody, 03 medical and health sciences, Mice, 0302 clinical medicine, 10E8, Protein Domains, 4E10, Virology, Animals, Humans, membrane interaction, Amino Acid Sequence, 030304 developmental biology, AIDS Vaccines, 0303 health sciences, biology, Germinal center, Fusion protein, Antibodies, Neutralizing, gp41, Transmembrane protein, HIV Envelope Protein gp41, 3. Good health, Cell biology, MPER, [SDV.BBM.BP]Life Sciences [q-bio]/Biochemistry, Molecular Biology/Biophysics, Disease Models, Animal, HEK293 Cells, [SDV.MP.VIR]Life Sciences [q-bio]/Microbiology and Parasitology/Virology, biology.protein, HIV-1, [SDV.IMM]Life Sciences [q-bio]/Immunology, Parasitology, Paratope, Female, LN01, Antibody, 030217 neurology & neurosurgery
Abstract

Summary Potent and broadly neutralizing antibodies (bnAbs) are the hallmark of HIV-1 protection by vaccination. The membrane-proximal external region (MPER) of the HIV-1 gp41 fusion protein is targeted by the most broadly reactive HIV-1 neutralizing antibodies. Here, we examine the structural and molecular mechansims of neutralization by anti-MPER bnAb, LN01, which was isolated from lymph-node-derived germinal center B cells of an elite controller and exhibits broad neutralization breadth. LN01 engages both MPER and the transmembrane (TM) region, which together form a continuous helix in complex with LN01. The tilted TM orientation allows LN01 to interact simultaneously with the peptidic component of the MPER epitope and membrane via two specific lipid binding sites of the antibody paratope. Although LN01 carries a high load of somatic mutations, most key residues interacting with the MPER epitope and lipids are germline encoded, lending support for the LN01 epitope as a candidate for lineage-based vaccine development., Graphical Abstract, Highlights • bNAb LN01 neutralizes 92% of a 118-strain virus panel • LN01 targets the HIV-1 gp41 MPER, the TM region, and lipids • LN01-complexed MPER forms a continuous helix with TM • Most LN01 paratope residues interacting with MPER-TM and lipids are germline encoded, The gp41 membrane-proximal external region (MPER) is a highly conserved region of HIV-1 Env. Pinto et al. characterize the broadly neutralizing anti-MPER mAb LN01, which shows low autoreactivity. LN01 interacts with a complex epitope comprising MPER, the transmembrane region, and lipids, providing insights for vaccine design.

Published
2019
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4. Molecular Basis of DNA Packaging in Bacteria Revealed by All-Atoms Molecular Dynamic Simulations: The case of histone like proteins in Borrelia burgdoferi

Author

Christophe Chipot, François Dehez, Cécilia Hognon, Antonio Monari, Joanna Timmins, Simon Garaude, Laboratoire de Physique et Chimie Théoriques (LPCT), Institut de Chimie du CNRS (INC)-Université de Lorraine (UL)-Centre National de la Recherche Scientifique (CNRS), Groupe Infection virale et cancer (IBS-VIC), 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)-Centre National de la Recherche Scientifique (CNRS)-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), Department of Physics [Illinois at Urbana-Champaign, USA], University of Illinois at Urbana-Champaign [Urbana], University of Illinois System-University of Illinois System, Laboratoire International Associé (LIA), University of Illinois System-University of Illinois System-Centre National de la Recherche Scientifique (CNRS), Université Grenoble Alpes [2016-2019] (UGA [2016-2019])-Institut de Recherche Interdisciplinaire de Grenoble (IRIG), and 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)

Subjects
0303 health sciences, biology, Chemistry, [SDV]Life Sciences [q-bio], 010402 general chemistry, biology.organism_classification, 01 natural sciences, 0104 chemical sciences, Cell biology, 03 medical and health sciences, Molecular dynamics, Histone, Dna compaction, Gene expression, biology.protein, [CHIM]Chemical Sciences, General Materials Science, Epigenetics, Physical and Theoretical Chemistry, Borrelia burgdorferi, Dna packaging, Bacteria, ComputingMilieux_MISCELLANEOUS, 030304 developmental biology
Abstract

DNA compaction is essential to ensure the packaging of the genetic material in living cells and also plays a key role in the epigenetic regulation of gene expression. In both humans and bacteria, D...

