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Betancurt-Anzola L, Martínez-Carranza M, Delarue M, Zatopek KM, Gardner AF, Sauguet L. Molecular basis for proofreading by the unique exonuclease domain of Family-D DNA polymerases. Nat Commun 2023; 14:8306. [PMID: 38097591 PMCID: PMC10721889 DOI: 10.1038/s41467-023-44125-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2023] [Accepted: 11/30/2023] [Indexed: 12/17/2023] Open
Abstract
Replicative DNA polymerases duplicate entire genomes at high fidelity. This feature is shared among the three domains of life and is facilitated by their dual polymerase and exonuclease activities. Family D replicative DNA polymerases (PolD), found exclusively in Archaea, contain an unusual RNA polymerase-like catalytic core, and a unique Mre11-like proofreading active site. Here, we present cryo-EM structures of PolD trapped in a proofreading mode, revealing an unanticipated correction mechanism that extends the repertoire of protein domains known to be involved in DNA proofreading. Based on our experimental structures, mutants of PolD were designed and their contribution to mismatch bypass and exonuclease kinetics was determined. This study sheds light on the convergent evolution of structurally distinct families of DNA polymerases, and the domain acquisition and exchange mechanism that occurred during the evolution of the replisome in the three domains of life.
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Affiliation(s)
- Leonardo Betancurt-Anzola
- Architecture and Dynamics of Biological Macromolecules, Institut Pasteur, Université Paris Cité, CNRS, UMR 3528, Paris, France
- New England Biolabs Inc., 240 County Road, Ipswich, MA, 01938, USA
- New England Biolabs France, 5 Rue Henri Auguste Desbruères, 91000, Évry-Courcouronnes, France
- Sorbonne Université, Collège Doctoral, ED 515, Paris, France
| | - Markel Martínez-Carranza
- Architecture and Dynamics of Biological Macromolecules, Institut Pasteur, Université Paris Cité, CNRS, UMR 3528, Paris, France
| | - Marc Delarue
- Architecture and Dynamics of Biological Macromolecules, Institut Pasteur, Université Paris Cité, CNRS, UMR 3528, Paris, France
| | - Kelly M Zatopek
- New England Biolabs Inc., 240 County Road, Ipswich, MA, 01938, USA.
| | - Andrew F Gardner
- New England Biolabs Inc., 240 County Road, Ipswich, MA, 01938, USA.
| | - Ludovic Sauguet
- Architecture and Dynamics of Biological Macromolecules, Institut Pasteur, Université Paris Cité, CNRS, UMR 3528, Paris, France.
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2
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Hsieh YC, Delarue M, Orland H, Koehl P. Analyzing the Geometry and Dynamics of Viral Structures: A Review of Computational Approaches Based on Alpha Shape Theory, Normal Mode Analysis, and Poisson-Boltzmann Theories. Viruses 2023; 15:1366. [PMID: 37376665 DOI: 10.3390/v15061366] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2023] [Revised: 06/05/2023] [Accepted: 06/09/2023] [Indexed: 06/29/2023] Open
Abstract
The current SARS-CoV-2 pandemic highlights our fragility when we are exposed to emergent viruses either directly or through zoonotic diseases. Fortunately, our knowledge of the biology of those viruses is improving. In particular, we have more and more structural information on virions, i.e., the infective form of a virus that includes its genomic material and surrounding protective capsid, and on their gene products. It is important to have methods that enable the analyses of structural information on such large macromolecular systems. We review some of those methods in this paper. We focus on understanding the geometry of virions and viral structural proteins, their dynamics, and their energetics, with the ambition that this understanding can help design antiviral agents. We discuss those methods in light of the specificities of those structures, mainly that they are huge. We focus on three of our own methods based on the alpha shape theory for computing geometry, normal mode analyses to study dynamics, and modified Poisson-Boltzmann theories to study the organization of ions and co-solvent and solvent molecules around biomacromolecules. The corresponding software has computing times that are compatible with the use of regular desktop computers. We show examples of their applications on some outer shells and structural proteins of the West Nile Virus.
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Affiliation(s)
- Yin-Chen Hsieh
- Institute for Arctic and Marine Biology, Department of Biosciences, Fisheries, and Economics, UiT The Arctic University of Norway, 9037 Tromso, Norway
| | - Marc Delarue
- Institut Pasteur, Université Paris-Cité and CNRS, UMR 3528, Unité Architecture et Dynamique des Macromolécules Biologiques, 75015 Paris, France
| | - Henri Orland
- Institut de Physique Théorique, CEA, CNRS, Université Paris-Saclay, 91191 Gif-sur-Yvette, France
| | - Patrice Koehl
- Department of Computer Science, University of California, Davis, CA 95616, USA
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Czernecki D, Nourisson A, Legrand P, Delarue M. Reclassification of family A DNA polymerases reveals novel functional subfamilies and distinctive structural features. Nucleic Acids Res 2023; 51:4488-4507. [PMID: 37070157 PMCID: PMC10201439 DOI: 10.1093/nar/gkad242] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2022] [Revised: 03/07/2023] [Accepted: 03/24/2023] [Indexed: 04/19/2023] Open
Abstract
Family A DNA polymerases (PolAs) form an important and well-studied class of extant polymerases participating in DNA replication and repair. Nonetheless, despite the characterization of multiple subfamilies in independent, dedicated works, their comprehensive classification thus far is missing. We therefore re-examine all presently available PolA sequences, converting their pairwise similarities into positions in Euclidean space, separating them into 19 major clusters. While 11 of them correspond to known subfamilies, eight had not been characterized before. For every group, we compile their general characteristics, examine their phylogenetic relationships and perform conservation analysis in the essential sequence motifs. While most subfamilies are linked to a particular domain of life (including phages), one subfamily appears in Bacteria, Archaea and Eukaryota. We also show that two new bacterial subfamilies contain functional enzymes. We use AlphaFold2 to generate high-confidence prediction models for all clusters lacking an experimentally determined structure. We identify new, conserved features involving structural alterations, ordered insertions and an apparent structural incorporation of a uracil-DNA glycosylase (UDG) domain. Finally, genetic and structural analyses of a subset of T7-like phages indicate a splitting of the 3'-5' exo and pol domains into two separate genes, observed in PolAs for the first time.
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Affiliation(s)
- Dariusz Czernecki
- Institut Pasteur, Université Paris Cité, CNRS UMR 3528, Unit of Architecture and Dynamics of Biological Macromolecules, 75015 Paris, France
- Sorbonne Université, Collège Doctoral, ED 515, 75005 Paris, France
| | - Antonin Nourisson
- Institut Pasteur, Université Paris Cité, CNRS UMR 3528, Unit of Architecture and Dynamics of Biological Macromolecules, 75015 Paris, France
- Sorbonne Université, Collège Doctoral, ED 515, 75005 Paris, France
| | - Pierre Legrand
- Institut Pasteur, Université Paris Cité, CNRS UMR 3528, Unit of Architecture and Dynamics of Biological Macromolecules, 75015 Paris, France
- Synchrotron SOLEIL, L’Orme des Merisiers, 91190 Saint-Aubin, France
| | - Marc Delarue
- Institut Pasteur, Université Paris Cité, CNRS UMR 3528, Unit of Architecture and Dynamics of Biological Macromolecules, 75015 Paris, France
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4
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Madru C, Martínez-Carranza M, Laurent S, Alberti AC, Chevreuil M, Raynal B, Haouz A, Le Meur RA, Delarue M, Henneke G, Flament D, Krupovic M, Legrand P, Sauguet L. DNA-binding mechanism and evolution of replication protein A. Nat Commun 2023; 14:2326. [PMID: 37087464 PMCID: PMC10122647 DOI: 10.1038/s41467-023-38048-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2023] [Accepted: 04/13/2023] [Indexed: 04/24/2023] Open
Abstract
Replication Protein A (RPA) is a heterotrimeric single stranded DNA-binding protein with essential roles in DNA replication, recombination and repair. Little is known about the structure of RPA in Archaea, the third domain of life. By using an integrative structural, biochemical and biophysical approach, we extensively characterize RPA from Pyrococcus abyssi in the presence and absence of DNA. The obtained X-ray and cryo-EM structures reveal that the trimerization core and interactions promoting RPA clustering on ssDNA are shared between archaea and eukaryotes. However, we also identified a helical domain named AROD (Acidic Rpa1 OB-binding Domain), and showed that, in Archaea, RPA forms an unanticipated tetrameric supercomplex in the absence of DNA. The four RPA molecules clustered within the tetramer could efficiently coat and protect stretches of ssDNA created by the advancing replisome. Finally, our results provide insights into the evolution of this primordial replication factor in eukaryotes.
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Affiliation(s)
- Clément Madru
- Architecture and Dynamics of Biological Macromolecules, Institut Pasteur, Université Paris Cité, CNRS, UMR 3528, Paris, France
| | - Markel Martínez-Carranza
- Architecture and Dynamics of Biological Macromolecules, Institut Pasteur, Université Paris Cité, CNRS, UMR 3528, Paris, France
| | - Sébastien Laurent
- Univ Brest, Ifremer, CNRS, Biologie et Ecologie des Ecoystèmes marins profonds (BEEP), F-29280, Plouzané, France
| | - Alessandra C Alberti
- Architecture and Dynamics of Biological Macromolecules, Institut Pasteur, Université Paris Cité, CNRS, UMR 3528, Paris, France
| | - Maelenn Chevreuil
- Molecular Biophysics Platform, C2RT, Institut Pasteur, Université Paris Cité, CNRS, UMR 3528, Paris, France
| | - Bertrand Raynal
- Molecular Biophysics Platform, C2RT, Institut Pasteur, Université Paris Cité, CNRS, UMR 3528, Paris, France
| | - Ahmed Haouz
- Crystallography Platform, C2RT, Institut Pasteur, Université Paris Cité, CNRS, UMR 3528, Paris, France
| | - Rémy A Le Meur
- Biological NMR Platform & HDX, C2RT, Institut Pasteur, Université Paris Cité, CNRS, UMR 3528, Paris, France
| | - Marc Delarue
- Architecture and Dynamics of Biological Macromolecules, Institut Pasteur, Université Paris Cité, CNRS, UMR 3528, Paris, France
| | - Ghislaine Henneke
- Univ Brest, Ifremer, CNRS, Biologie et Ecologie des Ecoystèmes marins profonds (BEEP), F-29280, Plouzané, France
| | - Didier Flament
- Univ Brest, Ifremer, CNRS, Biologie et Ecologie des Ecoystèmes marins profonds (BEEP), F-29280, Plouzané, France
| | - Mart Krupovic
- Archaeal Virology Unit, Institut Pasteur, Université Paris Cité, CNRS, UMR 6047, Paris, France
| | - Pierre Legrand
- Architecture and Dynamics of Biological Macromolecules, Institut Pasteur, Université Paris Cité, CNRS, UMR 3528, Paris, France
- Synchrotron SOLEIL, HelioBio group, L'Orme des Merisiers, 91190, Saint-Aubin, France
| | - Ludovic Sauguet
- Architecture and Dynamics of Biological Macromolecules, Institut Pasteur, Université Paris Cité, CNRS, UMR 3528, Paris, France.
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5
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Bethlehem RAI, Seidlitz J, White SR, Vogel JW, Anderson KM, Adamson C, Adler S, Alexopoulos GS, Anagnostou E, Areces-Gonzalez A, Astle DE, Auyeung B, Ayub M, Bae J, Ball G, Baron-Cohen S, Beare R, Bedford SA, Benegal V, Beyer F, Blangero J, Blesa Cábez M, Boardman JP, Borzage M, Bosch-Bayard JF, Bourke N, Calhoun VD, Chakravarty MM, Chen C, Chertavian C, Chetelat G, Chong YS, Cole JH, Corvin A, Costantino M, Courchesne E, Crivello F, Cropley VL, Crosbie J, Crossley N, Delarue M, Delorme R, Desrivieres S, Devenyi GA, Di Biase MA, Dolan R, Donald KA, Donohoe G, Dunlop K, Edwards AD, Elison JT, Ellis CT, Elman JA, Eyler L, Fair DA, Feczko E, Fletcher PC, Fonagy P, Franz CE, Galan-Garcia L, Gholipour A, Giedd J, Gilmore JH, Glahn DC, Goodyer IM, Grant PE, Groenewold NA, Gunning FM, Gur RE, Gur RC, Hammill CF, Hansson O, Hedden T, Heinz A, Henson RN, Heuer K, Hoare J, Holla B, Holmes AJ, Holt R, Huang H, Im K, Ipser J, Jack CR, Jackowski AP, Jia T, Johnson KA, Jones PB, Jones DT, Kahn RS, Karlsson H, Karlsson L, Kawashima R, Kelley EA, Kern S, Kim KW, Kitzbichler MG, Kremen WS, Lalonde F, Landeau B, Lee S, Lerch J, Lewis JD, Li J, Liao W, Liston C, Lombardo MV, Lv J, Lynch C, Mallard TT, Marcelis M, Markello RD, Mathias SR, Mazoyer B, McGuire P, Meaney MJ, Mechelli A, Medic N, Misic B, Morgan SE, Mothersill D, Nigg J, Ong MQW, Ortinau C, Ossenkoppele R, Ouyang M, Palaniyappan L, Paly L, Pan PM, Pantelis C, Park MM, Paus T, Pausova Z, Paz-Linares D, Pichet Binette A, Pierce K, Qian X, Qiu J, Qiu A, Raznahan A, Rittman T, Rodrigue A, Rollins CK, Romero-Garcia R, Ronan L, Rosenberg MD, Rowitch DH, Salum GA, Satterthwaite TD, Schaare HL, Schachar RJ, Schultz AP, Schumann G, Schöll M, Sharp D, Shinohara RT, Skoog I, Smyser CD, Sperling RA, Stein DJ, Stolicyn A, Suckling J, Sullivan G, Taki Y, Thyreau B, Toro R, Traut N, Tsvetanov KA, Turk-Browne NB, Tuulari JJ, Tzourio C, Vachon-Presseau É, Valdes-Sosa MJ, Valdes-Sosa PA, Valk SL, van Amelsvoort T, Vandekar SN, Vasung L, Victoria LW, Villeneuve S, Villringer A, Vértes PE, Wagstyl K, Wang YS, Warfield SK, Warrier V, Westman E, Westwater ML, Whalley HC, Witte AV, Yang N, Yeo B, Yun H, Zalesky A, Zar HJ, Zettergren A, Zhou JH, Ziauddeen H, Zugman A, Zuo XN, Bullmore ET, Alexander-Bloch AF. Brain charts for the human lifespan. Nature 2022; 604:525-533. [PMID: 35388223 PMCID: PMC9021021 DOI: 10.1038/s41586-022-04554-y] [Citation(s) in RCA: 400] [Impact Index Per Article: 200.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2021] [Accepted: 02/16/2022] [Indexed: 02/02/2023]
Abstract
Over the past few decades, neuroimaging has become a ubiquitous tool in basic research and clinical studies of the human brain. However, no reference standards currently exist to quantify individual differences in neuroimaging metrics over time, in contrast to growth charts for anthropometric traits such as height and weight1. Here we assemble an interactive open resource to benchmark brain morphology derived from any current or future sample of MRI data ( http://www.brainchart.io/ ). With the goal of basing these reference charts on the largest and most inclusive dataset available, acknowledging limitations due to known biases of MRI studies relative to the diversity of the global population, we aggregated 123,984 MRI scans, across more than 100 primary studies, from 101,457 human participants between 115 days post-conception to 100 years of age. MRI metrics were quantified by centile scores, relative to non-linear trajectories2 of brain structural changes, and rates of change, over the lifespan. Brain charts identified previously unreported neurodevelopmental milestones3, showed high stability of individuals across longitudinal assessments, and demonstrated robustness to technical and methodological differences between primary studies. Centile scores showed increased heritability compared with non-centiled MRI phenotypes, and provided a standardized measure of atypical brain structure that revealed patterns of neuroanatomical variation across neurological and psychiatric disorders. In summary, brain charts are an essential step towards robust quantification of individual variation benchmarked to normative trajectories in multiple, commonly used neuroimaging phenotypes.
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Affiliation(s)
- R A I Bethlehem
- Autism Research Centre, Department of Psychiatry, University of Cambridge, Cambridge, UK.
- Brain Mapping Unit, Department of Psychiatry, University of Cambridge, Cambridge, UK.
| | - J Seidlitz
- Department of Psychiatry, University of Pennsylvania, Philadelphia, PA, USA.
- Department of Child and Adolescent Psychiatry and Behavioral Science, The Children's Hospital of Philadelphia, Philadelphia, PA, USA.