Published
2019
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5. Induced Night-Vision by Singlet-Oxygen-Mediated Activation of Rhodopsin

Author

Hugo Gattuso, Antonio Monari, Miriam Navarrete-Miguel, Christophe Chipot, Wensheng Cai, Hong Zhang, Daniel Roca-Sanjuán, Angelo Giussani, Marco Marazzi, François Dehez, Laboratoire de Physique et Chimie Théoriques (LPCT), Institut de Chimie du CNRS (INC)-Université de Lorraine (UL)-Centre National de la Recherche Scientifique (CNRS), Universidad de Alcalá - University of Alcalá (UAH), Instituto de Ciencia Molecular (ICMol), Universitat de València (UV), Tianjin Key Laboratory of Biosensing and Molecular Recognition, Nankai University (NKU), 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], and University of Illinois System-University of Illinois System

Subjects
genetic structures, biology, 010405 organic chemistry, Singlet oxygen, Photoreceptor protein, Retinal, 010402 general chemistry, 01 natural sciences, Visual sensitivity, eye diseases, Transmembrane protein, 0104 chemical sciences, chemistry.chemical_compound, chemistry, Rhodopsin, Night vision, biology.protein, Biophysics, [CHIM]Chemical Sciences, General Materials Science, Physical and Theoretical Chemistry, ComputingMilieux_MISCELLANEOUS, Visual phototransduction
Abstract

In humans, vision is limited to a small fraction of the whole electromagnetic spectrum. One possible strategy for enhancing vision in deep-red or poor-light conditions consists of recruiting chlorophyll derivatives in the rod photoreceptor cells of the eye, as suggested in the case of some deep-sea fish. Here, we employ all-atom molecular simulations and high-level quantum chemistry calculations to rationalize how chlorin e6 (Ce6), widely used in photodynamic therapy although accompanied by enhanced visual sensitivity, mediates vision in the dark, shining light on a fascinating but largely unknown molecular mechanism. First, we identify persistent interaction sites between Ce6 and the extracellular loops of rhodopsin, the transmembrane photoreceptor protein responsible for the first steps in vision. Triggered by Ce6 deep-red light absorption, the retinal within rhodopsin can be isomerized thus starting the visual phototransduction cascade. Our data largely exclude previously hypothesized energy-transfer mechanisms while clearly lending credence to a retinal isomerization indirectly triggered by singlet oxygen, proposing an alternative mechanism to rationalize photosensitizer-mediated night vision.

Published
2019
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6. Mechanism of the allosteric activation of the ClpP protease machinery by substrates and active-site inhibitors

Author

Audrey Hessel, Katharina Weinhäupl, Adrián Velázquez-Campoy, Christophe Chipot, Cécile Morlot, Paul Schanda, Jan Felix, François Dehez, Olga Abian, Hugo Pacheco de Freitas Fraga, Irina Gutsche, Diego F. Gauto, Instituto de Investigação e Inovação em Saúde, Laboratory for Protein Biochemistry and Biomolecular Engineering, Department of Biochemistry, Physiology and Microbiology, Universiteit Gent = Ghent University [Belgium] (UGENT), Institut de biologie structurale (IBS - UMR 5075 ), 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)-Centre National de la Recherche Scientifique (CNRS), Laboratoire de Physique et Chimie Théoriques (LPCT), Institut de Chimie du CNRS (INC)-Université de Lorraine (UL)-Centre National de la Recherche Scientifique (CNRS), Department of Physics [Illinois at Urbana-Champaign, USA], University of Illinois at Urbana-Champaign [Urbana], University of Illinois System-University of Illinois System, Laboratoire International Associé CNRS and University of Illinois at Urbana−Champaign, Vandoeuvre-les-Nancy F-54506, France., Unidad Asociada IQFR-CSIC-BIFI [Zaragoza, Spain], University of Zaragoza - Universidad de Zaragoza [Zaragoza]-Instituto de Biocomputación y Física de Sistemas Complejos - BIFI [Zaragoza, Spain], Grenoble Partnership for Structural Biology (PSB), Innovative EM/NMR approach for the characterization of the drug target ClpP APPID: 301, 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), Centre National de la Recherche Scientifique (France), Agence Nationale de la Recherche (France), Ministerio de Economía y Competitividad (España), Instituto de Salud Carlos III, European Science Foundation, European Commission, SCOAP, Universiteit Gent = Ghent University (UGENT), Centre National de la Recherche Scientifique (CNRS)-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), and University of Illinois System

Subjects
DYNAMICS, [SDV]Life Sciences [q-bio], medicine.medical_treatment, Crystallography, X-Ray, Biochemistry, 01 natural sciences, Serine, Structural Biology, Catalytic Domain, CRYSTAL-STRUCTURE, Research Articles, ComputingMilieux_MISCELLANEOUS, chemistry.chemical_classification, 0303 health sciences, Multidisciplinary, biology, Chemistry, Thermus thermophilus / enzymology, SciAdv r-articles, Endopeptidase Clp, Bacterial Proteins / chemistry, 3. Good health, INSIGHTS, Drug development, ESCHERICHIA-COLI, NMR-SPECTROSCOPY, Endopeptidase Clp / antagonists & inhibitors, Research Article, medicine.drug, PROTEINS, Protein subunit, Allosteric regulation, TUBERCULOSIS, 010402 general chemistry, 03 medical and health sciences, Bacterial Proteins, Allosteric Regulation, medicine, Protease Inhibitors, Bacterial Proteins / antagonists & inhibitors, 030304 developmental biology, COMPLEX, Protease, 010405 organic chemistry, Thermus thermophilus, Biology and Life Sciences, Active site, Isothermal titration calorimetry, 0104 chemical sciences, MODEL, SERINE-PROTEASE, Enzyme, Endopeptidase Clp / chemistry, Chaperone (protein), Proteasome inhibitor, biology.protein, Biophysics, Protease Inhibitors / chemistry
Abstract