- Lifespan Brain Institute, The Children's Hospital of Philadelphia and Penn Medicine, Philadelphia, PA, USA.
| | - S R White
- Department of Psychiatry, University of Cambridge, Cambridge, UK
- MRC Biostatistics Unit, University of Cambridge, Cambridge, UK
| | - J W Vogel
- Department of Psychiatry, University of Pennsylvania, Philadelphia, PA, USA
- Lifespan Informatics & Neuroimaging Center, University of Pennsylvania, Philadelphia, PA, USA
| | - K M Anderson
- Department of Psychology, Yale University, New Haven, CT, USA
| | - C Adamson
- Developmental Imaging, Murdoch Children's Research Institute, Melbourne, Victoria, Australia
- Department of Medicine, Monash University, Melbourne, Victoria, Australia
| | - S Adler
- UCL Great Ormond Street Institute for Child Health, London, UK
| | - G S Alexopoulos
- Weill Cornell Institute of Geriatric Psychiatry, Department of Psychiatry, Weill Cornell Medicine, New York, USA
| | - E Anagnostou
- Department of Pediatrics University of Toronto, Toronto, Canada
- Holland Bloorview Kids Rehabilitation Hospital, Toronto, Canada
| | - A Areces-Gonzalez
- The Clinical Hospital of Chengdu Brain Science Institute, MOE Key Lab for NeuroInformation, University of Electronic Science and Technology of China, Chengdu, China
- University of Pinar del Río "Hermanos Saiz Montes de Oca", Pinar del Río, Cuba
| | - D E Astle
- MRC Cognition and Brain Sciences Unit, University of Cambridge, Cambridge, UK
| | - B Auyeung
- Autism Research Centre, Department of Psychiatry, University of Cambridge, Cambridge, UK
- Department of Psychology, School of Philosophy, Psychology and Language Sciences, University of Edinburgh, Edinburgh, UK
| | - M Ayub
- Queen's University, Department of Psychiatry, Centre for Neuroscience Studies, Kingston, Ontario, Canada
- University College London, Mental Health Neuroscience Research Department, Division of Psychiatry, London, UK
| | - J Bae
- Department of Neuropsychiatry, Seoul National University Bundang Hospital, Seongnam, Korea
| | - G Ball
- Developmental Imaging, Murdoch Children's Research Institute, Melbourne, Victoria, Australia
- Department of Paediatrics, University of Melbourne, Melbourne, Victoria, Australia
| | - S Baron-Cohen
- Autism Research Centre, Department of Psychiatry, University of Cambridge, Cambridge, UK
- Cambridge Lifetime Asperger Syndrome Service (CLASS), Cambridgeshire and Peterborough NHS Foundation Trust, Cambridge, UK
| | - R Beare
- Developmental Imaging, Murdoch Children's Research Institute, Melbourne, Victoria, Australia
- Department of Medicine, Monash University, Melbourne, Victoria, Australia
| | - S A Bedford
- Autism Research Centre, Department of Psychiatry, University of Cambridge, Cambridge, UK
| | - V Benegal
- Centre for Addiction Medicine, National Institute of Mental Health and Neurosciences (NIMHANS), Bengaluru, India
| | - F Beyer
- Department of Neurology, Max Planck Institute for Human Cognitive and Brain Sciences, Leipzig, Germany
| | - J Blangero
- Department of Human Genetics, South Texas Diabetes and Obesity Institute, University of Texas Rio Grande Valley, Edinburg, TX, USA
| | - M Blesa Cábez
- MRC Centre for Reproductive Health, University of Edinburgh, Edinburgh, UK
| | - J P Boardman
- MRC Centre for Reproductive Health, University of Edinburgh, Edinburgh, UK
| | - M Borzage
- Fetal and Neonatal Institute, Division of Neonatology, Children's Hospital Los Angeles, Department of Pediatrics, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
| | - J F Bosch-Bayard
- McGill Centre for Integrative Neuroscience, Ludmer Centre for Neuroinformatics and Mental Health, Montreal Neurological Institute, Montreal, Quebec, Canada
- McGill University, Montreal, Quebec, Canada
| | - N Bourke
- Department of Brain Sciences, Imperial College London, London, UK
- Care Research and Technology Centre, Dementia Research Institute, London, UK
| | - V D Calhoun
- Tri-institutional Center for Translational Research in Neuroimaging and Data Science (TReNDS), Georgia State University, Georgia Institute of Technology, and Emory University, Atlanta, GA, USA
| | - M M Chakravarty
- McGill University, Montreal, Quebec, Canada
- Computational Brain Anatomy (CoBrA) Laboratory, Cerebral Imaging Centre, Douglas Mental Health University Institute, Montreal, Quebec, Canada
| | - C Chen
- Penn Statistics in Imaging and Visualization Center, Department of Biostatistics, Epidemiology, and Informatics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - C Chertavian
- Lifespan Brain Institute, The Children's Hospital of Philadelphia and Penn Medicine, Philadelphia, PA, USA
| | - G Chetelat
- Normandie Univ, UNICAEN, INSERM, U1237, PhIND "Physiopathology and Imaging of Neurological Disorders", Institut Blood and Brain @ Caen-Normandie, Cyceron, Caen, France
| | - Y S Chong
- Singapore Institute for Clinical Sciences, Agency for Science, Technology and Research, Singapore, Singapore
- Department of Obstetrics and Gynaecology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
| | - J H Cole
- Centre for Medical Image Computing (CMIC), University College London, London, UK
- Dementia Research Centre (DRC), University College London, London, UK
| | - A Corvin
- Department of Psychiatry, Trinity College, Dublin, Ireland
| | - M Costantino
- Cerebral Imaging Centre, Douglas Mental Health University Institute, Verdun, Quebec, Canada
- Undergraduate program in Neuroscience, McGill University, Montreal, Quebec, Canada
| | - E Courchesne
- Department of Neuroscience, University of California, San Diego, San Diego, CA, USA
- Autism Center of Excellence, University of California, San Diego, San Diego, CA, USA
| | - F Crivello
- Institute of Neurodegenerative Disorders, CNRS UMR5293, CEA, University of Bordeaux, Bordeaux, France
| | - V L Cropley
- Melbourne Neuropsychiatry Centre, University of Melbourne, Melbourne, Victoria, Australia
| | - J Crosbie
- The Hospital for Sick Children, Toronto, Ontario, Canada
| | - N Crossley
- Department of Psychiatry, School of Medicine, Pontificia Universidad Católica de Chile, Santiago, Chile
- Department of Psychosis Studies, Institute of Psychiatry, Psychology and Neuroscience, King's College London, London, UK
- Instituto Milenio Intelligent Healthcare Engineering, Santiago, Chile
| | - M Delarue
- Normandie Univ, UNICAEN, INSERM, U1237, PhIND "Physiopathology and Imaging of Neurological Disorders", Institut Blood and Brain @ Caen-Normandie, Cyceron, Caen, France
| | - R Delorme
- Child and Adolescent Psychiatry Department, Robert Debré University Hospital, AP-HP, Paris, France
- Human Genetics and Cognitive Functions, Institut Pasteur, Paris, France
| | - S Desrivieres
- Social, Genetic and Developmental Psychiatry Centre, Institute of Psychiatry, Psychology and Neuroscience, King's College London, London, UK
| | - G A Devenyi
- Cerebral Imaging Centre, McGill Department of Psychiatry, Douglas Mental Health University Institute, Montreal, QC, Canada
- Department of Psychiatry, McGill University, Montreal, QC, Canada
| | - M A Di Biase
- Melbourne Neuropsychiatry Centre, University of Melbourne, Melbourne, Victoria, Australia
- Department of Psychiatry, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
| | - R Dolan
- Max Planck UCL Centre for Computational Psychiatry and Ageing Research, University College London, London, UK
- Wellcome Centre for Human Neuroimaging, London, UK
| | - K A Donald
- Division of Developmental Paediatrics, Department of Paediatrics and Child Health, Red Cross War Memorial Children's Hospital, Cape Town, South Africa
- Neuroscience Institute, University of Cape Town, Cape Town, South Africa
| | - G Donohoe
- Center for Neuroimaging, Cognition & Genomics (NICOG), School of Psychology, National University of Ireland Galway, Galway, Ireland
| | - K Dunlop
- Weil Family Brain and Mind Research Institute, Department of Psychiatry, Weill Cornell Medicine, New York, NY, USA
| | - A D Edwards
- Centre for the Developing Brain, King's College London, London, UK
- Evelina London Children's Hospital, London, UK
- MRC Centre for Neurodevelopmental Disorders, London, UK
| | - J T Elison
- Institute of Child Development, Department of Pediatrics, Masonic Institute for the Developing Brain, University of Minnesota, Minneapolis, MN, USA
| | - C T Ellis
- Department of Psychology, Yale University, New Haven, CT, USA
- Haskins Laboratories, New Haven, CT, USA
| | - J A Elman
- Department of Psychiatry, Center for Behavior Genetics of Aging, University of California, San Diego, La Jolla, CA, USA
| | - L Eyler
- Desert-Pacific Mental Illness Research Education and Clinical Center, VA San Diego Healthcare, San Diego, CA, USA
- Department of Psychiatry, University of California San Diego, Los Angeles, CA, USA
| | - D A Fair
- Institute of Child Development, Department of Pediatrics, Masonic Institute for the Developing Brain, University of Minnesota, Minneapolis, MN, USA
| | - E Feczko
- Institute of Child Development, Department of Pediatrics, Masonic Institute for the Developing Brain, University of Minnesota, Minneapolis, MN, USA
| | - P C Fletcher
- Department of Psychiatry, University of Cambridge, and Wellcome Trust MRC Institute of Metabolic Science, Cambridge Biomedical Campus, Cambridge, UK
- Cambridgeshire and Peterborough NHS Foundation Trust, Cambridge, UK
| | - P Fonagy
- Department of Clinical, Educational and Health Psychology, University College London, London, UK
- Anna Freud National Centre for Children and Families, London, UK
| | - C E Franz
- Department of Psychiatry, Center for Behavior Genetics of Aging, University of California, San Diego, La Jolla, CA, USA
| | | | - A Gholipour
- Computational Radiology Laboratory, Boston Children's Hospital, Boston, MA, USA
| | - J Giedd
- Department of Child and Adolescent Psychiatry, University of California, San Diego, San Diego, CA, USA
- Department of Psychiatry, University of California San Diego, San Diego, CA, USA
| | - J H Gilmore
- Department of Psychiatry, University of North Carolina, Chapel Hill, NC, USA
| | - D C Glahn
- Department of Psychiatry, Boston Children's Hospital and Harvard Medical School, Boston, MA, USA
- Harvard Medical School, Boston, MA, USA
| | - I M Goodyer
- Department of Psychiatry, University of Cambridge, Cambridge, UK
| | - P E Grant
- Division of Newborn Medicine and Neuroradiology, Fetal Neonatal Neuroimaging and Developmental Science Center, Boston Children's Hospital, Harvard Medical School, Boston, MA, USA
| | - N A Groenewold
- Neuroscience Institute, University of Cape Town, Cape Town, South Africa
- Department of Paediatrics and Child Health, Red Cross War Memorial Children's Hospital, SA-MRC Unit on Child & Adolescent Health, University of Cape Town, Cape Town, South Africa
| | - F M Gunning
- Weill Cornell Institute of Geriatric Psychiatry, Department of Psychiatry, Weill Cornell Medicine, New York, NY, USA
| | - R E Gur
- Department of Psychiatry, University of Pennsylvania, Philadelphia, PA, USA
- Lifespan Brain Institute, The Children's Hospital of Philadelphia and Penn Medicine, Philadelphia, PA, USA
| | - R C Gur
- Department of Psychiatry, University of Pennsylvania, Philadelphia, PA, USA
- Lifespan Brain Institute, The Children's Hospital of Philadelphia and Penn Medicine, Philadelphia, PA, USA
| | - C F Hammill
- The Hospital for Sick Children, Toronto, Ontario, Canada
- Mouse Imaging Centre, Toronto, Ontario, Canada
| | - O Hansson
- Clinical Memory Research Unit, Department of Clinical Sciences Malmö, Lund University, Malmö, Sweden
- Memory Clinic, Skåne University Hospital, Malmö, Sweden
| | - T Hedden
- Department of Neurology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Athinoula A. Martinos Center for Biomedical Imaging, Department of Radiology, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
| | - A Heinz
- Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Department of Psychiatry and Psychotherapy, Charité Campus Mitte, Berlin, Germany
| | - R N Henson
- Department of Psychiatry, University of Cambridge, Cambridge, UK
- MRC Cognition and Brain Sciences Unit, University of Cambridge, Cambridge, UK
| | - K Heuer
- Department of Neuropsychology, Max Planck Institute for Human Cognitive and Brain Sciences, Leipzig, Germany
- Université de Paris, Paris, France
| | - J Hoare
- Department of Psychiatry, University of Cape Town, Cape Town, South Africa
| | - B Holla
- Department of Integrative Medicine, NIMHANS, Bengaluru, India
- Accelerator Program for Discovery in Brain disorders using Stem cells (ADBS), Department of Psychiatry, NIMHANS, Bengaluru, India
| | - A J Holmes
- Departments of Psychology and Psychiatry, Yale University, New Haven, CT, USA
| | - R Holt
- Autism Research Centre, Department of Psychiatry, University of Cambridge, Cambridge, UK
| | - H Huang
- Radiology Research, Children's Hospital of Philadelphia, Philadelphia, PA, USA
- The Department of Radiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - K Im
- Department of Psychiatry, Boston Children's Hospital and Harvard Medical School, Boston, MA, USA
- Division of Newborn Medicine and Neuroradiology, Fetal Neonatal Neuroimaging and Developmental Science Center, Boston Children's Hospital, Harvard Medical School, Boston, MA, USA
| | - J Ipser
- Department of Psychiatry and Mental Health, Clinical Neuroscience Institute, University of Cape Town, Cape Town, South Africa
| | - C R Jack
- Department of Radiology, Mayo Clinic, Rochester, MN, USA
| | - A P Jackowski
- Department of Psychiatry, Universidade Federal de São Paulo, São Paulo, Brazil
- National Institute of Developmental Psychiatry, Beijing, China
| | - T Jia
- Institute of Science and Technology for Brain-Inspired Intelligence, Fudan University, Shanghai, China
- Key Laboratory of Computational Neuroscience and BrainInspired Intelligence (Fudan University), Ministry of Education, Shanghai, China
- Centre for Population Neuroscience and Precision Medicine (PONS), Institute of Psychiatry, Psychology and Neuroscience, SGDP Centre, King's College London, London, UK
| | - K A Johnson
- Harvard Medical School, Boston, MA, USA
- Harvard Aging Brain Study, Department of Neurology, Massachusetts General Hospital, Boston, MA, USA
- Center for Alzheimer Research and Treatment, Department of Neurology, Brigham and Women's Hospital, Boston, MA, USA
- Department of Radiology, Massachusetts General Hospital, Boston, MA, USA
| | - P B Jones
- Department of Psychiatry, University of Cambridge, Cambridge, UK
- Cambridgeshire and Peterborough NHS Foundation Trust, Cambridge, UK
| | - D T Jones
- Department of Radiology, Mayo Clinic, Rochester, MN, USA
- Department of Neurology, Mayo Clinic, Rochester, MN, USA
| | - R S Kahn
- Department of Psychiatry, Icahn School of Medicine, Mount Sinai, NY, USA
| | - H Karlsson
- Department of Clinical Medicine, Department of Psychiatry and Turku Brain and Mind Center, FinnBrain Birth Cohort Study, University of Turku and Turku University Hospital, Turku, Finland
- Centre for Population Health Research, Turku University Hospital and University of Turku, Turku, Finland
| | - L Karlsson
- Department of Clinical Medicine, Department of Psychiatry and Turku Brain and Mind Center, FinnBrain Birth Cohort Study, University of Turku and Turku University Hospital, Turku, Finland
- Centre for Population Health Research, Turku University Hospital and University of Turku, Turku, Finland
| | - R Kawashima
- Institute of Development, Aging and Cancer, Tohoku University, Seiryocho, Aobaku, Sendai, Japan
| | - E A Kelley
- Queen's University, Departments of Psychology and Psychiatry, Centre for Neuroscience Studies, Kingston, Ontario, Canada
| | - S Kern
- Neuropsychiatric Epidemiology Unit, Department of Psychiatry and Neurochemistry, Institute of Neuroscience and Physiology, the Sahlgrenska Academy, Centre for Ageing and Health (AGECAP) at the University of Gothenburg, Gothenburg, Sweden
- Region Västra Götaland, Sahlgrenska University Hospital, Psychiatry, Cognition and Old Age Psychiatry Clinic, Gothenburg, Sweden
| | - K W Kim
- Department of Brain and Cognitive Sciences, Seoul National University College of Natural Sciences, Seoul, South Korea
- Department of Neuropsychiatry, Seoul National University Bundang Hospital, Seongnam, South Korea
- Department of Psychiatry, Seoul National University College of Medicine, Seoul, South Korea
- Institute of Human Behavioral Medicine, SNU-MRC, Seoul, South Korea
| | - M G Kitzbichler
- Brain Mapping Unit, Department of Psychiatry, University of Cambridge, Cambridge, UK
- Department of Psychiatry, University of Cambridge, Cambridge, UK
| | - W S Kremen
- Department of Psychiatry, Center for Behavior Genetics of Aging, University of California, San Diego, La Jolla, CA, USA
| | - F Lalonde
- Section on Developmental Neurogenomics, Human Genetics Branch, National Institute of Mental Health, Bethesda, MD, USA
| | - B Landeau
- Normandie Univ, UNICAEN, INSERM, U1237, PhIND "Physiopathology and Imaging of Neurological Disorders", Institut Blood and Brain @ Caen-Normandie, Cyceron, Caen, France
| | - S Lee
- Department of Brain & Cognitive Sciences, Seoul National University College of Natural Sciences, Seoul, South Korea
| | - J Lerch
- Mouse Imaging Centre, Toronto, Ontario, Canada
- Department of Medical Biophysics, University of Toronto, Toronto, Ontario, Canada
- Wellcome Centre for Integrative Neuroimaging, FMRIB, Nuffield Department of Clinical Neuroscience, University of Oxford, Oxford, UK
| | - J D Lewis
- Montreal Neurological Institute, McGill University, Montreal, Quebec, Canada
| | - J Li
- The Clinical Hospital of Chengdu Brain Science Institute, University of Electronic Science and Technology of China, Chengdu, China
| | - W Liao
- The Clinical Hospital of Chengdu Brain Science Institute, University of Electronic Science and Technology of China, Chengdu, China
| | - C Liston
- Department of Psychiatry and Brain and Mind Research Institute, Weill Cornell Medicine, New York, NY, USA
| | - M V Lombardo
- Autism Research Centre, Department of Psychiatry, University of Cambridge, Cambridge, UK
- Laboratory for Autism and Neurodevelopmental Disorders, Center for Neuroscience and Cognitive Systems @UniTn, Istituto Italiano di Tecnologia, Rovereto, Italy
| | - J Lv
- Melbourne Neuropsychiatry Centre, University of Melbourne, Melbourne, Victoria, Australia
- School of Biomedical Engineering and Brain and Mind Centre, The University of Sydney, Sydney, New South Wales, Australia
| | - C Lynch
- Weil Family Brain and Mind Research Institute, Department of Psychiatry, Weill Cornell Medicine, New York, NY, USA
| | - T T Mallard
- Department of Psychology, University of Texas, Austin, TX, USA
| | - M Marcelis
- Department of Psychiatry and Neuropsychology, School of Mental Health and Neuroscience, EURON, Maastricht University Medical Centre, Maastricht, The Netherlands
- Institute for Mental Health Care Eindhoven (GGzE), Eindhoven, The Netherlands
| | - R D Markello
- McConnell Brain Imaging Centre, Montreal Neurological Institute, McGill University, Montreal, Quebec, Canada
| | - S R Mathias
- Department of Psychiatry, Boston Children's Hospital and Harvard Medical School, Boston, MA, USA
| | - B Mazoyer
- Institute of Neurodegenerative Disorders, CNRS UMR5293, CEA, University of Bordeaux, Bordeaux, France
- Ludmer Centre for Neuroinformatics and Mental Health, Douglas Mental Health University Institute, Montreal, Quebec, Canada
| | - P McGuire
- Department of Psychosis Studies, Institute of Psychiatry, Psychology and Neuroscience, King's College London, London, UK
| | - M J Meaney
- Ludmer Centre for Neuroinformatics and Mental Health, Douglas Mental Health University Institute, Montreal, Quebec, Canada
- Singapore Institute for Clinical Sciences, Singapore, Singapore
| | - A Mechelli
- Bordeaux University Hospital, Bordeaux, France
| | - N Medic
- Department of Psychiatry, University of Cambridge, Cambridge, UK
| | - B Misic
- McConnell Brain Imaging Centre, Montreal Neurological Institute, McGill University, Montreal, Quebec, Canada
| | - S E Morgan
- Department of Psychiatry, University of Cambridge, Cambridge, UK
- Department of Computer Science and Technology, University of Cambridge, Cambridge, UK
- The Alan Turing Institute, London, UK
| | - D Mothersill
- Department of Psychology, School of Business, National College of Ireland, Dublin, Ireland
- School of Psychology and Center for Neuroimaging and Cognitive Genomics, National University of Ireland Galway, Galway, Ireland
- Department of Psychiatry, Trinity College Dublin, Dublin, Ireland
| | - J Nigg
- Department of Psychiatry, School of Medicine, Oregon Health and Science University, Portland, OR, USA
| | - M Q W Ong
- Center for Sleep and Cognition, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
| | - C Ortinau
- Department of Pediatrics, Washington University in St Louis, St Louis, MO, USA
| | - R Ossenkoppele
- Alzheimer Center Amsterdam, Department of Neurology, Amsterdam Neuroscience, Vrije Universiteit Amsterdam, Amsterdam UMC, Amsterdam, The Netherlands
- Lund University, Clinical Memory Research Unit, Lund, Sweden
| | - M Ouyang
- Radiology Research, Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | - L Palaniyappan
- Robarts Research Institute and The Brain and Mind Institute, University of Western Ontario, London, Ontario, Canada
| | - L Paly
- Normandie Univ, UNICAEN, INSERM, U1237, PhIND "Physiopathology and Imaging of Neurological Disorders", Institut Blood and Brain @ Caen-Normandie, Cyceron, Caen, France
| | - P M Pan
- Department of Psychiatry, Federal University of Sao Poalo (UNIFESP), Sao Poalo, Brazil
- National Institute of Developmental Psychiatry for Children and Adolescents (INPD), Sao Poalo, Brazil
| | - C Pantelis
- Melbourne Neuropsychiatry Centre, Department of Psychiatry, The University of Melbourne and Melbourne Health, Carlton South, Victoria, Australia
- Melbourne School of Engineering, The University of Melbourne, Parkville, Victoria, Australia
- Florey Institute of Neuroscience and Mental Health, Parkville, Victoria, Australia
| | - M M Park
- Department of Psychiatry, Schulich School of Medicine and Dentistry, Western University, London, Ontario, Canada
| | - T Paus
- Department of Psychiatry, Faculty of Medicine and Centre Hospitalier Universitaire Sainte-Justine, University of Montreal, Montreal, Quebec, Canada
- Departments of Psychiatry and Psychology, University of Toronto, Toronto, Ontario, Canada
| | - Z Pausova
- The Hospital for Sick Children, Toronto, Ontario, Canada
- Departments of Physiology and Nutritional Sciences, University of Toronto, Toronto, Ontario, Canada
| | - D Paz-Linares
- The Clinical Hospital of Chengdu Brain Science Institute, MOE Key Lab for NeuroInformation, University of Electronic Science and Technology of China, Chengdu, China
- Cuban Neuroscience Center, Havana, Cuba
| | - A Pichet Binette
- Department of Psychiatry, Faculty of Medicine, McGill University, Montreal, Quebec, Canada
- Douglas Mental Health University Institute, Montreal, Quebec, Canada
| | - K Pierce
- Department of Neuroscience, University of California, San Diego, San Diego, CA, USA
| | - X Qian
- Center for Sleep and Cognition, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
| | - J Qiu
- School of Psychology, Southwest University, Chongqing, China
| | - A Qiu
- Department of Biomedical Engineering, The N.1 Institute for Health, National University of Singapore, Singapore, Singapore
| | - A Raznahan
- Section on Developmental Neurogenomics, Human Genetics Branch, National Institute of Mental Health, Bethesda, MD, USA
| | - T Rittman
- Department of Clinical Neurosciences, University of Cambridge, Cambridge, UK
| | - A Rodrigue
- Department of Psychiatry, Boston Children's Hospital and Harvard Medical School, Boston, MA, USA
| | - C K Rollins
- Department of Neurology, Harvard Medical School, Boston, MA, USA
- Department of Neurology, Boston Children's Hospital, Boston, MA, USA
| | - R Romero-Garcia
- Department of Psychiatry, University of Cambridge, Cambridge, UK
- Instituto de Biomedicina de Sevilla (IBiS) HUVR/CSIC/Universidad de Sevilla, Dpto. de Fisiología Médica y Biofísica, Seville, Spain
| | - L Ronan
- Department of Psychiatry, University of Cambridge, Cambridge, UK
| | - M D Rosenberg
- Department of Psychology and Neuroscience Institute, University of Chicago, Chicago, IL, USA
| | - D H Rowitch
- Department of Paediatrics and Wellcome-MRC Cambridge Stem Cell Institute, University of Cambridge, Cambridge, UK
| | - G A Salum
- Department of Psychiatry, Universidade Federal do Rio Grande do Sul (UFRGS), Hospital de Clinicas de Porto Alegre, Porto Alegre, Brazil
- National Institute of Developmental Psychiatry (INPD), São Paulo, Brazil
| | - T D Satterthwaite
- Department of Psychiatry, University of Pennsylvania, Philadelphia, PA, USA
- Lifespan Informatics & Neuroimaging Center, University of Pennsylvania, Philadelphia, PA, USA
| | - H L Schaare
- Otto Hahn Group Cognitive Neurogenetics, Max Planck Institute for Human Cognitive and Brain Sciences, Leipzig, Germany
- Institute of Neuroscience and Medicine (INM-7: Brain and Behaviour), Research Centre Juelich, Juelich, Germany
| | - R J Schachar
- The Hospital for Sick Children, Toronto, Ontario, Canada
| | - A P Schultz
- Harvard Medical School, Boston, MA, USA
- Harvard Aging Brain Study, Department of Neurology, Massachusetts General Hospital, Boston, MA, USA
- Athinoula A. Martinos Center for Biomedical Imaging, Department of Radiology, Massachusetts General Hospital, Charlestown, MA, USA
| | - G Schumann
- Centre for Population Neuroscience and Stratified Medicine (PONS), Institute for Science and Technology for Brain-inspired Intelligence, Fudan University, Shanghai, China
- PONS-Centre, Charite Mental Health, Dept of Psychiatry and Psychotherapy, Charite Campus Mitte, Berlin, Germany
| | - M Schöll
- Wallenberg Centre for Molecular and Translational Medicine, University of Gothenburg, Gothenburg, Sweden
- Department of Psychiatry and Neurochemistry, University of Gothenburg, Gothenburg, Sweden
- Dementia Research Centre, Queen's Square Institute of Neurology, University College London, London, UK
| | - D Sharp
- Department of Brain Sciences, Imperial College London, London, UK
- Care Research and Technology Centre, UK Dementia Research Institute, London, UK
| | - R T Shinohara
- Penn Statistics in Imaging and Visualization Center, Department of Biostatistics, Epidemiology, and Informatics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
- Center for Biomedical Image Computing and Analytics, Department of Radiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - I Skoog
- Neuropsychiatric Epidemiology Unit, Department of Psychiatry and Neurochemistry, Institute of Neuroscience and Physiology, the Sahlgrenska Academy, Centre for Ageing and Health (AGECAP) at the University of Gothenburg, Gothenburg, Sweden
- Region Västra Götaland, Sahlgrenska University Hospital, Psychiatry, Cognition and Old Age Psychiatry Clinic, Gothenburg, Sweden
| | - C D Smyser
- Departments of Neurology, Pediatrics, and Radiology, Washington University School of Medicine, St Louis, MO, USA
| | - R A Sperling
- Harvard Medical School, Boston, MA, USA
- Harvard Aging Brain Study, Department of Neurology, Massachusetts General Hospital, Boston, MA, USA
- Center for Alzheimer Research and Treatment, Department of Neurology, Brigham and Women's Hospital, Boston, MA, USA
| | - D J Stein
- SA MRC Unit on Risk and Resilience in Mental Disorders, Dept of Psychiatry and Neuroscience Institute, University of Cape Town, Cape Town, South Africa
| | - A Stolicyn
- Division of Psychiatry, Centre for Clinical Brain Sciences, University of Edinburgh, Edinburgh, UK
| | - J Suckling
- Department of Psychiatry, University of Cambridge, Cambridge, UK
- Cambridgeshire and Peterborough NHS Foundation Trust, Cambridge, UK
| | - G Sullivan
- MRC Centre for Reproductive Health, University of Edinburgh, Edinburgh, UK
| | - Y Taki
- Institute of Development, Aging and Cancer, Tohoku University, Seiryocho, Aobaku, Sendai, Japan
| | - B Thyreau
- Institute of Development, Aging and Cancer, Tohoku University, Seiryocho, Aobaku, Sendai, Japan
| | - R Toro
- Université de Paris, Paris, France
- Department of Neuroscience, Institut Pasteur, Paris, France
| | - N Traut
- Department of Neuroscience, Institut Pasteur, Paris, France
- Center for Research and Interdisciplinarity (CRI), Université Paris Descartes, Paris, France
| | - K A Tsvetanov
- Department of Clinical Neurosciences, University of Cambridge, Cambridge, UK
- Department of Psychology, University of Cambridge, Cambridge, UK
| | - N B Turk-Browne
- Department of Psychology, Yale University, New Haven, CT, USA
- Wu Tsai Institute, Yale University, New Haven, CT, USA
| | - J J Tuulari
- Department of Clinical Medicine, Department of Psychiatry and Turku Brain and Mind Center, FinnBrain Birth Cohort Study, University of Turku and Turku University Hospital, Turku, Finland
- Department of Clinical Medicine, University of Turku, Turku, Finland
- Turku Collegium for Science, Medicine and Technology, University of Turku, Turku, Finland
| | - C Tzourio
- Univ. Bordeaux, Inserm, Bordeaux Population Health Research Center, U1219, CHU Bordeaux, Bordeaux, France
| | - É Vachon-Presseau
- Faculty of Dental Medicine and Oral Health Sciences, McGill University, Montreal, Quebec, Canada
| | | | - P A Valdes-Sosa
- The Clinical Hospital of Chengdu Brain Science Institute, University of Electronic Science and Technology of China, Chengdu, China
- Alan Edwards Centre for Research on Pain (AECRP), McGill University, Montreal, Quebec, Canada
| | - S L Valk
- Institute for Neuroscience and Medicine 7, Forschungszentrum Jülich, Jülich, Germany
- Max Planck Institute for Human Cognitive and Brain Sciences, Leipzig, Germany
| | - T van Amelsvoort
- Department of Psychiatry and Neurosychology, Maastricht University, Maastricht, The Netherlands
| | - S N Vandekar
- Department of Biostatistics, Vanderbilt University, Nashville, TN, USA
- Department of Biostatistics, Vanderbilt University Medical Center, Nashville, TN, USA
| | - L Vasung
- McConnell Brain Imaging Centre, Montreal Neurological Institute, McGill University, Montreal, Quebec, Canada
| | - L W Victoria
- Weill Cornell Institute of Geriatric Psychiatry, Department of Psychiatry, Weill Cornell Medicine, New York, NY, USA
| | - S Villeneuve
- McConnell Brain Imaging Centre, Montreal Neurological Institute, McGill University, Montreal, Quebec, Canada
- Department of Psychiatry, Faculty of Medicine, McGill University, Montreal, Quebec, Canada
- Douglas Mental Health University Institute, Montreal, Quebec, Canada
| | - A Villringer
- Department of Neurology, Max Planck Institute for Human Cognitive and Brain Sciences, Leipzig, Germany
- Clinic for Cognitive Neurology, University of Leipzig Medical Center, Leipzig, Germany
| | - P E Vértes
- Department of Psychiatry, University of Cambridge, Cambridge, UK
- The Alan Turing Institute, London, UK
| | - K Wagstyl
- Wellcome Centre for Human Neuroimaging, London, UK
| | - Y S Wang
- State Key Laboratory of Cognitive Neuroscience and Learning, Beijing Normal University, Beijing, China
- Developmental Population Neuroscience Research Center, IDG/McGovern Institute for Brain Research, Beijing Normal University, Beijing, China
- National Basic Science Data Center, Beijing, China
- Research Center for Lifespan Development of Brain and Mind, Institute of Psychology, Chinese Academy of Sciences, Beijing, China
| | - S K Warfield
- Computational Radiology Laboratory, Boston Children's Hospital, Boston, MA, USA
| | - V Warrier
- Department of Psychiatry, University of Cambridge, Cambridge, UK
| | - E Westman
- Division of Clinical Geriatrics, Center for Alzheimer Research, Department of Neurobiology, Care Sciences and Society, Karolinska Institutet, Stockholm, Sweden
| | - M L Westwater
- Department of Psychiatry, University of Cambridge, Cambridge, UK
| | - H C Whalley
- Division of Psychiatry, Centre for Clinical Brain Sciences, University of Edinburgh, Edinburgh, UK
| | - A V Witte
- Department of Neurology, Max Planck Institute for Human Cognitive and Brain Sciences, Leipzig, Germany
- Clinic for Cognitive Neurology, University of Leipzig Medical Center, Leipzig, Germany
- Faculty of Medicine, CRC 1052 'Obesity Mechanisms', University of Leipzig, Leipzig, Germany
| | - N Yang
- State Key Laboratory of Cognitive Neuroscience and Learning, Beijing Normal University, Beijing, China
- Developmental Population Neuroscience Research Center, IDG/McGovern Institute for Brain Research, Beijing Normal University, Beijing, China
- National Basic Science Data Center, Beijing, China
- Research Center for Lifespan Development of Brain and Mind, Institute of Psychology, Chinese Academy of Sciences, Beijing, China
| | - B Yeo
- Department of Electrical and Computer Engineering, National University of Singapore, Singapore, Singapore
- Centre for Sleep and Cognition and Centre for Translational MR Research, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
- N.1 Institute for Health & Institute for Digital Medicine, National University of Singapore, Singapore, Singapore
- Integrative Sciences and Engineering Programme (ISEP), National University of Singapore, Singapore, Singapore
| | - H Yun
- Division of Newborn Medicine and Neuroradiology, Fetal Neonatal Neuroimaging and Developmental Science Center, Boston Children's Hospital, Harvard Medical School, Boston, MA, USA
| | - A Zalesky
- Melbourne Neuropsychiatry Centre, University of Melbourne, Melbourne, Victoria, Australia
- Department of Biomedical Engineering, University of Melbourne, Melbourne, Victoria, Australia
| | - H J Zar
- Department of Paediatrics and Child Health, Red Cross War Memorial Children's Hospital, SA-MRC Unit on Child & Adolescent Health, University of Cape Town, Cape Town, South Africa
| | - A Zettergren
- Neuropsychiatric Epidemiology Unit, Department of Psychiatry and Neurochemistry, Institute of Neuroscience and Physiology, the Sahlgrenska Academy, Centre for Ageing and Health (AGECAP) at the University of Gothenburg, Gothenburg, Sweden
| | - J H Zhou
- Center for Sleep and Cognition, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
- Department of Electrical and Computer Engineering, National University of Singapore, Singapore, Singapore
- Center for Translational Magnetic Resonance Research, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
| | - H Ziauddeen
- Department of Psychiatry, University of Cambridge, Cambridge, UK
- Cambridgeshire and Peterborough NHS Foundation Trust, Cambridge, UK
- Wellcome Trust-MRC Institute of Metabolic Science, University of Cambridge, Cambridge, UK
| | - A Zugman
- National Institute of Developmental Psychiatry for Children and Adolescents (INPD), Sao Poalo, Brazil
- National Institute of Mental Health (NIMH), National Institutes of Health (NIH), Bethesda, MD, USA
- Department of Psychiatry, Escola Paulista de Medicina, São Paulo, Brazil
| | - X N Zuo
- State Key Laboratory of Cognitive Neuroscience and Learning, Beijing Normal University, Beijing, China
- Developmental Population Neuroscience Research Center, IDG/McGovern Institute for Brain Research, Beijing Normal University, Beijing, China
- National Basic Science Data Center, Beijing, China
- Research Center for Lifespan Development of Brain and Mind, Institute of Psychology, Chinese Academy of Sciences, Beijing, China
- Key Laboratory of Brain and Education, School of Education Science, Nanning Normal University, Nanning, China
| | - E T Bullmore
- Department of Psychiatry, University of Cambridge, Cambridge, UK
| | - A F Alexander-Bloch
- Department of Psychiatry, University of Pennsylvania, Philadelphia, PA, USA
- Department of Child and Adolescent Psychiatry and Behavioral Science, The Children's Hospital of Philadelphia, Philadelphia, PA, USA
- Lifespan Brain Institute, The Children's Hospital of Philadelphia and Penn Medicine, Philadelphia, PA, USA
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Tekpinar M, Neron B, Delarue M. Correction to "Extracting Dynamical Correlations and Identifying Key Residues for Allosteric Communication in Proteins by correlationplus". J Chem Inf Model 2021; 61:5720. [PMID: 34756028 DOI: 10.1021/acs.jcim.1c01333] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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Czernecki D, Hu H, Romoli F, Delarue M. Structural dynamics and determinants of 2-aminoadenine specificity in DNA polymerase DpoZ of vibriophage ϕVC8. Nucleic Acids Res 2021; 49:11974-11985. [PMID: 34751404 PMCID: PMC8599892 DOI: 10.1093/nar/gkab955] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2021] [Revised: 09/29/2021] [Accepted: 10/04/2021] [Indexed: 11/12/2022] Open
Abstract
All genetic information in cellular life is stored in DNA copolymers composed of four basic building blocks (ATGC-DNA). In contrast, a group of bacteriophages belonging to families Siphoviridae and Podoviridae has abandoned the usage of one of them, adenine (A), replacing it with 2-aminoadenine (Z). The resulting ZTGC-DNA is more stable than its ATGC-DNA counterpart, owing to the additional hydrogen bond present in the 2-aminoadenine:thymine (Z:T) base pair, while the additional amino group also confers resistance to the host endonucleases. Recently, two classes of replicative proteins found in ZTGC-DNA-containing phages were characterized and one of them, DpoZ from DNA polymerase A (PolA) family, was shown to possess significant Z-vs-A specificity. Here, we present the crystallographic structure of the apo form of DpoZ of vibriophage ϕVC8, composed of the 3′-5′ exonuclease and polymerase domains. We captured the enzyme in two conformations that involve the tip of the thumb subdomain and the exonuclease domain. We highlight insertions and mutations characteristic of ϕVC8 DpoZ and its close homologues. Through mutagenesis and functional assays we suggest that the preference of ϕVC8 DpoZ towards Z relies on a polymerase backtracking process, more efficient when the nascent base pair is A:T than when it is Z:T.