18 pags., 6 figs., 1 tab. -- Open Access funded by Creative Commons Atribution Licence 4.0, Coordinated conformational transitions in oligomeric enzymatic complexes modulate function in response to substrates and play a crucial role in enzyme inhibition and activation. Caseinolytic protease (ClpP) is a tetradecameric complex, which has emerged as a drug target against multiple pathogenic bacteria. Activation of different ClpPs by inhibitors has been independently reported from drug development efforts, but no rationale for inhibitor-induced activation has been hitherto proposed. Using an integrated approach that includes x-ray crystallography, solid- and solution-state nuclear magnetic resonance, molecular dynamics simulations, and isothermal titration calorimetry, we show that the proteasome inhibitor bortezomib binds to the ClpP active-site serine, mimicking a peptide substrate, and induces a concerted allosteric activation of the complex. The bortezomib-activated conformation also exhibits a higher affinity for its cognate unfoldase ClpX. We propose a universal allosteric mechanism, where substrate binding to a single subunit locks ClpP into an active conformation optimized for chaperone association and protein processive degradation., This work used the platforms of the Grenoble Instruct center (ISBG; UMS 3518 CNRS-CEA-UJF-EMBL) with support from INSTRUCT (“Innovative EM/NMR approach for the characterization of the drug target ClpP APPID: 301“), FRISBI (ANR-10-INSB-05-02), and GRAL (ANR-10-LABX-49-01) within the Grenoble Partnership for Structural Biology (PSB). We thank the ESRF for beamtime at ID30A and ID23-1. Funding: This work was supported by Spanish Ministerio de Economia y Competitividad (BFU2016-78232-P) and Instituto de Salud Carlos III co-funded by European Union (PI15/00663 and PI18/00349, ERDF/ ESF, “Investing in your future”). This work was financially supported by the European Research Council (ERC-Stg-2012-311318 to P.S.). J.F. is supported by an EMBO long-term post-doctoral fellowship (ALTF441-2017).

Published
2019
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7. Triggering Tautomerization of Curcumin by Confinement into Liposomes

Author

Ewa Rogalska, Stéphane Parant, Maxime Girardon, Antonio Monari, Christophe Chipot, Andreea Pasc, Nadia Canilho, François Dehez, Laboratoire Lorrain de Chimie Moléculaire (L2CM), Institut de Chimie du CNRS (INC)-Université de Lorraine (UL)-Centre National de la Recherche Scientifique (CNRS), Laboratoire de Physique et Chimie Théoriques (LPCT), 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, PhotoNS, and Université de Lorraine (UL)-Centre National de la Recherche Scientifique (CNRS)

Subjects
Liposome, food.ingredient, 010304 chemical physics, Organic Chemistry, 02 engineering and technology, 021001 nanoscience & nanotechnology, Photochemistry, 01 natural sciences, Fluorescence, Tautomer, Lecithin, Analytical Chemistry, chemistry.chemical_compound, food, chemistry, 0103 physical sciences, Curcumin, [CHIM]Chemical Sciences, Physical and Theoretical Chemistry, 0210 nano-technology, ComputingMilieux_MISCELLANEOUS
Abstract

International audience

Published
2019
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8. Conformational transitions of the serotonin 5-HT3 receptor

Author

Emmanuelle Neumann, Ghérici Hassaine, Hugues Nury, Jonathan Perot, Anders A. Jensen, François Dehez, Christophe Chipot, Jacques Neyton, Lucie Polovinkin, Pierre-Jean Corringer, Guy Schoehn, Solène N Lefebvre, Institut de biologie structurale (IBS - UMR 5075 ), 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)-Centre National de la Recherche Scientifique (CNRS), Theranyx SA (Theranyx), 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), Récepteurs Canaux - Channel Receptors, Centre National de la Recherche Scientifique (CNRS)-Institut Pasteur [Paris], Laboratoire de Physique et Chimie Théoriques (LPCT), Institut de Chimie du CNRS (INC)-Université de Lorraine (UL)-Centre National de la Recherche Scientifique (CNRS), Department of Physics [Illinois at Urbana-Champaign, USA], University of Illinois at Urbana-Champaign [Urbana], University of Illinois System-University of Illinois System, Laboratoire International Associé (LIA), University of Illinois System-University of Illinois System-Centre National de la Recherche Scientifique (CNRS), The work was funded by the Marie Curie CIG NeuroPenta and ERC Starting grant 637733 (to H.N.). It used the platforms of the Grenoble Instruct-ERIC Center (ISBG: UMS 3518 CNRS-CEA-UGA-EMBL) with support from FRISBI (ANR-10 INSB-05-02) and GRAL (ANR-10-LABX-49-01) within the Grenoble PSB. The electron microscopy facility is supported by the Rhône-Alpes Region, the FRM, the FEDER and the GIS-IBISA., 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), European Project: 637733,H2020,ERC-2014-STG,PentaBrain(2015), Centre National de la Recherche Scientifique (CNRS)-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), University of Copenhagen = Københavns Universitet (UCPH)-University of Copenhagen = Københavns Universitet (UCPH), and Institut Pasteur [Paris] (IP)-Centre National de la Recherche Scientifique (CNRS)