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Affiliation(s)
- Dariusz Czernecki
- Unit of Architecture and Dynamics of Biological Macromolecules, CNRS UMR 3528, 25-28 rue du Docteur Roux, Institut Pasteur, 75015 Paris, France.,Sorbonne Université, Collège Doctoral, ED 515, 75005 Paris, France
| | - Haidai Hu
- Unit of Architecture and Dynamics of Biological Macromolecules, CNRS UMR 3528, 25-28 rue du Docteur Roux, Institut Pasteur, 75015 Paris, France
| | - Filippo Romoli
- Unit of Architecture and Dynamics of Biological Macromolecules, CNRS UMR 3528, 25-28 rue du Docteur Roux, Institut Pasteur, 75015 Paris, France
| | - Marc Delarue
- Unit of Architecture and Dynamics of Biological Macromolecules, CNRS UMR 3528, 25-28 rue du Docteur Roux, Institut Pasteur, 75015 Paris, France
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Tekpinar M, Neron B, Delarue M. Extracting Dynamical Correlations and Identifying Key Residues for Allosteric Communication in Proteins by correlationplus. J Chem Inf Model 2021; 61:4832-4838. [PMID: 34652149 DOI: 10.1021/acs.jcim.1c00742] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Extracting dynamical pairwise correlations and identifying key residues from large molecular dynamics trajectories or normal-mode analysis of coarse-grained models are important for explaining various processes like ligand binding, mutational effects, and long-distance interactions. Efficient and flexible tools to perform this task can provide new insights about residues involved in allosteric regulation and protein function. In addition, combining and comparing dynamical coupling information with sequence coevolution data can help to understand better protein function. To this aim, we developed a Python package called correlationplus to calculate, visualize, and analyze pairwise correlations. In this way, the package aids to identify key residues and interactions in proteins. The source code of correlationplus is available under LGPL version 3 at https://github.com/tekpinar/correlationplus. The current version of the package (0.2.0) can be installed with common installation methods like conda or pip in addition to source code installation. Moreover, docker images are also available for usage of the code without installation.
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Affiliation(s)
- Mustafa Tekpinar
- Unit of Architecture and Dynamics of Biological Macromolecules, Pasteur Institute, UMR 3528 CNRS, 25 Rue du Dr. Roux, 75015 Paris, France
| | - Bertrand Neron
- Computational Biology Department, Bioinformatics and Biostatistics Hub, 28 Rue du Dr. Roux, 75015 Paris, France
| | - Marc Delarue
- Unit of Architecture and Dynamics of Biological Macromolecules, Pasteur Institute, UMR 3528 CNRS, 25 Rue du Dr. Roux, 75015 Paris, France
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Koehl P, Orland H, Delarue M. Parameterizing elastic network models to capture the dynamics of proteins. J Comput Chem 2021; 42:1643-1661. [PMID: 34117647 DOI: 10.1002/jcc.26701] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2020] [Revised: 12/14/2020] [Accepted: 05/23/2021] [Indexed: 11/09/2022]
Abstract
Coarse-grained normal mode analyses of protein dynamics rely on the idea that the geometry of a protein structure contains enough information for computing its fluctuations around its equilibrium conformation. This geometry is captured in the form of an elastic network (EN), namely a network of edges between its residues. The normal modes of a protein are then identified with the normal modes of its EN. Different approaches have been proposed to construct ENs, focusing on the choice of the edges that they are comprised of, and on their parameterizations by the force constants associated with those edges. Here we propose new tools to guide choices on these two facets of EN. We study first different geometric models for ENs. We compare cutoff-based ENs, whose edges have lengths that are smaller than a cutoff distance, with Delaunay-based ENs and find that the latter provide better representations of the geometry of protein structures. We then derive an analytical method for the parameterization of the EN such that its dynamics leads to atomic fluctuations that agree with experimental B-factors. To limit overfitting, we attach a parameter referred to as flexibility constant to each atom instead of to each edge in the EN. The parameterization is expressed as a non-linear optimization problem whose parameters describe both rigid-body and internal motions. We show that this parameterization leads to improved ENs, whose dynamics mimic MD simulations better than ENs with uniform force constants, and reduces the number of normal modes needed to reproduce functional conformational changes.
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Affiliation(s)
- Patrice Koehl
- Department of Computer Sciences and Genome Center, University of California, Davis, California, USA
| | - Henri Orland
- Institut de Physique Théorique, Université Paris-Saclay, Gif sur Yvette, France
| | - Marc Delarue
- Unité de Dynamique Structurale des Macromolécules, Institut Pasteur, UMR 3528 du CNRS, Paris, France
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10
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Czernecki D, Bonhomme F, Kaminski PA, Delarue M. Characterization of a triad of genes in cyanophage S-2L sufficient to replace adenine by 2-aminoadenine in bacterial DNA. Nat Commun 2021; 12:4710. [PMID: 34354070 PMCID: PMC8342488 DOI: 10.1038/s41467-021-25064-x] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2021] [Accepted: 07/21/2021] [Indexed: 11/09/2022] Open
Abstract
Cyanophage S-2L is known to profoundly alter the biophysical properties of its DNA by replacing all adenines (A) with 2-aminoadenines (Z), which still pair with thymines but with a triple hydrogen bond. It was recently demonstrated that a homologue of adenylosuccinate synthetase (PurZ) and a dATP triphosphohydrolase (DatZ) are two important pieces of the metabolism of 2-aminoadenine, participating in the synthesis of ZTGC-DNA. Here, we determine that S-2L PurZ can use either dATP or ATP as a source of energy, thereby also depleting the pool of nucleotides in dATP. Furthermore, we identify a conserved gene (mazZ) located between purZ and datZ genes in S-2L and related phage genomes. We show that it encodes a (d)GTP-specific diphosphohydrolase, thereby providing the substrate of PurZ in the 2-aminoadenine synthesis pathway. High-resolution crystal structures of S-2L PurZ and MazZ with their respective substrates provide a rationale for their specificities. The Z-cluster made of these three genes - datZ, mazZ and purZ - was expressed in E. coli, resulting in a successful incorporation of 2-aminoadenine in the bacterial chromosomal and plasmidic DNA. This work opens the possibility to study synthetic organisms containing ZTGC-DNA.
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Affiliation(s)
- Dariusz Czernecki
- Unit of Architecture and Dynamics of Biological Macromolecules, CNRS UMR 3528, 25-28 rue du Docteur Roux, Institut Pasteur, Paris, France
- Sorbonne Université, Collège Doctoral, ED 515, Paris, France
| | - Frédéric Bonhomme
- Unit of Epigenetic Chemical Biology, CNRS UMR 3523, 25-28 rue du Docteur Roux, Institut Pasteur, Paris, France
| | - Pierre-Alexandre Kaminski
- Unit of Biology of Pathogenic Gram-Positive Bacteria, CNRS UMR 2001, 25-28 rue du Docteur Roux, Institut Pasteur, Paris, France
| | - Marc Delarue
- Unit of Architecture and Dynamics of Biological Macromolecules, CNRS UMR 3528, 25-28 rue du Docteur Roux, Institut Pasteur, Paris, France.
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11
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Di-Luoffo M, Ben-Meriem Z, Lefebvre P, Delarue M, Guillermet-Guibert J. PI3K functions as a hub in mechanotransduction. Trends Biochem Sci 2021; 46:878-888. [PMID: 34112586 DOI: 10.1016/j.tibs.2021.05.005] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2021] [Revised: 04/22/2021] [Accepted: 05/12/2021] [Indexed: 01/18/2023]
Abstract
Mammalian cells integrate different types of stimuli that govern their fate. These stimuli encompass biochemical as well as biomechanical cues (shear, tensile, and compressive stresses) that are usually studied separately. The phosphatidylinositol 3-kinase (PI3K) enzymes, producing signaling phosphoinositides at plasma and intracellular membranes, are key in intracellular signaling and vesicular trafficking pathways. Recent evidence in cancer research demonstrates that these enzymes are essential in mechanotransduction. Despite this, the importance of the integration of biomechanical cues and PI3K-driven biochemical signals is underestimated. In this opinion article, we make the hypothesis that modeling of biomechanical cues is critical to understand PI3K oncogenicity. We also identify known/missing knowledge in terms of isoform specificity and molecular pathways of activation, knowledge that is needed for clinical applications.
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Affiliation(s)
- M Di-Luoffo
- Centre de Recherches en Cancérologie de Toulouse (CRCT), Université de Toulouse, Institut National de la Santé et de la Recherche Médicale (Inserm) U1037, Centre National de la Recherche Scientifique (CNRS) U5071, Toulouse, France; Laboratoire D'analyse et D'architectures Des Systems (LAAS)-CNRS (Centre National de la Recherche Scientifique), Toulouse, France
| | - Z Ben-Meriem
- Centre de Recherches en Cancérologie de Toulouse (CRCT), Université de Toulouse, Institut National de la Santé et de la Recherche Médicale (Inserm) U1037, Centre National de la Recherche Scientifique (CNRS) U5071, Toulouse, France; Laboratoire D'analyse et D'architectures Des Systems (LAAS)-CNRS (Centre National de la Recherche Scientifique), Toulouse, France
| | - P Lefebvre
- Centre de Recherches en Cancérologie de Toulouse (CRCT), Université de Toulouse, Institut National de la Santé et de la Recherche Médicale (Inserm) U1037, Centre National de la Recherche Scientifique (CNRS) U5071, Toulouse, France; Laboratoire D'analyse et D'architectures Des Systems (LAAS)-CNRS (Centre National de la Recherche Scientifique), Toulouse, France
| | - M Delarue
- Centre de Recherches en Cancérologie de Toulouse (CRCT), Université de Toulouse, Institut National de la Santé et de la Recherche Médicale (Inserm) U1037, Centre National de la Recherche Scientifique (CNRS) U5071, Toulouse, France; Laboratoire D'analyse et D'architectures Des Systems (LAAS)-CNRS (Centre National de la Recherche Scientifique), Toulouse, France
| | - J Guillermet-Guibert
- Centre de Recherches en Cancérologie de Toulouse (CRCT), Université de Toulouse, Institut National de la Santé et de la Recherche Médicale (Inserm) U1037, Centre National de la Recherche Scientifique (CNRS) U5071, Toulouse, France; TouCAN (Laboratoire d'Excellence Toulouse Cancer), Toulouse, France.
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12
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Koehl P, Delarue M, Orland H. Simultaneous Identification of Multiple Binding Sites in Proteins: A Statistical Mechanics Approach. J Phys Chem B 2021; 125:5052-5067. [PMID: 33973782 DOI: 10.1021/acs.jpcb.1c02658] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
We present an extension of the Poisson-Boltzmann model in which the solute of interest is immersed in an assembly of self-orienting Langevin water dipoles, anions, cations, and hydrophobic molecules, all of variable densities. Interactions between charges are controlled by electrostatics, while hydrophobic interactions are modeled with a Yukawa potential. We impose steric constraints by assuming that the system is represented on a cubic lattice. We also assume incompressibility; i.e., all sites of the lattice are occupied. This model, which we refer to as the Hydrophobic Dipolar Poisson-Boltzmann Langevin (HDPBL) model, leads to a system of two equations whose solutions give the water dipole, salt, and hydrophobic molecule densities, all of them in the presence of the others in a self-consistent way. We use those to study the organization of the ions, cosolvent, and solvent molecules around proteins. In particular, peaks of densities are expected to reveal, simultaneously, the presence of compatible binding sites of different kinds on a protein. We have tested and validated the ability of HDPBL to detect pockets in proteins that bind to hydrophobic ligands, polar ligands, and charged small probes as well as to characterize the binding sites of lipids for membrane proteins.
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Affiliation(s)
- Patrice Koehl
- Department of Computer Science and Genome Center, University of California, Davis, California 95616, United States
| | - Marc Delarue
- Architecture et Dynamique des Macromolécules Biologiques, Département de Biologie Structurale et Chimie, UMR 3528 du CNRS, Institut Pasteur, 75015 Paris, France
| | - Henri Orland
- Institut de Physique Théorique, Université Paris-Saclay, CEA, 91191 Gif/Yvette Cedex, France
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13
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Madru C, Tekpinar AD, Rosario S, Czernecki D, Brûlé S, Sauguet L, Delarue M. Fast and efficient purification of SARS-CoV-2 RNA dependent RNA polymerase complex expressed in Escherichia coli. PLoS One 2021; 16:e0250610. [PMID: 33914787 PMCID: PMC8084133 DOI: 10.1371/journal.pone.0250610] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2020] [Accepted: 04/09/2021] [Indexed: 01/18/2023] Open
Abstract
To stop the COVID-19 pandemic due to the Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2), which caused more than 2.5 million deaths to date, new antiviral molecules are urgently needed. The replication of SARS-CoV-2 requires the RNA-dependent RNA polymerase (RdRp), making RdRp an excellent target for antiviral agents. RdRp is a multi-subunit complex composed of 3 viral proteins named nsp7, nsp8 and nsp12 that ensure the ~30 kb RNA genome’s transcription and replication. The main strategies employed so far for the overproduction of RdRp consist of expressing and purifying the three subunits separately before assembling the complex in vitro. However, nsp12 shows limited solubility in bacterial expression systems and is often produced in insect cells. Here, we describe an alternative strategy to co-express the full SARS-CoV-2 RdRp in E. coli, using a single plasmid. Characterization of the purified recombinant SARS-CoV-2 RdRp shows that it forms a complex with the expected (nsp7)(nsp8)2(nsp12) stoichiometry. RNA polymerization activity was measured using primer-extension assays showing that the purified enzyme is functional. The purification protocol can be achieved in one single day, surpassing in speed all other published protocols. Our construct is ideally suited for screening RdRp and its variants against very large chemical compounds libraries and has been made available to the scientific community through the Addgene plasmid depository (Addgene ID: 165451).
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Affiliation(s)
- Clément Madru
- Unit of Structural Dynamics of Macromolecules, Institut Pasteur & CNRS UMR, Paris, France
| | - Ayten Dizkirici Tekpinar
- Unit of Structural Dynamics of Macromolecules, Institut Pasteur & CNRS UMR, Paris, France
- Department of Molecular Biology and Genetics, Faculty of Science, Van Yüzüncü Yıl University, Van, Turkey
| | - Sandrine Rosario
- Unit of Structural Dynamics of Macromolecules, Institut Pasteur & CNRS UMR, Paris, France
| | - Dariusz Czernecki
- Unit of Structural Dynamics of Macromolecules, Institut Pasteur & CNRS UMR, Paris, France
- École Doctorale Complexité du Vivant, Sorbonne Université, Paris, France
| | - Sébastien Brûlé
- Molecular Biophysics Platform, C2RT, Institut Pasteur, CNRS UMR, Paris, France
| | - Ludovic Sauguet
- Unit of Structural Dynamics of Macromolecules, Institut Pasteur & CNRS UMR, Paris, France
- * E-mail: (LS); (MD)
| | - Marc Delarue
- Unit of Structural Dynamics of Macromolecules, Institut Pasteur & CNRS UMR, Paris, France
- * E-mail: (LS); (MD)
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14
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Abstract
Optimal transport (OT) has become a discipline by itself that offers solutions to a wide range of theoretical problems in probability and mathematics with applications in several applied fields such as imaging sciences, machine learning, and in data sciences in general. The traditional OT problem suffers from a severe limitation: its balance condition imposes that the two distributions to be compared be normalized and have the same total mass. However, it is important for many applications to be able to relax this constraint and allow for mass creation and/or destruction. This is true, for example, in all problems requiring partial matching. In this paper, we propose an approach to solving a generalized version of the OT problem, which we refer to as the discrete variable-mass optimal-transport (VMOT) problem, using techniques adapted from statistical physics. Our first contribution is to fully describe this formalism, including all the proofs of its main claims. In particular, we derive a strongly concave effective free-energy function that captures the constraints of the VMOT problem at a finite temperature. From its maximum we derive a weak distance (i.e., a divergence) between possibly unbalanced distribution functions. The temperature-dependent OT distance decreases monotonically to the standard variable-mass OT distance, providing a robust framework for temperature annealing. Our second contribution is to show that the implementation of this formalism has the same properties as the regularized OT algorithms in time complexity, making it a competitive approach to solving the VMOT problem. We illustrate applications of the framework to the problem of partial two- and three-dimensional shape-matching problems.
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Affiliation(s)
- Patrice Koehl
- Department of Computer Science and Genome Center, University of California, Davis, California 95616, USA
| | - Marc Delarue
- Unité de Dynamique Structurale des Macromolécules, Department of Structural Biology and Chemistry, UMR 3528 du CNRS, Institut Pasteur, 75015 Paris, France
| | - Henri Orland
- Institut de Physique Théorique, Université Paris-Saclay, CEA, 91191 Gif/Yvette Cedex, France
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15
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Fourati Z, Sauguet L, Delarue M. Structural evidence for the binding of monocarboxylates and dicarboxylates at pharmacologically relevant extracellular sites of a pentameric ligand-gated ion channel. Acta Crystallogr D Struct Biol 2020; 76:668-675. [PMID: 32627739 PMCID: PMC7336382 DOI: 10.1107/s205979832000772x] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2019] [Accepted: 06/05/2020] [Indexed: 11/21/2022] Open
Abstract
GLIC is a bacterial homologue of the pentameric ligand-gated ion channels (pLGICs) that mediate the fast chemical neurotransmission of nerve signalling in eukaryotes. Because the activation and allosteric modulation features are conserved among prokaryotic and eukaryotic pLGICs, GLIC is commonly used as a model to study the allosteric transition and structural pharmacology of pLGICs. It has previously been shown that GLIC is inhibited by some carboxylic acid derivatives. Here, experimental evidence for carboxylate binding to GLIC is provided by solving its X-ray structures with a series of monocarboxylate and dicarboxylate derivatives, and two carboxylate-binding sites are described: (i) the `intersubunit' site that partially overlaps the canonical pLGIC orthosteric site and (ii) the `intrasubunit' vestibular site, which is only occupied by a subset of the described derivatives. While the intersubunit site is widely conserved in all pLGICs, the intrasubunit site is only conserved in cationic eukaryotic pLGICs. This study sheds light on the importance of these two extracellular modulation sites as potential drug targets in pLGICs.
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Affiliation(s)
- Zaineb Fourati
- Unité Dynamique Structurale des Macromolécules, Institut Pasteur, 25 Rue du Docteur Roux, F-75015 Paris, France
- Centre National de la Recherche Scientifique, CNRS UMR3528, Biologie Structurale des Processus Cellulaires et Maladies Infectieuses, 25 Rue du Docteur Roux, F-75015 Paris, France
| | - Ludovic Sauguet
- Unité Dynamique Structurale des Macromolécules, Institut Pasteur, 25 Rue du Docteur Roux, F-75015 Paris, France
- Centre National de la Recherche Scientifique, CNRS UMR3528, Biologie Structurale des Processus Cellulaires et Maladies Infectieuses, 25 Rue du Docteur Roux, F-75015 Paris, France
| | - Marc Delarue
- Unité Dynamique Structurale des Macromolécules, Institut Pasteur, 25 Rue du Docteur Roux, F-75015 Paris, France
- Centre National de la Recherche Scientifique, CNRS UMR3528, Biologie Structurale des Processus Cellulaires et Maladies Infectieuses, 25 Rue du Docteur Roux, F-75015 Paris, France
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16
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Madru C, Henneke G, Raia P, Hugonneau-Beaufet I, Pehau-Arnaudet G, England P, Lindahl E, Delarue M, Carroni M, Sauguet L. Structural basis for the increased processivity of D-family DNA polymerases in complex with PCNA. Nat Commun 2020; 11:1591. [PMID: 32221299 PMCID: PMC7101311 DOI: 10.1038/s41467-020-15392-9] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2019] [Accepted: 03/05/2020] [Indexed: 11/09/2022] Open
Abstract
Replicative DNA polymerases (DNAPs) have evolved the ability to copy the genome with high processivity and fidelity. In Eukarya and Archaea, the processivity of replicative DNAPs is greatly enhanced by its binding to the proliferative cell nuclear antigen (PCNA) that encircles the DNA. We determined the cryo-EM structure of the DNA-bound PolD–PCNA complex from Pyrococcus abyssi at 3.77 Å. Using an integrative structural biology approach — combining cryo-EM, X-ray crystallography, protein–protein interaction measurements, and activity assays — we describe the molecular basis for the interaction and cooperativity between a replicative DNAP and PCNA. PolD recruits PCNA via a complex mechanism, which requires two different PIP-boxes. We infer that the second PIP-box, which is shared with the eukaryotic Polα replicative DNAP, plays a dual role in binding either PCNA or primase, and could be a master switch between an initiation and a processive phase during replication. Replicative DNA polymerases (DNAPs) have evolved the ability to copy the genome with high processivity and fidelity. Here, the authors present a cryo-EM structure of the DNA-bound PolD–PCNA complex from Pyrococcus abyssi to reveal the molecular basis for the interaction and cooperativity between a replicative DNAP and PCNA.
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Affiliation(s)
- Clément Madru
- Unit of Structural Dynamics of Macromolecules, Institut Pasteur and CNRS UMR 3528, Paris, France
| | - Ghislaine Henneke
- CNRS, Ifremer, Université de Brest, Laboratoire de Microbiologie des Environnements Extrêmes, Plouzané, France
| | - Pierre Raia
- Unit of Structural Dynamics of Macromolecules, Institut Pasteur and CNRS UMR 3528, Paris, France.,Sorbonne Université, École Doctorale Complexité du Vivant (ED515), Paris, France
| | - Inès Hugonneau-Beaufet
- Unit of Structural Dynamics of Macromolecules, Institut Pasteur and CNRS UMR 3528, Paris, France
| | | | - Patrick England
- Molecular Biophysics Platform, C2RT, Institut Pasteur, CNRS UMR 3528, Paris, France
| | - Erik Lindahl
- Department of Biochemistry and Biophysics, Science for Life Laboratory, Stockholm University, Stockholm, Sweden.,Department of Applied Physics, KTH Royal Institute of Technology, Stockholm, Sweden
| | - Marc Delarue
- Unit of Structural Dynamics of Macromolecules, Institut Pasteur and CNRS UMR 3528, Paris, France
| | - Marta Carroni
- Department of Biochemistry and Biophysics, Science for Life Laboratory, Stockholm University, Stockholm, Sweden.
| | - Ludovic Sauguet
- Unit of Structural Dynamics of Macromolecules, Institut Pasteur and CNRS UMR 3528, Paris, France.
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17
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Delarue M, Berceanu A, Laude MC, Louvrier A. Giant Blisters. J Stomatol Oral Maxillofac Surg 2019; 120:497-498. [PMID: 30664956 DOI: 10.1016/j.jormas.2019.01.007] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/03/2018] [Revised: 12/30/2018] [Accepted: 01/08/2019] [Indexed: 06/09/2023]
Affiliation(s)
- M Delarue
- Centre Hospitalier Universitaire de Besançon, Service de chirurgie maxillo-faciale, 25030, Besançon, France.
| | - A Berceanu
- Centre Hospitalier Universitaire de Besançon, Service de Soins Intensifs Hématologie, 25030, Besançon, France
| | - M-C Laude
- Centre Hospitalier Universitaire de Besançon, Service de Soins Intensifs Hématologie, 25030, Besançon, France
| | - A Louvrier
- Centre Hospitalier Universitaire de Besançon, Service de chirurgie maxillo-faciale, 25030, Besançon, France; INSERM, EFS BFC, UMR 1098, Interactions hôte-greffon-tumeur - Ingénierie cellulaire et génique, Université de Bourgogne Franche-Comté, Besançon, France
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18
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Fourati Z, Howard RJ, Heusser SA, Hu H, Ruza RR, Sauguet L, Lindahl E, Delarue M. Structural Basis for a Bimodal Allosteric Mechanism of General Anesthetic Modulation in Pentameric Ligand-Gated Ion Channels. Cell Rep 2019; 23:993-1004. [PMID: 29694907 DOI: 10.1016/j.celrep.2018.03.108] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2017] [Revised: 02/02/2018] [Accepted: 03/23/2018] [Indexed: 10/17/2022] Open
Abstract
Ion channel modulation by general anesthetics is a vital pharmacological process with implications for receptor biophysics and drug development. Functional studies have implicated conserved sites of both potentiation and inhibition in pentameric ligand-gated ion channels, but a detailed structural mechanism for these bimodal effects is lacking. The prokaryotic model protein GLIC recapitulates anesthetic modulation of human ion channels, and it is accessible to structure determination in both apparent open and closed states. Here, we report ten X-ray structures and electrophysiological characterization of GLIC variants in the presence and absence of general anesthetics, including the surgical agent propofol. We show that general anesthetics can allosterically favor closed channels by binding in the pore or favor open channels via various subsites in the transmembrane domain. Our results support an integrated, multi-site mechanism for allosteric modulation, and they provide atomic details of both potentiation and inhibition by one of the most common general anesthetics.
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Affiliation(s)
- Zaineb Fourati
- Unit of Structural Dynamics of Macromolecules, Institut Pasteur and UMR 3528 du CNRS, 75015 Paris, France
| | - Rebecca J Howard
- Department of Biochemistry and Biophysics and Science for Life Laboratory, Stockholm University, 17165 Solna, Sweden
| | - Stephanie A Heusser
- Department of Biochemistry and Biophysics and Science for Life Laboratory, Stockholm University, 17165 Solna, Sweden
| | - Haidai Hu
- Unit of Structural Dynamics of Macromolecules, Institut Pasteur and UMR 3528 du CNRS, 75015 Paris, France; Sorbonne Universités, UPMC University Paris 6, 75005 Paris, France
| | - Reinis R Ruza
- Unit of Structural Dynamics of Macromolecules, Institut Pasteur and UMR 3528 du CNRS, 75015 Paris, France
| | - Ludovic Sauguet
- Unit of Structural Dynamics of Macromolecules, Institut Pasteur and UMR 3528 du CNRS, 75015 Paris, France
| | - Erik Lindahl
- Department of Biochemistry and Biophysics and Science for Life Laboratory, Stockholm University, 17165 Solna, Sweden; Swedish e-Science Research Center, KTH Royal Institute of Technology, 11428 Stockholm, Sweden
| | - Marc Delarue
- Unit of Structural Dynamics of Macromolecules, Institut Pasteur and UMR 3528 du CNRS, 75015 Paris, France.
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Koehl P, Delarue M, Orland H. Statistical Physics Approach to the Optimal Transport Problem. Phys Rev Lett 2019; 123:040603. [PMID: 31491256 DOI: 10.1103/physrevlett.123.040603] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/29/2019] [Revised: 06/03/2019] [Indexed: 06/10/2023]
Abstract
Originally defined for the optimal allocation of resources, optimal transport (OT) has found many theoretical and practical applications in multiple domains of science and physics. In this Letter we develop a new method for solving the discrete version of this problem using techniques derived from statistical physics. We derive a strongly concave free energy function that captures the constraints of the OT problem at a finite temperature. Its maximum defines an optimal transport plan, or registration between the two discrete probability measures that are compared, as well as a pseudodistance between those measures that satisfies the triangular inequalities. The computation of this pseudodistance is fast and numerically stable. The temperature dependent OT pseudodistance is shown to decrease monotonically with respect to the inverse of the temperature and to converge to the standard OT distance at zero temperature, providing a robust framework for temperature annealing. We illustrate applications of this framework to the problem of image comparison.
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Affiliation(s)
- Patrice Koehl
- Department of Computer Science and Genome Center, University of California, Davis, California 95616, USA
| | - Marc Delarue
- Unité de Dynamique Structurale des Macromolécules, Department of Structural Biology and Chemistry, UMR 3528 du CNRS, Institut Pasteur, 75015 Paris, France
| | - Henri Orland
- Institut de Physique Théorique, CEA-Saclay, 91191 Gif/Yvette Cedex, France
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20
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Abstract
Optimal transport (OT) has become a discipline by itself that offers solutions to a wide range of theoretical problems in probability and mathematics. Despite its appealing theoretical properties, solving the OT problem involves the resolution of a linear program whose computational cost can quickly become prohibitive whenever the size of the problem exceeds a few hundred points. The recent introduction of entropy regularization, however, has led to the development of fast algorithms for solving an approximate OT problem. The successes of those algorithms have resulted in a popularization of the applications of OT in several applied fields such as imaging sciences and machine learning, and in data sciences in general. Problems remain, however, as to the numerical convergence of those regularized approximations towards the actual OT solution. In addition, the physical meaning of this regularization is unclear. In this paper, we propose an approach to solving the discrete OT problem using techniques adapted from statistical physics. Our first contribution is to fully describe this formalism, including all the proofs of its main claims. In particular we derive a strongly concave effective free energy function that captures the constraints of the optimal transport problem at a finite temperature. Its maximum defines a pseudo distance between the two set of weighted points that are compared, which satisfies the triangular inequalities. The temperature dependent OT pseudo distance decreases monotonically to the standard OT distance, providing a robust framework for temperature annealing. Our second contribution is to show that the implementation of this formalism has the same properties as the regularized OT algorithms in time complexity, making it a competitive approach to solving the OT problem. We illustrate applications of the framework to the problem of protein fold recognition based on sequence information only.
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Affiliation(s)
- Patrice Koehl
- Department of Computer Science and Genome Center, University of California, Davis, California 95616, USA
| | - Marc Delarue
- Unité de Dynamique Structurale des Macromolécules, Department of Structural Biology and Chemistry, UMR 3528 du CNRS, Institut Pasteur, 75015 Paris, France
| | - Henri Orland
- Institut de Physique Théorique, CEA-Saclay, 91191 Gif/Yvette Cedex, France
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21
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Loc'h J, Gerodimos CA, Rosario S, Tekpinar M, Lieber MR, Delarue M. Structural evidence for an in trans base selection mechanism involving Loop1 in polymerase μ at an NHEJ double-strand break junction. J Biol Chem 2019; 294:10579-10595. [PMID: 31138645 DOI: 10.1074/jbc.ra119.008739] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2019] [Revised: 05/13/2019] [Indexed: 11/06/2022] Open
Abstract
Eukaryotic DNA polymerase (Pol) X family members such as Pol μ and terminal deoxynucleotidyl transferase (TdT) are important components for the nonhomologous DNA end-joining (NHEJ) pathway. TdT participates in a specialized version of NHEJ, V(D)J recombination. It has primarily nontemplated polymerase activity but can take instructions across strands from the downstream dsDNA, and both activities are highly dependent on a structural element called Loop1. However, it is unclear whether Pol μ follows the same mechanism, because the structure of its Loop1 is disordered in available structures. Here, we used a chimeric TdT harboring Loop1 of Pol μ that recapitulated the functional properties of Pol μ in ligation experiments. We solved three crystal structures of this TdT chimera bound to several DNA substrates at 1.96-2.55 Å resolutions, including a full DNA double-strand break (DSB) synapsis. We then modeled the full Pol μ sequence in the context of one these complexes. The atomic structure of an NHEJ junction with a Pol X construct that mimics Pol μ in a reconstituted system explained the distinctive properties of Pol μ compared with TdT. The structure suggested a mechanism of base selection relying on Loop1 and taking instructions via the in trans templating base independently of the primer strand. We conclude that our atomic-level structural observations represent a paradigm shift for the mechanism of base selection in the Pol X family of DNA polymerases.
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Affiliation(s)
- Jérôme Loc'h
- From the Unité de Dynamique Structurale des Macromolécules, Institut Pasteur, UMR 3528 du CNRS, 25 Rue du Dr. Roux, 75015 Paris, France and
| | - Christina A Gerodimos
- the Departments of Pathology, Biochemistry and Molecular Biology, and Molecular Microbiology and Immunology and the Department of Biological Sciences, Section of Molecular and Computational Biology, Norris Comprehensive Cancer Center, University of Southern California Keck School of Medicine, Los Angeles, California 90033
| | - Sandrine Rosario
- From the Unité de Dynamique Structurale des Macromolécules, Institut Pasteur, UMR 3528 du CNRS, 25 Rue du Dr. Roux, 75015 Paris, France and
| | - Mustafa Tekpinar
- From the Unité de Dynamique Structurale des Macromolécules, Institut Pasteur, UMR 3528 du CNRS, 25 Rue du Dr. Roux, 75015 Paris, France and
| | - Michael R Lieber
- the Departments of Pathology, Biochemistry and Molecular Biology, and Molecular Microbiology and Immunology and the Department of Biological Sciences, Section of Molecular and Computational Biology, Norris Comprehensive Cancer Center, University of Southern California Keck School of Medicine, Los Angeles, California 90033
| | - Marc Delarue
- From the Unité de Dynamique Structurale des Macromolécules, Institut Pasteur, UMR 3528 du CNRS, 25 Rue du Dr. Roux, 75015 Paris, France and
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22
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Randrianjatovo-Gbalou I, Delarue M. Rapid enzymatic synthesis of long RNA polymers: A simple protocol to generate RNA libraries with random sequences. Methods 2019; 161:83-90. [PMID: 30926532 DOI: 10.1016/j.ymeth.2019.03.025] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2019] [Revised: 03/22/2019] [Accepted: 03/23/2019] [Indexed: 11/28/2022] Open
Abstract
RNA aptamers have several advantages over DNA aptamers due to their propensity to fold into three-dimensional structures. However, the synthesis of large RNA libraries remains a challenge as it requires more precautions to conserve their functional integrity, especially when such libraries are intended for aptamers or ribozymes selection. Here, we present an enzymatic method that enables the rapid synthesis of RNA polymers thanks to the efficient incorporation of ribonucleotides (NTPs) as well as chemically modified ribonucleotides by human DNA polymerase Theta (θ) mutants. These mutants have the ability to generate long single-stranded RNA polynucleotides of random sequences due to their improved template-free terminal nucleotidyltransferase activity. Here we describe the detailed protocols to produce large and diverse libraries of RNA, to make them ready to use in repeated cycles of Systematic Evolution of Ligands by Exponential enrichment (SELEX) and to synthesize C2'-modified nucleic acids with higher nuclease resistance.