Subjects
0301 basic medicine, Multidisciplinary, Allosteric modulator, [SDV.BBM.BS]Life Sciences [q-bio]/Biochemistry, Molecular Biology/Structural Biology [q-bio.BM], Allosteric regulation, Gating, 03 medical and health sciences, chemistry.chemical_compound, 030104 developmental biology, 0302 clinical medicine, chemistry, Biophysics, Serotonin, Binding site, Neurotransmitter, Receptor, 030217 neurology & neurosurgery, Ion channel
Abstract

International audience; The serotonin 5-HT3 receptor is a pentameric ligand-gated ion channel (pLGIC). It belongs to a large family of receptors that function as allosteric signal transducers across the plasma membrane1,2; upon binding of neurotransmitter molecules to extracellular sites, the receptors undergo complex conformational transitions that result in transient opening of a pore permeable to ions. 5-HT3 receptors are therapeutic targets for emesis and nausea, irritable bowel syndrome and depression3. In spite of several reported pLGIC structures4-8, no clear unifying view has emerged on the conformational transitions involved in channel gating. Here we report four cryo-electron microscopy structures of the full-length mouse 5-HT3 receptor in complex with the anti-emetic drug tropisetron, with serotonin, and with serotonin and a positive allosteric modulator, at resolutions ranging from 3.2 Å to 4.5 Å. The tropisetron-bound structure resembles those obtained with an inhibitory nanobody5 or without ligand9. The other structures include an 'open' state and two ligand-bound states. We present computational insights into the dynamics of the structures, their pore hydration and free-energy profiles, and characterize movements at the gate level and cation accessibility in the pore. Together, these data deepen our understanding of the gating mechanism of pLGICs and capture ligand binding in unprecedented detail.

Published
2018
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9. Dynamics and interactions of AAC3 in DPC are not functionally relevant

Author

Christophe Chipot, Vilius Kurauskas, François Dehez, Beate Bersch, Paul Schanda, Audrey Hessel, 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), Laboratoire de Physique et Chimie Théoriques (LPCT), Institut de Chimie du CNRS (INC)-Université de Lorraine (UL)-Centre National de la Recherche Scientifique (CNRS), 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, Université Grenoble Alpes [2016-2019] (UGA [2016-2019])-Institut de Recherche Interdisciplinaire de Grenoble (IRIG), and 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)

Subjects
0301 basic medicine, biology, Membrane transport protein, Dynamics (mechanics), Nuclear magnetic resonance spectroscopy, 010402 general chemistry, 01 natural sciences, 0104 chemical sciences, 03 medical and health sciences, chemistry.chemical_compound, Adenosine diphosphate, 030104 developmental biology, chemistry, Structural Biology, biology.protein, Biophysics, [SDV.BBM]Life Sciences [q-bio]/Biochemistry, Molecular Biology, Molecular Biology, Adenosine triphosphate, ComputingMilieux_MISCELLANEOUS
Abstract

International audience

Published
2018
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10. α-Helix Unwinding as Force Buffer in Spectrins

Author

Hirohide Takahashi, Felix Rico, Simon Scheuring, Christophe Chipot, BIO-AFM-LAB Bio Atomic Force Microscopy Laboratory (Bio-AFM-Lab), Aix Marseille Université (AMU)-Institut National de la Santé et de la Recherche Médicale (INSERM), Weill Medical College of Cornell University [New York], Laboratoire International Associé Centre National de la Recherche Scientifique, University of Illinois at Urbana-Champaign [Urbana], University of Illinois System-University of Illinois System, Department of Physics [Illinois at Urbana-Champaign, USA], 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
0301 basic medicine, [PHYS.PHYS.PHYS-BIO-PH]Physics [physics]/Physics [physics]/Biological Physics [physics.bio-ph], General Physics and Astronomy, macromolecular substances, Spring (mathematics), 01 natural sciences, 03 medical and health sciences, Molecular dynamics, unwinding, 0103 physical sciences, General Materials Science, Spectrin, Cytoskeleton, High-Speed Force Spectroscopy, Actin, unfolding, 010304 chemical physics, Chemistry, General Engineering, Force spectroscopy, 030104 developmental biology, Membrane, Helix, Biophysics, Force Spectroscopy, AFM
Abstract