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Affiliation(s)
- Irina Randrianjatovo-Gbalou
- Unit of Structural Dynamics of Biological Macromolecules and CNRS UMR 3528, Institut Pasteur, 25 rue du Docteur Roux, 75724 Paris Cedex 15, France.
| | - Marc Delarue
- Unit of Structural Dynamics of Biological Macromolecules and CNRS UMR 3528, Institut Pasteur, 25 rue du Docteur Roux, 75724 Paris Cedex 15, France
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23
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Raia P, Carroni M, Henry E, Pehau-Arnaudet G, Brûlé S, Béguin P, Henneke G, Lindahl E, Delarue M, Sauguet L. Structure of the DP1-DP2 PolD complex bound with DNA and its implications for the evolutionary history of DNA and RNA polymerases. PLoS Biol 2019; 17:e3000122. [PMID: 30657780 PMCID: PMC6355029 DOI: 10.1371/journal.pbio.3000122] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2018] [Revised: 01/31/2019] [Accepted: 01/10/2019] [Indexed: 02/01/2023] Open
Abstract
PolD is an archaeal replicative DNA polymerase (DNAP) made of a proofreading exonuclease subunit (DP1) and a larger polymerase catalytic subunit (DP2). Recently, we reported the individual crystal structures of the DP1 and DP2 catalytic cores, thereby revealing that PolD is an atypical DNAP that has all functional properties of a replicative DNAP but with the catalytic core of an RNA polymerase (RNAP). We now report the DNA-bound cryo-electron microscopy (cryo-EM) structure of the heterodimeric DP1-DP2 PolD complex from Pyrococcus abyssi, revealing a unique DNA-binding site. Comparison of PolD and RNAPs extends their structural similarities and brings to light the minimal catalytic core shared by all cellular transcriptases. Finally, elucidating the structure of the PolD DP1-DP2 interface, which is conserved in all eukaryotic replicative DNAPs, clarifies their evolutionary relationships with PolD and sheds light on the domain acquisition and exchange mechanism that occurred during the evolution of the eukaryotic replisome.
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Affiliation(s)
- Pierre Raia
- Unit of Structural Dynamics of Macromolecules, Pasteur Institute and CNRS UMR 3528, Paris, France
- Sorbonne Université, Ecole Doctorale Complexité du Vivant (ED515), Paris, France
| | - Marta Carroni
- Science for Life Laboratory, Department of Biochemistry and Biophysics, Stockholm University, Sweden
| | - Etienne Henry
- CNRS, IFREMER, Univ Brest, Laboratoire de Microbiologie des Environnements Extrêmes, Plouzané, France
| | | | - Sébastien Brûlé
- Molecular Biophysics Platform, Pasteur Institute, C2RT and CNRS UMR 3528, Paris, France
| | - Pierre Béguin
- Unit of Molecular Biology of Gene in Extremophiles, Pasteur Institute, Paris, France
| | - Ghislaine Henneke
- IFREMER, CNRS, Univ Brest, Laboratoire de Microbiologie des Environnements Extrêmes, Plouzané, France
| | - Erik Lindahl
- Science for Life Laboratory, Department of Biochemistry and Biophysics, Stockholm University, Sweden
| | - Marc Delarue
- Unit of Structural Dynamics of Macromolecules, Pasteur Institute and CNRS UMR 3528, Paris, France
| | - Ludovic Sauguet
- Unit of Structural Dynamics of Macromolecules, Pasteur Institute and CNRS UMR 3528, Paris, France
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24
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Delarue M, Koehl P. Combined approaches from physics, statistics, and computer science for ab initio protein structure prediction: ex unitate vires (unity is strength)? F1000Res 2018; 7. [PMID: 30079234 PMCID: PMC6058471 DOI: 10.12688/f1000research.14870.1] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 07/19/2018] [Indexed: 11/20/2022] Open
Abstract
Connecting the dots among the amino acid sequence of a protein, its structure, and its function remains a central theme in molecular biology, as it would have many applications in the treatment of illnesses related to misfolding or protein instability. As a result of high-throughput sequencing methods, biologists currently live in a protein sequence-rich world. However, our knowledge of protein structure based on experimental data remains comparatively limited. As a consequence, protein structure prediction has established itself as a very active field of research to fill in this gap. This field, once thought to be reserved for theoretical biophysicists, is constantly reinventing itself, borrowing ideas informed by an ever-increasing assembly of scientific domains, from biology, chemistry, (statistical) physics, mathematics, computer science, statistics, bioinformatics, and more recently data sciences. We review the recent progress arising from this integration of knowledge, from the development of specific computer architecture to allow for longer timescales in physics-based simulations of protein folding to the recent advances in predicting contacts in proteins based on detection of coevolution using very large data sets of aligned protein sequences.
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Affiliation(s)
- Marc Delarue
- Unité Dynamique Structurale des Macromolécules, Institut Pasteur, and UMR 3528 du CNRS, Paris, France
| | - Patrice Koehl
- Department of Computer Science, Genome Center, University of California, Davis, Davis, California, USA
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25
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Delarue M, Brittingham GP, Pfeffer S, Surovtsev IV, Pinglay S, Kennedy KJ, Schaffer M, Gutierrez JI, Sang D, Poterewicz G, Chung JK, Plitzko JM, Groves JT, Jacobs-Wagner C, Engel BD, Holt LJ. mTORC1 Controls Phase Separation and the Biophysical Properties of the Cytoplasm by Tuning Crowding. Cell 2018. [PMID: 29937223 DOI: 10.1016/j.cell.2018.1005.1042] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/30/2023]
Abstract
Macromolecular crowding has a profound impact on reaction rates and the physical properties of the cell interior, but the mechanisms that regulate crowding are poorly understood. We developed genetically encoded multimeric nanoparticles (GEMs) to dissect these mechanisms. GEMs are homomultimeric scaffolds fused to a fluorescent protein that self-assemble into bright, stable particles of defined size and shape. By combining tracking of GEMs with genetic and pharmacological approaches, we discovered that the mTORC1 pathway can modulate the effective diffusion coefficient of particles ≥20 nm in diameter more than 2-fold by tuning ribosome concentration, without any discernable effect on the motion of molecules ≤5 nm. This change in ribosome concentration affected phase separation both in vitro and in vivo. Together, these results establish a role for mTORC1 in controlling both the mesoscale biophysical properties of the cytoplasm and biomolecular condensation.
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Affiliation(s)
- M Delarue
- Institute for Systems Genetics, New York University Langone Health, New York, NY 10016, USA
| | - G P Brittingham
- Institute for Systems Genetics, New York University Langone Health, New York, NY 10016, USA
| | - S Pfeffer
- Department of Molecular Structural Biology, Max Planck Institute of Biochemistry, 82152 Martinsried, Germany
| | - I V Surovtsev
- Department of Molecular, Cellular, and Developmental Biology, Yale University, New Haven, CT 06511, USA; Howard Hughes Medical Institute, Chevy Chase, MD 20815, USA; Microbial Sciences Institute, Yale West Campus, West Haven, CT 06516, USA
| | - S Pinglay
- Institute for Systems Genetics, New York University Langone Health, New York, NY 10016, USA
| | - K J Kennedy
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA 95720, USA
| | - M Schaffer
- Department of Molecular Structural Biology, Max Planck Institute of Biochemistry, 82152 Martinsried, Germany
| | - J I Gutierrez
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA 95720, USA
| | - D Sang
- Institute for Systems Genetics, New York University Langone Health, New York, NY 10016, USA
| | - G Poterewicz
- Institute for Systems Genetics, New York University Langone Health, New York, NY 10016, USA
| | - J K Chung
- Department of Chemistry, University of California, Berkeley, Berkeley, CA 95720, USA
| | - J M Plitzko
- Department of Molecular Structural Biology, Max Planck Institute of Biochemistry, 82152 Martinsried, Germany
| | - J T Groves
- Department of Chemistry, University of California, Berkeley, Berkeley, CA 95720, USA; Howard Hughes Medical Institute, Chevy Chase, MD 20815, USA
| | - C Jacobs-Wagner
- Department of Molecular, Cellular, and Developmental Biology, Yale University, New Haven, CT 06511, USA; Howard Hughes Medical Institute, Chevy Chase, MD 20815, USA; Microbial Sciences Institute, Yale West Campus, West Haven, CT 06516, USA; Department of Microbial Pathogenesis, Yale School of Medicine, New Haven, CT 06511, USA
| | - B D Engel
- Department of Molecular Structural Biology, Max Planck Institute of Biochemistry, 82152 Martinsried, Germany.
| | - L J Holt
- Institute for Systems Genetics, New York University Langone Health, New York, NY 10016, USA.
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26
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Randrianjatovo-Gbalou I, Rosario S, Sismeiro O, Varet H, Legendre R, Coppée JY, Huteau V, Pochet S, Delarue M. Enzymatic synthesis of random sequences of RNA and RNA analogues by DNA polymerase theta mutants for the generation of aptamer libraries. Nucleic Acids Res 2018; 46:6271-6284. [PMID: 29788485 PMCID: PMC6158600 DOI: 10.1093/nar/gky413] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2018] [Revised: 04/12/2018] [Accepted: 05/04/2018] [Indexed: 12/17/2022] Open
Abstract
Nucleic acid aptamers, especially RNA, exhibit valuable advantages compared to protein therapeutics in terms of size, affinity and specificity. However, the synthesis of libraries of large random RNAs is still difficult and expensive. The engineering of polymerases able to directly generate these libraries has the potential to replace the chemical synthesis approach. Here, we start with a DNA polymerase that already displays a significant template-free nucleotidyltransferase activity, human DNA polymerase theta, and we mutate it based on the knowledge of its three-dimensional structure as well as previous mutational studies on members of the same polA family. One mutant exhibited a high tolerance towards ribonucleotides (NTPs) and displayed an efficient ribonucleotidyltransferase activity that resulted in the assembly of long RNA polymers. HPLC analysis and RNA sequencing of the products were used to quantify the incorporation of the four NTPs as a function of initial NTP concentrations and established the randomness of each generated nucleic acid sequence. The same mutant revealed a propensity to accept other modified nucleotides and to extend them in long fragments. Hence, this mutant can deliver random natural and modified RNA polymers libraries ready to use for SELEX, with custom lengths and balanced or unbalanced ratios.
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Affiliation(s)
- Irina Randrianjatovo-Gbalou
- Unit of Structural Dynamics of Biological Macromolecules, CNRS UMR 3528, Institut Pasteur, 25 rue du Docteur Roux, 75724 Paris Cedex 15, France
| | - Sandrine Rosario
- Unit of Structural Dynamics of Biological Macromolecules, CNRS UMR 3528, Institut Pasteur, 25 rue du Docteur Roux, 75724 Paris Cedex 15, France
| | - Odile Sismeiro
- Transcriptome and EpiGenome platform, BioMics, Center of Innovation and Technological Research, Institut Pasteur, 28 rue du Docteur Roux, 75724 Paris Cedex 15, France
| | - Hugo Varet
- Transcriptome and EpiGenome platform, BioMics, Center of Innovation and Technological Research, Institut Pasteur, 28 rue du Docteur Roux, 75724 Paris Cedex 15, France
- Hub informatique et Biostatistique, Centre de Bioinformatique, Biostatistique et Biologie Intégrative (C3BI, USR 3756 IP-CNRS), Institut Pasteur, 28 Rue du Docteur Roux, 75724 Paris Cedex 15, France
| | - Rachel Legendre
- Transcriptome and EpiGenome platform, BioMics, Center of Innovation and Technological Research, Institut Pasteur, 28 rue du Docteur Roux, 75724 Paris Cedex 15, France
- Hub informatique et Biostatistique, Centre de Bioinformatique, Biostatistique et Biologie Intégrative (C3BI, USR 3756 IP-CNRS), Institut Pasteur, 28 Rue du Docteur Roux, 75724 Paris Cedex 15, France
| | - Jean-Yves Coppée
- Transcriptome and EpiGenome platform, BioMics, Center of Innovation and Technological Research, Institut Pasteur, 28 rue du Docteur Roux, 75724 Paris Cedex 15, France
| | - Valérie Huteau
- Unité de Chimie et Biocatalyse, CNRS UMR 3523, Institut Pasteur, 28 rue du Docteur Roux, 75724 Paris Cedex 15, France
| | - Sylvie Pochet
- Unité de Chimie et Biocatalyse, CNRS UMR 3523, Institut Pasteur, 28 rue du Docteur Roux, 75724 Paris Cedex 15, France
| | - Marc Delarue
- Unit of Structural Dynamics of Biological Macromolecules, CNRS UMR 3528, Institut Pasteur, 25 rue du Docteur Roux, 75724 Paris Cedex 15, France
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27
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Delarue M, Brittingham GP, Pfeffer S, Surovtsev IV, Pinglay S, Kennedy KJ, Schaffer M, Gutierrez JI, Sang D, Poterewicz G, Chung JK, Plitzko JM, Groves JT, Jacobs-Wagner C, Engel BD, Holt LJ. mTORC1 Controls Phase Separation and the Biophysical Properties of the Cytoplasm by Tuning Crowding. Cell 2018; 174:338-349.e20. [PMID: 29937223 PMCID: PMC10080728 DOI: 10.1016/j.cell.2018.05.042] [Citation(s) in RCA: 229] [Impact Index Per Article: 38.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2017] [Revised: 03/26/2018] [Accepted: 05/17/2018] [Indexed: 12/14/2022]
Abstract
Macromolecular crowding has a profound impact on reaction rates and the physical properties of the cell interior, but the mechanisms that regulate crowding are poorly understood. We developed genetically encoded multimeric nanoparticles (GEMs) to dissect these mechanisms. GEMs are homomultimeric scaffolds fused to a fluorescent protein that self-assemble into bright, stable particles of defined size and shape. By combining tracking of GEMs with genetic and pharmacological approaches, we discovered that the mTORC1 pathway can modulate the effective diffusion coefficient of particles ≥20 nm in diameter more than 2-fold by tuning ribosome concentration, without any discernable effect on the motion of molecules ≤5 nm. This change in ribosome concentration affected phase separation both in vitro and in vivo. Together, these results establish a role for mTORC1 in controlling both the mesoscale biophysical properties of the cytoplasm and biomolecular condensation.
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Affiliation(s)
- M Delarue
- Institute for Systems Genetics, New York University Langone Health, New York, NY 10016, USA
| | - G P Brittingham
- Institute for Systems Genetics, New York University Langone Health, New York, NY 10016, USA
| | - S Pfeffer
- Department of Molecular Structural Biology, Max Planck Institute of Biochemistry, 82152 Martinsried, Germany
| | - I V Surovtsev
- Department of Molecular, Cellular, and Developmental Biology, Yale University, New Haven, CT 06511, USA; Howard Hughes Medical Institute, Chevy Chase, MD 20815, USA; Microbial Sciences Institute, Yale West Campus, West Haven, CT 06516, USA
| | - S Pinglay
- Institute for Systems Genetics, New York University Langone Health, New York, NY 10016, USA
| | - K J Kennedy
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA 95720, USA
| | - M Schaffer
- Department of Molecular Structural Biology, Max Planck Institute of Biochemistry, 82152 Martinsried, Germany
| | - J I Gutierrez
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA 95720, USA
| | - D Sang
- Institute for Systems Genetics, New York University Langone Health, New York, NY 10016, USA
| | - G Poterewicz
- Institute for Systems Genetics, New York University Langone Health, New York, NY 10016, USA
| | - J K Chung
- Department of Chemistry, University of California, Berkeley, Berkeley, CA 95720, USA
| | - J M Plitzko
- Department of Molecular Structural Biology, Max Planck Institute of Biochemistry, 82152 Martinsried, Germany
| | - J T Groves
- Department of Chemistry, University of California, Berkeley, Berkeley, CA 95720, USA; Howard Hughes Medical Institute, Chevy Chase, MD 20815, USA
| | - C Jacobs-Wagner
- Department of Molecular, Cellular, and Developmental Biology, Yale University, New Haven, CT 06511, USA; Howard Hughes Medical Institute, Chevy Chase, MD 20815, USA; Microbial Sciences Institute, Yale West Campus, West Haven, CT 06516, USA; Department of Microbial Pathogenesis, Yale School of Medicine, New Haven, CT 06511, USA
| | - B D Engel
- Department of Molecular Structural Biology, Max Planck Institute of Biochemistry, 82152 Martinsried, Germany.
| | - L J Holt
- Institute for Systems Genetics, New York University Langone Health, New York, NY 10016, USA.
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28
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Loc'h J, Delarue M. Terminal deoxynucleotidyltransferase: the story of an untemplated DNA polymerase capable of DNA bridging and templated synthesis across strands. Curr Opin Struct Biol 2018; 53:22-31. [PMID: 29656238 DOI: 10.1016/j.sbi.2018.03.019] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2018] [Revised: 03/27/2018] [Accepted: 03/30/2018] [Indexed: 01/08/2023]
Abstract
Terminal deoxynucleotidyltransferase (TdT) is a member of the polX family which is involved in DNA repair. It has been known for years as an untemplated DNA polymerase used during V(D)J recombination to generate diversity at the CDR3 region of immunoglobulins and T-cell receptors. Recently, however, TdT was crystallized in the presence of a complete DNA synapsis made of two double-stranded DNA (dsDNA), each with a 3' protruding end, and overlapping with only one micro-homology base-pair, thus giving structural insight for the first time into DNA synthesis across strands. It was subsequently shown that TdT indeed has an in trans template-dependent activity in the presence of an excess of the downstream DNA duplex. A possible biological role of this dual activity is discussed.
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Affiliation(s)
- Jérôme Loc'h
- Unit of Structural Dynamics of Biological Macromolecules and UMR 3528 du CNRS, Institut Pasteur, 75015 Paris, France
| | - Marc Delarue
- Unit of Structural Dynamics of Biological Macromolecules and UMR 3528 du CNRS, Institut Pasteur, 75015 Paris, France.