Spectrins are cytoskeletal proteins located at the inner face of the plasma membrane, making connections between membrane anchors and the actin cortex, and between actin filaments. Spectrins share a common structure forming a bundle of 3 α-helices and play a major role during cell deformation. Here, we used high-speed force spectroscopy and steered molecular dynamics simulations to understand the mechanical stability of spectrin, revealing a molecular force buffering function. We find that spectrin acts as a soft spring at short extensions (70-100 Å). Under continuous external stretching, its α-helices unwind, leading to a viscous mechanical response over larger extensions (100-300 Å), represented by a constant-force plateau in force/extension curves. This viscous force buffering emerges from a quasi-equilibrium competition between disruption and re-formation of α-helical hydrogen bonds. Our results suggest that, in contrast to β-sheet proteins, which unfold in a catastrophic event, α-helical spectrins dominantly unwind, providing a viscous force buffer over extensions about 5 times their folded length.

Published
2018
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11. Mitochondrial ADP/ATP Carrier in Dodecylphosphocholine Binds Cardiolipins with Non-native Affinity

Author

Christophe Chipot, François Dehez, Edmund R.S. Kunji, Martin S. King, Paul Schanda, Laboratoire International Associé Centre National de la Recherche Scientifique, University of Illinois at Urbana-Champaign [Urbana], University of Illinois System-University of Illinois System, Institut de biologie structurale (IBS - UMR 5075 ), 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)-Centre National de la Recherche Scientifique (CNRS), Wellcome Trust-Medical Research Council Cambridge Stem Cell Institute, University of Cambridge [UK] (CAM), King, Martin [0000-0001-6030-5154], Kunji, Edmund [0000-0002-0610-4500], Apollo - University of Cambridge Repository, Centre National de la Recherche Scientifique (CNRS)-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), Laboratoire International Associé (LIA), University of Illinois System-University of Illinois System-Centre National de la Recherche Scientifique (CNRS), Structure et Réactivité des Systèmes Moléculaires Complexes (SRSMC), Centre National de la Recherche Scientifique (CNRS)-Université de Lorraine (UL), MRC Mitochondrial Biology Unit, Dunn Human Nutrition Unit, Medical Research Council, and Department of Physics [Illinois at Urbana-Champaign, USA]

Subjects
0301 basic medicine, Cardiolipins, Phosphorylcholine, Biophysics, Biology, Article, 03 medical and health sciences, Molecular dynamics, Protein structure, [CHIM]Chemical Sciences, Binding selectivity, ComputingMilieux_MISCELLANEOUS, reproductive and urinary physiology, 030102 biochemistry & molecular biology, [SDV.BBM.BS]Life Sciences [q-bio]/Biochemistry, Molecular Biology/Structural Biology [q-bio.BM], Yeast, Mitochondria, 030104 developmental biology, Membrane protein, Biochemistry, Solubilization, embryonic structures, ATP–ADP translocase, Mitochondrial ADP, ATP Translocases, Protein Binding
Abstract

International audience; Biophysical investigation of membrane proteins generally requires their extraction from native sources using detergents, a step that can lead, possibly irreversibly, to protein denaturation. The propensity of dodecylphosphocholine (DPC), a detergent widely utilized in NMR studies of membrane proteins, to distort their structure has been the subject of much controversy. It has been recently proposed that the binding specificity of the yeast mitochondrial ADP/ATP carrier (yAAC3) toward cardiolipins is preserved in DPC, thereby suggesting that DPC is a suitable environment in which to study membrane proteins. In this communication, we used all-atom molecular dynamics simulations to investigate the specific binding of cardiolipins to yAAC3. Our data demonstrate that the interaction interface observed in a native-like environment differs markedly from that inferred from an NMR investigation in DPC, implying that in this detergent, the protein structure is distorted. We further investigated yAAC3 solubilized in DPC and in the milder dodecylmaltoside with thermal-shift assays. The loss of thermal transition observed in DPC confirms that the protein is no longer properly folded in this environment.

Published
2017
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12. A central cavity within the holo-translocon suggests a mechanism for membrane protein insertion

Author

Ian Collinson, Aurélien Deniaud, Juri Rappsilber, Patrick Schultz, Nathan R. Zaccai, Manikandan Karuppasamy, Remy Martin, Kèvin Knoops, Juan Zou, Christiane Schaffitzel, Klaus Schulten, Giuseppe Zaccai, Imre Berger, Gabor Papai, Qiyang Jiang, Mathieu Botte, Jelger A. Lycklama a Nijeholt, Abhishek Roy, Laboratoire européen de biologie moléculaire - European Molecular Biology Laboratory (EMBL Grenoble), European Molecular Biology Laboratory [Grenoble] (EMBL), School of Biochemistry, University of Bristol [Bristol], Institut de Génétique et de Biologie Moléculaire et Cellulaire (IGBMC), Université de Strasbourg (UNISTRA)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS), Wellcome Trust Centre for Cell Biology, University of Edinburgh, Department of Physics, University of Illinois at Urbana-Champaign [Urbana], University of Illinois System-University of Illinois System, Department of Physics [Illinois at Urbana-Champaign, USA], Institut de génétique et biologie moléculaire et cellulaire (IGBMC), Université Louis Pasteur - Strasbourg I-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS), Institut de biologie structurale (IBS - UMR 5075 ), 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)-Centre National de la Recherche Scientifique (CNRS), Centre National de la Recherche Scientifique (CNRS)-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), Thomas, Frank, Zaccai, Nathan [0000-0002-1476-2044], and Apollo - University of Cambridge Repository