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29
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Abdollahi N, Albani A, Anthony E, Baud A, Cardon M, Clerc R, Czernecki D, Conte R, David L, Delaune A, Djerroud S, Fourgoux P, Guiglielmoni N, Laurentie J, Lehmann N, Lochard C, Montagne R, Myrodia V, Opuu V, Parey E, Polit L, Privé S, Quignot C, Ruiz-Cuevas M, Sissoko M, Sompairac N, Vallerix A, Verrecchia V, Delarue M, Guérois R, Ponty Y, Sacquin-Mora S, Carbone A, Froidevaux C, Le Crom S, Lespinet O, Weigt M, Abboud S, Bernardes J, Bouvier G, Dequeker C, Ferré A, Fuchs P, Lelandais G, Poulain P, Richard H, Schweke H, Laine E, Lopes A. Meet-U: Educating through research immersion. PLoS Comput Biol 2018; 14:e1005992. [PMID: 29543809 PMCID: PMC5854232 DOI: 10.1371/journal.pcbi.1005992] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
We present a new educational initiative called Meet-U that aims to train students for collaborative work in computational biology and to bridge the gap between education and research. Meet-U mimics the setup of collaborative research projects and takes advantage of the most popular tools for collaborative work and of cloud computing. Students are grouped in teams of 4–5 people and have to realize a project from A to Z that answers a challenging question in biology. Meet-U promotes "coopetition," as the students collaborate within and across the teams and are also in competition with each other to develop the best final product. Meet-U fosters interactions between different actors of education and research through the organization of a meeting day, open to everyone, where the students present their work to a jury of researchers and jury members give research seminars. This very unique combination of education and research is strongly motivating for the students and provides a formidable opportunity for a scientific community to unite and increase its visibility. We report on our experience with Meet-U in two French universities with master’s students in bioinformatics and modeling, with protein–protein docking as the subject of the course. Meet-U is easy to implement and can be straightforwardly transferred to other fields and/or universities. All the information and data are available at www.meet-u.org.
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Affiliation(s)
- Nika Abdollahi
- Departments of Computer Science and of Life Sciences, Sorbonne Université (SU) / UPMC, Paris, France
| | - Alexandre Albani
- Departments of Computer Science and of Life Sciences, Sorbonne Université (SU) / UPMC, Paris, France
| | - Eric Anthony
- Department of Biology and of Computer Science, Univ. Paris-Sud, Université Paris-Saclay (UPSay), Orsay, France
| | - Agnes Baud
- Departments of Computer Science and of Life Sciences, Sorbonne Université (SU) / UPMC, Paris, France
| | - Mélissa Cardon
- Departments of Computer Science and of Life Sciences, Sorbonne Université (SU) / UPMC, Paris, France
| | - Robert Clerc
- Departments of Computer Science and of Life Sciences, Sorbonne Université (SU) / UPMC, Paris, France
| | - Dariusz Czernecki
- Departments of Computer Science and of Life Sciences, Sorbonne Université (SU) / UPMC, Paris, France
| | - Romain Conte
- Departments of Computer Science and of Life Sciences, Sorbonne Université (SU) / UPMC, Paris, France
| | - Laurent David
- Departments of Computer Science and of Life Sciences, Sorbonne Université (SU) / UPMC, Paris, France
| | - Agathe Delaune
- Departments of Computer Science and of Life Sciences, Sorbonne Université (SU) / UPMC, Paris, France
| | - Samia Djerroud
- Departments of Computer Science and of Life Sciences, Sorbonne Université (SU) / UPMC, Paris, France
| | - Pauline Fourgoux
- Department of Biology and of Computer Science, Univ. Paris-Sud, Université Paris-Saclay (UPSay), Orsay, France
| | - Nadège Guiglielmoni
- Department of Biology and of Computer Science, Univ. Paris-Sud, Université Paris-Saclay (UPSay), Orsay, France
| | - Jeanne Laurentie
- Departments of Computer Science and of Life Sciences, Sorbonne Université (SU) / UPMC, Paris, France
| | - Nathalie Lehmann
- Departments of Computer Science and of Life Sciences, Sorbonne Université (SU) / UPMC, Paris, France
| | - Camille Lochard
- Department of Biology and of Computer Science, Univ. Paris-Sud, Université Paris-Saclay (UPSay), Orsay, France
| | - Rémi Montagne
- Department of Biology and of Computer Science, Univ. Paris-Sud, Université Paris-Saclay (UPSay), Orsay, France
| | - Vasiliki Myrodia
- Departments of Computer Science and of Life Sciences, Sorbonne Université (SU) / UPMC, Paris, France
| | - Vaitea Opuu
- Department of Biology and of Computer Science, Univ. Paris-Sud, Université Paris-Saclay (UPSay), Orsay, France
| | - Elise Parey
- Departments of Computer Science and of Life Sciences, Sorbonne Université (SU) / UPMC, Paris, France
| | - Lélia Polit
- Departments of Computer Science and of Life Sciences, Sorbonne Université (SU) / UPMC, Paris, France
| | - Sylvain Privé
- Department of Biology and of Computer Science, Univ. Paris-Sud, Université Paris-Saclay (UPSay), Orsay, France
| | - Chloé Quignot
- Departments of Computer Science and of Life Sciences, Sorbonne Université (SU) / UPMC, Paris, France
| | - Maria Ruiz-Cuevas
- Departments of Computer Science and of Life Sciences, Sorbonne Université (SU) / UPMC, Paris, France
| | - Mariam Sissoko
- Departments of Computer Science and of Life Sciences, Sorbonne Université (SU) / UPMC, Paris, France
| | - Nicolas Sompairac
- Departments of Computer Science and of Life Sciences, Sorbonne Université (SU) / UPMC, Paris, France
| | - Audrey Vallerix
- Department of Biology and of Computer Science, Univ. Paris-Sud, Université Paris-Saclay (UPSay), Orsay, France
| | - Violaine Verrecchia
- Department of Biology and of Computer Science, Univ. Paris-Sud, Université Paris-Saclay (UPSay), Orsay, France
| | - Marc Delarue
- Unit of Structural Dynamics of Macromolecules, CNRS, Institut Pasteur, Paris, France
| | - Raphael Guérois
- Institute for Integrative Biology of the Cell (I2BC), IBITECS, CEA, CNRS, Univ. Paris-Sud, UPSay, Gif-sur-Yvette cedex, France
| | - Yann Ponty
- AMIBio team, Laboratoire d’informatique de l’École polytechnique (LIX, UMR 7161) / Inria Saclay, UPSay, Palaiseau, France
| | - Sophie Sacquin-Mora
- Laboratoire de Biochimie Théorique, UPR 9080 CNRS Institut de Biologie Physico-Chimique, Paris, France
| | - Alessandra Carbone
- Sorbonne Université / UPMC, CNRS, IBPS, Laboratoire de Biologie Computationnelle et Quantitative (LCQB), UMR 7238, Paris, France
- Institut Universitaire de France
| | | | - Stéphane Le Crom
- Sorbonne Université / UPMC, Univ. Antilles, Univ. Nice Sophia Antipolis, CNRS, Evolution Paris Seine - Institut de Biologie Paris Seine (EPS - IBPS), Paris, France
| | - Olivier Lespinet
- Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Univ. Paris-Sud, UPSay, Gif-sur-Yvette cedex, France
| | - Martin Weigt
- Sorbonne Université / UPMC, CNRS, IBPS, Laboratoire de Biologie Computationnelle et Quantitative (LCQB), UMR 7238, Paris, France
| | - Samer Abboud
- Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Univ. Paris-Sud, UPSay, Gif-sur-Yvette cedex, France
| | - Juliana Bernardes
- Sorbonne Université / UPMC, CNRS, IBPS, Laboratoire de Biologie Computationnelle et Quantitative (LCQB), UMR 7238, Paris, France
| | - Guillaume Bouvier
- Department of Structural Biology and CheImistry (CNRS UMR3528) - Center of Bioinformatics, Biostatistics and Integrative Biology (CNRS USR3756) - Structural Bioinformatics Unit, Institut Pasteur, Paris, France
| | - Chloé Dequeker
- Sorbonne Université / UPMC, CNRS, IBPS, Laboratoire de Biologie Computationnelle et Quantitative (LCQB), UMR 7238, Paris, France
| | - Arnaud Ferré
- MaIAGE, INRA, UPSay, Jouy-en-Josas, France and LIMSI, CNRS, UPSay, Orsay, France
| | - Patrick Fuchs
- Sorbonne Université / UPMC, Ecole Normale Supérieure - PLS Research University, Département de Chimie, CNRS, Laboratoire des Biomolécules, UMR 7203 - Univ. Paris Diderot, Sorbonne Paris Cité, Paris, France
| | - Gaëlle Lelandais
- Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Univ. Paris-Sud, UPSay, Gif-sur-Yvette cedex, France
| | - Pierre Poulain
- Mitochondria, Metals and Oxidative Stress Group, Institut Jacques Monod, UMR 7592, Univ. Paris Diderot, CNRS, Sorbonne Paris Cité, Paris, France
| | - Hugues Richard
- Sorbonne Université / UPMC, CNRS, IBPS, Laboratoire de Biologie Computationnelle et Quantitative (LCQB), UMR 7238, Paris, France
| | - Hugo Schweke
- Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Univ. Paris-Sud, UPSay, Gif-sur-Yvette cedex, France
| | - Elodie Laine
- Sorbonne Université / UPMC, CNRS, IBPS, Laboratoire de Biologie Computationnelle et Quantitative (LCQB), UMR 7238, Paris, France
- * E-mail: (EL); (AL)
| | - Anne Lopes
- Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Univ. Paris-Sud, UPSay, Gif-sur-Yvette cedex, France
- * E-mail: (EL); (AL)
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Raia P, Béguin P, Henneke G, Delarue M, Sauguet L. Secret From the ABYSS: Structures of the D-Family DNA Polymerase (POLD) Reveal that DNA Replication and DNA Transcription Share a Joint Evolutionary History in Archaea. Biophys J 2018. [DOI: 10.1016/j.bpj.2017.11.1215] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022] Open
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31
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Howard RJ, Fourati Z, Heusser SA, Hu H, Ruza RR, Sauguet L, Lindahl E, Delarue M. Structural Details of an Allosteric Mechanism for Bimodal Anesthetic Modulation of Pentameric Ligand-Gated Ion Channels. Biophys J 2018. [DOI: 10.1016/j.bpj.2017.11.1137] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022] Open
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32
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33
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Nemecz Á, Hu H, Fourati Z, Van Renterghem C, Delarue M, Corringer PJ. Full mutational mapping of titratable residues helps to identify proton-sensors involved in the control of channel gating in the Gloeobacter violaceus pentameric ligand-gated ion channel. PLoS Biol 2017; 15:e2004470. [PMID: 29281623 PMCID: PMC5760087 DOI: 10.1371/journal.pbio.2004470] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2017] [Revised: 01/09/2018] [Accepted: 12/04/2017] [Indexed: 11/19/2022] Open
Abstract
The Gloeobacter violaceus ligand-gated ion channel (GLIC) has been extensively studied by X-ray crystallography and other biophysical techniques. This provided key insights into the general gating mechanism of pentameric ligand-gated ion channel (pLGIC) signal transduction. However, the GLIC is activated by lowering the pH and the location of its putative proton activation site(s) still remain(s) unknown. To this end, every Asp, Glu, and His residue was mutated individually or in combination and investigated by electrophysiology. In addition to the mutational analysis, key mutations were structurally resolved to address whether particular residues contribute to proton sensing, or alternatively to GLIC-gating, independently of the side chain protonation. The data show that multiple residues located below the orthosteric site, notably E26, D32, E35, and D122 in the lower part of the extracellular domain (ECD), along with E222, H235, E243, and H277 in the transmembrane domain (TMD), alter GLIC activation. D122 and H235 were found to also alter GLIC expression. E35 is identified as a key proton-sensing residue, whereby neutralization of its side chain carboxylate stabilizes the active state. Thus, proton activation occurs allosterically to the orthosteric site, at the level of multiple loci with a key contribution of the coupling interface between the ECD and TMD. Pentameric ligand-gated ion channels are an important class of receptors that are involved in many neurological diseases. They have been extensively studied but a full understanding of their mechanism of action has yet to be achieved. In an effort to bypass obstacles in the research of human receptors, bacterial versions have been used to characterize the family’s structure-function relationship. One key bacterial receptor, known as GLIC, has lead the way in structural resolution of various mechanistic states along the gating pathway, yet its activation by protons is significantly less understood than its human counterparts. To define the site(s) involved in proton gating, we systematically mutated all titratable residues near the pH50 of activation: Asp, Glu, and His. We determined that a previously established His residue in the transmembrane domain is structurally important but likely plays little or no role in proton gating. We instead found that proton activation is a complex multiple loci mechanism, with the key contribution stemming from the coupling interface between the extracellular and transmembrane domain, with E35 acting as a key proton-sensing residue.
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Affiliation(s)
- Ákos Nemecz
- Unité Récepteurs-Canaux, Unité Mixte de Recherche 3571 du Centre National de la Recherche Scientifique, Institut Pasteur, Paris, France
| | - Haidai Hu
- Unité de Dynamique Structurale des Macromolécules, Unité Mixte de Recherche 3528 du Centre National de la Recherche Scientifique, Institut Pasteur, Paris, France
| | - Zaineb Fourati
- Unité de Dynamique Structurale des Macromolécules, Unité Mixte de Recherche 3528 du Centre National de la Recherche Scientifique, Institut Pasteur, Paris, France
| | - Catherine Van Renterghem
- Unité Récepteurs-Canaux, Unité Mixte de Recherche 3571 du Centre National de la Recherche Scientifique, Institut Pasteur, Paris, France
| | - Marc Delarue
- Unité de Dynamique Structurale des Macromolécules, Unité Mixte de Recherche 3528 du Centre National de la Recherche Scientifique, Institut Pasteur, Paris, France
| | - Pierre-Jean Corringer
- Unité Récepteurs-Canaux, Unité Mixte de Recherche 3571 du Centre National de la Recherche Scientifique, Institut Pasteur, Paris, France
- * E-mail:
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Abstract
We propose a novel stochastic method to generate Brownian paths conditioned to start at an initial point and end at a given final point during a fixed time tf under a given potential U(x). These paths are sampled with a probability given by the overdamped Langevin dynamics. We show that these paths can be exactly generated by a local stochastic partial differential equation. This equation cannot be solved in general but we present several approximations that are valid either in the low temperature regime or in the presence of barrier crossing. We show that this method warrants the generation of statistically independent transition paths. It is computationally very efficient. We illustrate the method first on two simple potentials, the two-dimensional Mueller potential and the Mexican hat potential, and then on the multi-dimensional problem of conformational transitions in proteins using the "Mixed Elastic Network Model" as a benchmark.
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Affiliation(s)
- Marc Delarue
- Unité de Dynamique Structurale des Macromolécules, UMR 3528 du CNRS, Institut Pasteur, 75015 Paris, France
| | - Patrice Koehl
- Department of Computer Science and Genome Center, University of California, Davis, California 95616, USA
| | - Henri Orland
- Institut de Physique Théorique, CEA, URA 2306 du CNRS, F-91191 Gif-sur-Yvette, France and Beijing Computational Science Research Center, Building 9, East Zone, ZPark II, No.10 East Xibeiwang Road, Haidian District, Beijing 100193, China
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35
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Lev B, Murail S, Poitevin F, Cromer BA, Baaden M, Delarue M, Allen TW. String method solution of the gating pathways for a pentameric ligand-gated ion channel. Proc Natl Acad Sci U S A 2017; 114:E4158-E4167. [PMID: 28487483 PMCID: PMC5448215 DOI: 10.1073/pnas.1617567114] [Citation(s) in RCA: 48] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023] Open
Abstract
Pentameric ligand-gated ion channels control synaptic neurotransmission by converting chemical signals into electrical signals. Agonist binding leads to rapid signal transduction via an allosteric mechanism, where global protein conformational changes open a pore across the nerve cell membrane. We use all-atom molecular dynamics with a swarm-based string method to solve for the minimum free-energy gating pathways of the proton-activated bacterial GLIC channel. We describe stable wetted/open and dewetted/closed states, and uncover conformational changes in the agonist-binding extracellular domain, ion-conducting transmembrane domain, and gating interface that control communication between these domains. Transition analysis is used to compute free-energy surfaces that suggest allosteric pathways; stabilization with pH; and intermediates, including states that facilitate channel closing in the presence of an agonist. We describe a switching mechanism that senses proton binding by marked reorganization of subunit interface, altering the packing of β-sheets to induce changes that lead to asynchronous pore-lining M2 helix movements. These results provide molecular details of GLIC gating and insight into the allosteric mechanisms for the superfamily of pentameric ligand-gated channels.