Subjects
Models, Molecular, Protein Conformation, alpha-Helical, 0301 basic medicine, Methanocaldococcus, [SDV.BBM.BS] Life Sciences [q-bio]/Biochemistry, Molecular Biology/Structural Biology [q-bio.BM], Genetic Vectors, Gene Expression, membrane proteins, Article, Substrate Specificity, 03 medical and health sciences, Scattering, Small Angle, biophysical chemistry, Escherichia coli, Protein Interaction Domains and Motifs, Cloning, Molecular, Binding Sites, Multidisciplinary, electron microscopy, 030102 biochemistry & molecular biology, biology, [SDV.BBM.BS]Life Sciences [q-bio]/Biochemistry, Molecular Biology/Structural Biology [q-bio.BM], Escherichia coli Proteins, Thermus thermophilus, Cryoelectron Microscopy, Membrane Transport Proteins, SAXS, Periplasmic space, biology.organism_classification, Translocon, Recombinant Proteins, Transport protein, Neutron Diffraction, Protein Transport, 030104 developmental biology, Biochemistry, Membrane protein, Structural Homology, Protein, Chaperone (protein), ddc:000, biology.protein, Biophysics, Protein Conformation, beta-Strand, SEC Translocation Channels, Protein Binding, Biophysical chemistry
Abstract

The conserved SecYEG protein-conducting channel and the accessory proteins SecDF-YajC and YidC constitute the bacterial holo-translocon (HTL), capable of protein-secretion and membrane-protein insertion. By employing an integrative approach combining small-angle neutron scattering (SANS), low-resolution electron microscopy and biophysical analyses we determined the arrangement of the proteins and lipids within the super-complex. The results guided the placement of X-ray structures of individual HTL components and allowed the proposal of a model of the functional translocon. Their arrangement around a central lipid-containing pool conveys an unexpected, but compelling mechanism for membrane-protein insertion. The periplasmic domains of YidC and SecD are poised at the protein-channel exit-site of SecY, presumably to aid the emergence of translocating polypeptides. The SecY lateral gate for membrane-insertion is adjacent to the membrane ‘insertase’ YidC. Absolute-scale SANS employing a novel contrast-match-point analysis revealed a dynamic complex adopting open and compact configurations around an adaptable central lipid-filled chamber, wherein polytopic membrane-proteins could fold, sheltered from aggregation and proteolysis.

Published
2017
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13. Resolution Dependence of Magnetorotational Turbulence in the Isothermal Stratified Shearing Box

Author

Benjamin R. Ryan, Pierre Kestener, Sebastien Fromang, Charles F. Gammie, Astrophysique Interprétation Modélisation (AIM (UMR_7158 / UMR_E_9005 / UM_112)), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Institut national des sciences de l'Univers (INSU - CNRS)-Université Paris Diderot - Paris 7 (UPD7)-Centre National de la Recherche Scientifique (CNRS), Maison de la Simulation (MDLS), Université de Versailles Saint-Quentin-en-Yvelines (UVSQ)-Université Paris-Sud - Paris 11 (UP11)-Institut National de Recherche en Informatique et en Automatique (Inria)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS), Centre National de la Recherche Scientifique (CNRS)-Institut national des sciences de l'Univers (INSU - CNRS)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Paris Diderot - Paris 7 (UPD7), Université de Versailles Saint-Quentin-en-Yvelines (UVSQ)-Institut National de Recherche en Informatique et en Automatique (Inria)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS), Department of Physics [Illinois at Urbana-Champaign, USA], University of Illinois at Urbana-Champaign [Urbana], University of Illinois System-University of Illinois System, Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Institut national des sciences de l'Univers (INSU - CNRS)-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS)-Université Paris Cité (UPCité), Centre National de la Recherche Scientifique (CNRS)-Université Paris-Saclay-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Institut National de Recherche en Informatique et en Automatique (Inria)-Université de Versailles Saint-Quentin-en-Yvelines (UVSQ), Laboratoire AIM, Université Paris Diderot - Paris 7 ( UPD7 ) -Centre d'Etudes de Saclay, Maison de la Simulation ( MDLS ), Centre National de la Recherche Scientifique ( CNRS ) -Université Paris-Saclay-Commissariat à l'énergie atomique et aux énergies alternatives ( CEA ) -Institut National de Recherche en Informatique et en Automatique ( Inria ) -Université Paris-Sud - Paris 11 ( UP11 ) -Université de Versailles Saint-Quentin-en-Yvelines ( UVSQ ), and Centre National de la Recherche Scientifique (CNRS)-Université Paris-Saclay-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Institut National de Recherche en Informatique et en Automatique (Inria)-Université Paris-Sud - Paris 11 (UP11)-Université de Versailles Saint-Quentin-en-Yvelines (UVSQ)

Subjects
Angular momentum, 010504 meteorology & atmospheric sciences, [ PHYS.ASTR ] Physics [physics]/Astrophysics [astro-ph], FOS: Physical sciences, 01 natural sciences, accretion, Magnetorotational instability, 0103 physical sciences, Shear stress, 010303 astronomy & astrophysics, 0105 earth and related environmental sciences, Shearing (physics), Physics, High Energy Astrophysical Phenomena (astro-ph.HE), Turbulence, accretion disks, turbulence, Astronomy and Astrophysics, Scale height, Computational physics, Space and Planetary Science, Magnetohydrodynamics, Astrophysics - High Energy Astrophysical Phenomena, magnetohydrodynamics, [PHYS.ASTR]Physics [physics]/Astrophysics [astro-ph], Dimensionless quantity
Abstract

Magnetohydrodynamic (MHD) turbulence driven by the magnetorotational instability can provide diffusive transport of angular momentum in astrophysical disks, and a widely studied computational model for this process is the ideal, stratified, isothermal shearing box. Here we report results of a convergence study of such boxes up to a resolution of $N = 256$ zones per scale height, performed on blue waters at NCSA with ramses-gpu. We find that the time and vertically integrated dimensionless shear stress $\overline{\alpha} \sim N^{-1/3}$, i.e. the shear stress is resolution dependent. We also find that the magnetic field correlation length decreases with resolution, $\lambda \sim N^{-1/2}$. This variation is strongest at the disk midplane. We show that our measurements of $\alpha$ are consistent with earlier studies. We discuss possible reasons for the lack of convergence., Comment: 35 pages, 9 figures, submitted to ApJ. Comments welcome

Published
2017
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14. Adaptive Multilevel Splitting Method for Molecular Dynamics Calculation of Benzamidine-Trypsin Dissociation Time

Author

Christopher G. Mayne, Tony Lelièvre, Ivan Teo, Klaus Schulten, Department of Physics [Illinois at Urbana-Champaign, USA], University of Illinois at Urbana-Champaign [Urbana], University of Illinois System-University of Illinois System, The Beckman Institute for Advanced Science and Technology, Centre d'Enseignement et de Recherche en Mathématiques et Calcul Scientifique (CERMICS), École des Ponts ParisTech (ENPC), MATHematics for MatERIALS (MATHERIALS), École des Ponts ParisTech (ENPC)-École des Ponts ParisTech (ENPC)-Inria de Paris, Institut National de Recherche en Informatique et en Automatique (Inria)-Institut National de Recherche en Informatique et en Automatique (Inria), European Project: 614492,EC:FP7:ERC,ERC-2013-CoG,MSMATH(2014), Inria de Paris, Institut National de Recherche en Informatique et en Automatique (Inria)-Institut National de Recherche en Informatique et en Automatique (Inria)-Centre d'Enseignement et de Recherche en Mathématiques et Calcul Scientifique (CERMICS), and École des Ponts ParisTech (ENPC)-École des Ponts ParisTech (ENPC)

Subjects
0301 basic medicine, Field (physics), Computer science, Monte Carlo method, Molecular Dynamics Simulation, Ligands, 01 natural sciences, Article, Dissociation (chemistry), Benzamidine, 03 medical and health sciences, Search engine, Molecular dynamics, chemistry.chemical_compound, 0103 physical sciences, Trypsin, Rare Event Sampling, Statistical physics, Physical and Theoretical Chemistry, Simulation, 010304 chemical physics, Sampling (statistics), Benzamidines, Computer Science Applications, 030104 developmental biology, chemistry, Monte Carlo Method, Algorithms, [MATH.MATH-NA]Mathematics [math]/Numerical Analysis [math.NA], Protein Binding
Abstract

International audience Adaptive multilevel splitting (AMS) is a rare event sampling method that requires minimal parameter tuning and allows unbiased sampling of transition pathways of a given rare event. Previous simulation studies have verified the efficiency and accuracy of AMS in the calculation of transition times for simple systems in both Monte Carlo and molecular dynamics (MD) simulations. Now, AMS is applied for the first time to an MD simulation of protein–ligand dissociation, representing a leap in complexity from the previous test cases. Of interest is the dissociation rate, which is typically too low to be accessible to conventional MD. The present study joins other recent efforts to develop advanced sampling techniques in MD to calculate dissociation rates, which are gaining importance in the pharmaceutical field as indicators of drug efficacy. The system investigated here, benzamidine bound to trypsin, is an example common to many of these efforts. The AMS estimate of the dissociation rate was found to be (2.6 ± 2.4) × 102 s–1, which compares well with the experimental value.

Published
2016
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15. Stability of Glassy and Ferroelectric States in the Relaxors PbMg1/3Nb2/3O3 and PbMg1/3Nb2/3O3-12% PbTiO3

Author

Colla, Eugene V., Vigil, D., Timmerwilke, J., Weissman, Michael B., Viehland, Dwight D., Dkhil, B., Laboratoire Structures, Propriétés et Modélisation des solides (SPMS), CentraleSupélec-Centre National de la Recherche Scientifique (CNRS), Department of Physics [Illinois at Urbana-Champaign, USA], University of Illinois at Urbana-Champaign [Urbana], University of Illinois System-University of Illinois System, Department of Materials Science and Engineering [Blacksburg] (MSE), Virginia Tech [Blacksburg], Institut de Chimie du CNRS (INC)-CentraleSupélec-Centre National de la Recherche Scientifique (CNRS), Materials Science and Engineering (MSE), and Virginia Tech

Subjects
Condensed Matter - Materials Science, Phase transitions, Polarization, Physics, [PHYS.COND.CM-MS]Physics [physics]/Condensed Matter [cond-mat]/Materials Science [cond-mat.mtrl-sci], Materials Science (cond-mat.mtrl-sci), FOS: Physical sciences, PACS: 77.80.-e, 75.10.Nr, 77.84.-s, [PHYS.PHYS.PHYS-CHEM-PH]Physics [physics]/Physics [physics]/Chemical Physics [physics.chem-ph]
Abstract

The stability of the disordered glassy phase in the relaxors PbMg1/3Nb2/3O3 and (PbMg1/3Nb2/3O3)0.88(PbTiO3)0.12, called PMN and PMN-PT, was investigated by preparing partially polarized samples and allowing them to age at zero field in the temperature range for which the phase is history-dependent. The PMN-PT polarization would spontaneously increase until long-range order formed, first appearing as giant polarization noise. Thus the thermodynamically stable phase in PMN-PT appears to be ferroelectric. In contrast, a PMN sample lacking the sharp first-order field-driven transition found in some other samples spontaneously depolarized, consistent with its glassy state being thermodynamically stable. Detailed thermal depolarization results in PMN show two distinct broad peaks as well as a small fraction of material with a distribution of abrupt melting transitions., submitted to Phys. Rev. B. 9 text pages + 10 figs

Published
2007
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16. Quasivertical line in the phase diagram of single crystals of Pb Mg1 3 Nb2 3 O3 -x PbTiO3 (x=0.00, 0.06, 0.13, and 0.24) with a giant piezoelectric effect

Author

Raevskaya, S.I., Emelyanov, A.S., Savenko, F.I., Panchelyuga, M.S., Raevski, I.P., Prosandeev, S.A., Colla, E.V., Chen, H., Lu, S.G., Blinc, R., Kutnjak, Z., Gemeiner, P., Dkhil, B., Kamzina, L.S., Southern Federal University [Rostov-on-Don] (SFEDU), University of Arkansas for Medical Sciences (UAMS), Department of Physics [Illinois at Urbana-Champaign, USA], University of Illinois at Urbana-Champaign [Urbana], University of Illinois System-University of Illinois System, Tunghai University [Taichung], City University of Hong Kong [Hong Kong] (CUHK), Jozef Stefan Institute [Ljubljana] (IJS), Laboratoire Structures, Propriétés et Modélisation des solides (SPMS), Institut de Chimie du CNRS (INC)-CentraleSupélec-Centre National de la Recherche Scientifique (CNRS), A.F. Ioffe Physical-Technical Institute, and Russian Academy of Sciences [Moscow] (RAS)

Subjects
[SPI.MAT]Engineering Sciences [physics]/Materials
Abstract

We show that the phase diagram of the (001) Pb Mg1 3 Nb2 3 O3 -x PbTiO3 (PMN- x PT) (x=0.00, 0.06, 0.13, and 0.24) and (111) PMN-0.24PT lead-magnesium niobate mixed with lead titanate possesses a quasivertical line in the E electric field - T temperature plot, which hardly depends on the field. The existence of this line has been confirmed by independent studies of single crystals grown in different laboratories, by measuring the dielectric permittivity, compliances, and optical transmission, also in different laboratories. A thermal hysteresis inherent to first order phase transitions complicates the phase diagram. The piezoelectric coefficients of the (001) PMN- x PT (x = 0.06 and 0.13) have two peaks versus temperature, at finite fields. The first peak is due to the quasivertical phase boundary. The second is in the vicinity of a turning point of the Tm (E) temperature of the dielectric permittivity diffuse maximum. We show that the second peak prevails at reasonable fields, and the piezoelectric coefficients have comparatively large values at this peak, even at small x. © 2007 The American Physical Society.

Published
2007
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