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Affiliation(s)
- Bogdan Lev
- School of Science, RMIT University, Melbourne, VIC 3001, Australia
| | - Samuel Murail
- Laboratoire de Biochimie Théorique, CNRS, UPR9080, Université Paris Diderot, Sorbonne Paris Cité, F-75005 Paris, France
| | - Frédéric Poitevin
- Department of Structural Biology, Stanford University, Stanford, CA 94305
- Stanford PULSE Institute, SLAC National Accelerator Laboratory, Menlo Park, CA 94025
| | - Brett A Cromer
- School of Science, RMIT University, Melbourne, VIC 3001, Australia
- School of Health and Biomedical Sciences, RMIT University, Bundoora, VIC 3083, Australia
| | - Marc Baaden
- Laboratoire de Biochimie Théorique, CNRS, UPR9080, Université Paris Diderot, Sorbonne Paris Cité, F-75005 Paris, France
| | - Marc Delarue
- Department of Structural Biology and Chemistry, Institut Pasteur and UMR 3528 du CNRS, F-75015 Paris, France
| | - Toby W Allen
- School of Science, RMIT University, Melbourne, VIC 3001, Australia;
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36
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Menny A, Lefebvre SN, Schmidpeter PA, Drège E, Fourati Z, Delarue M, Edelstein SJ, Nimigean CM, Joseph D, Corringer PJ. Identification of a pre-active conformation of a pentameric channel receptor. eLife 2017; 6. [PMID: 28294942 PMCID: PMC5398890 DOI: 10.7554/elife.23955] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2016] [Accepted: 03/14/2017] [Indexed: 11/26/2022] Open
Abstract
Pentameric ligand-gated ion channels (pLGICs) mediate fast chemical signaling through global allosteric transitions. Despite the existence of several high-resolution structures of pLGICs, their dynamical properties remain elusive. Using the proton-gated channel GLIC, we engineered multiple fluorescent reporters, each incorporating a bimane and a tryptophan/tyrosine, whose close distance causes fluorescence quenching. We show that proton application causes a global compaction of the extracellular subunit interface, coupled to an outward motion of the M2-M3 loop near the channel gate. These movements are highly similar in lipid vesicles and detergent micelles. These reorganizations are essentially completed within 2 ms and occur without channel opening at low proton concentration, indicating that they report a pre-active intermediate state in the transition pathway toward activation. This provides a template to investigate the gating of eukaryotic neurotransmitter receptors, for which intermediate states also participate in activation. DOI:http://dx.doi.org/10.7554/eLife.23955.001 In the nervous system, proteins of the pLGIC family are found in the membrane that surrounds each neuron. These proteins have channels that can allow ions to pass through the membrane and are responsible for transmitting electrical signals from one neuron to the next. Small molecules called neurotransmitters interact with the pLGICs to open or close the ion channel. If the ability of the pLGIC channels to open is altered, it can lead to behavioral changes like addiction, or diseases such as schizophrenia or epilepsy. For a pLGIC channel to switch between the “open” and “closed” states, specific parts of the protein need to move in relation to each other. However, to study these transitions researchers have previously relied on comparing the three-dimensional structures of open and closed pLGICs extracted out of the cell membrane. Different techniques are needed to directly follow these movements within membranes. Bacteria also have proteins belonging to the pLGIC family, and Menny et al. have now investigated one such bacterial protein to understand how pLGICs open. First, a small fluorescent molecule that glows differently if the environment around it changes was attached to various parts of the bacterial channel. These fluorescent markers revealed how several parts of the protein move and they also made it possible to measure how quickly these movements take place. Some of these movements happen before the channel opens, suggesting that the activation of this pLGIC protein happens in stages and involves the protein adopting a temporary intermediate state. The next step will be to better understand the structure of the intermediate state, which could help us to understand how pLGICs work in the nervous systems of animals. In future this may aid the design of new drugs that can modify the activity of these channels in patients with neurological conditions or addictions. DOI:http://dx.doi.org/10.7554/eLife.23955.002
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Affiliation(s)
- Anaïs Menny
- Channel Receptors Unit, Institut Pasteur, Paris, France.,Unité Mixte de Recherche 3571, Centre National de la Recherche Scientifique, Paris, France.,Université Pierre et Marie Curie, Cellule Pasteur, Paris, France
| | - Solène N Lefebvre
- Channel Receptors Unit, Institut Pasteur, Paris, France.,Unité Mixte de Recherche 3571, Centre National de la Recherche Scientifique, Paris, France.,Université Pierre et Marie Curie, Cellule Pasteur, Paris, France
| | - Philipp Am Schmidpeter
- Departments of Anesthesiology, Physiology and Biophysics, Biochemistry, Weill Cornell Medicine, New York, United States
| | - Emmanuelle Drège
- BioCIS, Université Paris-Sud, CNRS, Université Paris-Saclay, Châtenay-Malabry, France
| | - Zaineb Fourati
- Unité de Dynamique Structurale des Macromolécules, Institut Pasteur, Paris, France.,Unité Mixte de Recherche 3528, Centre National de la Recherche Scientifique, Paris, France
| | - Marc Delarue
- Unité de Dynamique Structurale des Macromolécules, Institut Pasteur, Paris, France.,Unité Mixte de Recherche 3528, Centre National de la Recherche Scientifique, Paris, France
| | - Stuart J Edelstein
- Biologie Cellulaire de la Synapse, Institute of Biology, Ecole Normale Supérieure, Paris, France
| | - Crina M Nimigean
- Departments of Anesthesiology, Physiology and Biophysics, Biochemistry, Weill Cornell Medicine, New York, United States
| | - Delphine Joseph
- BioCIS, Université Paris-Sud, CNRS, Université Paris-Saclay, Châtenay-Malabry, France
| | - Pierre-Jean Corringer
- Channel Receptors Unit, Institut Pasteur, Paris, France.,Unité Mixte de Recherche 3571, Centre National de la Recherche Scientifique, Paris, France
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37
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Koehl P, Poitevin F, Navaza R, Delarue M. The Renormalization Group and Its Applications to Generating Coarse-Grained Models of Large Biological Molecular Systems. J Chem Theory Comput 2017; 13:1424-1438. [PMID: 28170254 DOI: 10.1021/acs.jctc.6b01136] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Understanding the dynamics of biomolecules is the key to understanding their biological activities. Computational methods ranging from all-atom molecular dynamics simulations to coarse-grained normal-mode analyses based on simplified elastic networks provide a general framework to studying these dynamics. Despite recent successes in studying very large systems with up to a 100,000,000 atoms, those methods are currently limited to studying small- to medium-sized molecular systems due to computational limitations. One solution to circumvent these limitations is to reduce the size of the system under study. In this paper, we argue that coarse-graining, the standard approach to such size reduction, must define a hierarchy of models of decreasing sizes that are consistent with each other, i.e., that each model contains the information of the dynamics of its predecessor. We propose a new method, Decimate, for generating such a hierarchy within the context of elastic networks for normal-mode analysis. This method is based on the concept of the renormalization group developed in statistical physics. We highlight the details of its implementation, with a special focus on its scalability to large systems of up to millions of atoms. We illustrate its application on two large systems, the capsid of a virus and the ribosome translation complex. We show that highly decimated representations of those systems, containing down to 1% of their original number of atoms, still capture qualitatively and quantitatively their dynamics. Decimate is available as an OpenSource resource.
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Affiliation(s)
- Patrice Koehl
- Department of Computer Sciences and Genome Center, University of California, Davis , Davis, California 95616, United States
| | - Frédéric Poitevin
- Department of Structural Biology, Stanford University , Stanford, California 94305, United States.,Stanford PULSE Institute, SLAC National Accelerator Laboratory, Standford University , Menlo Park, California 94025, United States
| | - Rafael Navaza
- Platform of Crystallogenesis and Crystallography, CiTech, Institut Pasteur , 75015 Paris, France
| | - Marc Delarue
- Unité de Dynamique Structurale des Macromolécules, UMR 3528 du CNRS, Institut Pasteur , 75015 Paris, France
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38
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Hu H, Nemecz A, Fourati Z, Corringer PJ, Delarue M. Uncommon Features of a Novel γ-Proteobacterial Pentameric Ligand-Gated Ion Channel Revealed by its Crystal Structure. Biophys J 2017. [DOI: 10.1016/j.bpj.2016.11.1739] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022] Open
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39
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Fourati Z, Ruza RR, Laverty D, Drege E, Delarue-Cochin S, Joseph D, Koehl P, Smart T, Delarue M. Barbiturates Bind in the GLIC Ion Channel Pore and Cause Inhibition by Stabilizing a Shut State. Biophys J 2017. [DOI: 10.1016/j.bpj.2016.11.2984] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022] Open
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40
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Lev B, Murail S, Poitevin F, Cromer BA, Baaden M, Delarue M, Allen TW. Gating Pathways for a Pentameric Ligand-Gated Ion Channel Solved by Atomistic String Method Simulations. Biophys J 2017. [DOI: 10.1016/j.bpj.2016.11.2553] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022] Open
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41
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Dolega ME, Delarue M, Ingremeau F, Prost J, Delon A, Cappello G. Cell-like pressure sensors reveal increase of mechanical stress towards the core of multicellular spheroids under compression. Nat Commun 2017; 8:14056. [PMID: 28128198 PMCID: PMC5290143 DOI: 10.1038/ncomms14056] [Citation(s) in RCA: 124] [Impact Index Per Article: 17.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2016] [Accepted: 11/21/2016] [Indexed: 12/22/2022] Open
Abstract
The surrounding microenvironment limits tumour expansion, imposing a compressive stress on the tumour, but little is known how pressure propagates inside the tumour. Here we present non-destructive cell-like microsensors to locally quantify mechanical stress distribution in three-dimensional tissue. Our sensors are polyacrylamide microbeads of well-defined elasticity, size and surface coating to enable internalization within the cellular environment. By isotropically compressing multicellular spheroids (MCS), which are spherical aggregates of cells mimicking a tumour, we show that the pressure is transmitted in a non-trivial manner inside the MCS, with a pressure rise towards the core. This observed pressure profile is explained by the anisotropic arrangement of cells and our results suggest that such anisotropy alone is sufficient to explain the pressure rise inside MCS composed of a single cell type. Furthermore, such pressure distribution suggests a direct link between increased mechanical stress and previously observed lack of proliferation within the spheroids core.
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Affiliation(s)
- M. E. Dolega
- Université Grenoble Alpes, Laboratoire Interdisciplinaire de Physique, CNRS, F-38000 Grenoble, France
| | - M. Delarue
- Institut Curie, CNRS, Université P. et M. Curie, UMR168, F-75231 Paris, France
| | - F. Ingremeau
- Université Grenoble Alpes, Laboratoire Interdisciplinaire de Physique, CNRS, F-38000 Grenoble, France
| | - J. Prost
- Institut Curie, CNRS, Université P. et M. Curie, UMR168, F-75231 Paris, France
| | - A. Delon
- Université Grenoble Alpes, Laboratoire Interdisciplinaire de Physique, CNRS, F-38000 Grenoble, France
| | - G. Cappello
- Université Grenoble Alpes, Laboratoire Interdisciplinaire de Physique, CNRS, F-38000 Grenoble, France
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42
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Hsieh YC, Poitevin F, Delarue M, Koehl P. Comparative Normal Mode Analysis of the Dynamics of DENV and ZIKV Capsids. Front Mol Biosci 2016; 3:85. [PMID: 28083537 PMCID: PMC5187361 DOI: 10.3389/fmolb.2016.00085] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2016] [Accepted: 12/12/2016] [Indexed: 11/13/2022] Open
Abstract
Key steps in the life cycle of a virus, such as the fusion event as the virus infects a host cell and its maturation process, relate to an intricate interplay between the structure and the dynamics of its constituent proteins, especially those that define its capsid, much akin to an envelope that protects its genomic material. We present a comprehensive, comparative analysis of such interplay for the capsids of two viruses from the flaviviridae family, Dengue (DENV) and Zika (ZIKV). We use for that purpose our own software suite, DD-NMA, which is based on normal mode analysis. We describe the elements of DD-NMA that are relevant to the analysis of large systems, such as virus capsids. In particular, we introduce our implementation of simplified elastic networks and justify their parametrization. Using DD-NMA, we illustrate the importance of packing interactions within the virus capsids on the dynamics of the E proteins of DENV and ZIKV. We identify differences between the computed atomic fluctuations of the E proteins in DENV and ZIKV and relate those differences to changes observed in their high resolution structures. We conclude with a discussion on additional analyses that are needed to fully characterize the dynamics of the two viruses.
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Affiliation(s)
- Yin-Chen Hsieh
- Department of Computer Science and Genome Center, University of California, Davis Davis, CA, USA
| | - Frédéric Poitevin
- Department of Structural Biology, Stanford UniversityStanford, CA, USA; SLAC National Accelerator Laboratory, Stanford PULSE InstituteMenlo Park, CA, USA
| | - Marc Delarue
- Unit of Structural Dynamics of Macromolecules, UMR 3528 du Centre National de la Recherche Scientifique, Institut Pasteur Paris, France
| | - Patrice Koehl
- Department of Computer Science and Genome Center, University of California, Davis Davis, CA, USA
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43
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Fourati Z, Ruza RR, Laverty D, Drège E, Delarue-Cochin S, Joseph D, Koehl P, Smart T, Delarue M. Barbiturates Bind in the GLIC Ion Channel Pore and Cause Inhibition by Stabilizing a Closed State. J Biol Chem 2016; 292:1550-1558. [PMID: 27986812 DOI: 10.1074/jbc.m116.766964] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2016] [Revised: 12/06/2016] [Indexed: 12/12/2022] Open
Abstract
Barbiturates induce anesthesia by modulating the activity of anionic and cationic pentameric ligand-gated ion channels (pLGICs). Despite more than a century of use in clinical practice, the prototypic binding site for this class of drugs within pLGICs is yet to be described. In this study, we present the first X-ray structures of barbiturates bound to GLIC, a cationic prokaryotic pLGIC with excellent structural homology to other relevant channels sensitive to general anesthetics and, as shown here, to barbiturates, at clinically relevant concentrations. Several derivatives of barbiturates containing anomalous scatterers were synthesized, and these derivatives helped us unambiguously identify a unique barbiturate binding site within the central ion channel pore in a closed conformation. In addition, docking calculations around the observed binding site for all three states of the receptor, including a model of the desensitized state, showed that barbiturates preferentially stabilize the closed state. The identification of this pore binding site sheds light on the mechanism of barbiturate inhibition of cationic pLGICs and allows the rationalization of several structural and functional features previously observed for barbiturates.
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Affiliation(s)
- Zaineb Fourati
- From the Unité de Dynamique Structurale des Macromolécules, UMR 3528 du CNRS, Institut Pasteur, 75015 Paris, France
| | - Reinis Reinholds Ruza
- From the Unité de Dynamique Structurale des Macromolécules, UMR 3528 du CNRS, Institut Pasteur, 75015 Paris, France
| | - Duncan Laverty
- the Department of Neuroscience, Physiology and Pharmacology, University College London, London WC1E 6BT, United Kingdom
| | - Emmanuelle Drège
- the UMR 8076 du CNRS, BioCIS, Faculté de Pharmacie, Université Paris Sud, 92296 Chatenay-Malabry, France
| | - Sandrine Delarue-Cochin
- the UMR 8076 du CNRS, BioCIS, Faculté de Pharmacie, Université Paris Sud, 92296 Chatenay-Malabry, France
| | - Delphine Joseph
- the UMR 8076 du CNRS, BioCIS, Faculté de Pharmacie, Université Paris Sud, 92296 Chatenay-Malabry, France
| | - Patrice Koehl
- the Department of Computer Science, University of California, Davis, California 95616
| | - Trevor Smart
- the Department of Neuroscience, Physiology and Pharmacology, University College London, London WC1E 6BT, United Kingdom.
| | - Marc Delarue
- From the Unité de Dynamique Structurale des Macromolécules, UMR 3528 du CNRS, Institut Pasteur, 75015 Paris, France.
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Abstract
Programmed cell death (PCD) is a ubiquitous genetically regulated process consisting of the activation of finely controlled signalling pathways that lead to cellular suicide. PCD can be part of a developmental programme (dPCD) or be triggered by environmental conditions (ePCD). In plant cells, as in animal cells, extensive chromatin condensation and degradation of the nuclear DNA are among the most conspicuous features of cells undergoing PCD. Changes in chromatin condensation could either reflect the structural changes required for internucleosomal fragmentation of nuclear DNA or relate to large-scale chromatin rearrangements associated with a major transcriptional switch occurring during cell death. The aim of this review is to give an update on plant PCD processes from a chromatin point of view. The first part will be dedicated to chromatin conformational changes associated with cell death observed in various developmental and physiological conditions, whereas the second part will be devoted to histone dynamics and DNA modifications associated with critical changes in genome expression during the cell death process.
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Affiliation(s)
- D Latrasse
- Institute of Plant Sciences Paris-Saclay IPS2, CNRS, INRA, Université Paris-Sud, Université Evry, Université Paris-Saclay, Batiment 630, 91405 Orsay, France
- Institute of Plant Sciences Paris-Saclay IPS2, Paris Diderot, Sorbonne Paris-Cité, Bâtiment 630, 91405 Orsay, France
| | - M Benhamed
- Institute of Plant Sciences Paris-Saclay IPS2, CNRS, INRA, Université Paris-Sud, Université Evry, Université Paris-Saclay, Batiment 630, 91405 Orsay, France
- Institute of Plant Sciences Paris-Saclay IPS2, Paris Diderot, Sorbonne Paris-Cité, Bâtiment 630, 91405 Orsay, France
| | - C Bergounioux
- Institute of Plant Sciences Paris-Saclay IPS2, CNRS, INRA, Université Paris-Sud, Université Evry, Université Paris-Saclay, Batiment 630, 91405 Orsay, France
- Institute of Plant Sciences Paris-Saclay IPS2, Paris Diderot, Sorbonne Paris-Cité, Bâtiment 630, 91405 Orsay, France
| | - C Raynaud
- Institute of Plant Sciences Paris-Saclay IPS2, CNRS, INRA, Université Paris-Sud, Université Evry, Université Paris-Saclay, Batiment 630, 91405 Orsay, France
- Institute of Plant Sciences Paris-Saclay IPS2, Paris Diderot, Sorbonne Paris-Cité, Bâtiment 630, 91405 Orsay, France
| | - M Delarue
- Institute of Plant Sciences Paris-Saclay IPS2, CNRS, INRA, Université Paris-Sud, Université Evry, Université Paris-Saclay, Batiment 630, 91405 Orsay, France
- Institute of Plant Sciences Paris-Saclay IPS2, Paris Diderot, Sorbonne Paris-Cité, Bâtiment 630, 91405 Orsay, France
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45
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Sauguet L, Raia P, Henneke G, Delarue M. Shared active site architecture between archaeal PolD and multi-subunit RNA polymerases revealed by X-ray crystallography. Nat Commun 2016; 7:12227. [PMID: 27548043 PMCID: PMC4996933 DOI: 10.1038/ncomms12227] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2016] [Accepted: 06/10/2016] [Indexed: 02/06/2023] Open
Abstract
Archaeal replicative DNA polymerase D (PolD) constitute an atypical class of DNA polymerases made of a proofreading exonuclease subunit (DP1) and a larger polymerase catalytic subunit (DP2), both with unknown structures. We have determined the crystal structures of Pyrococcus abyssi DP1 and DP2 at 2.5 and 2.2 Å resolution, respectively, revealing a catalytic core strikingly different from all other known DNA polymerases (DNAPs). Rather, the PolD DP2 catalytic core has the same ‘double-psi β-barrel' architecture seen in the RNA polymerase (RNAP) superfamily, which includes multi-subunit transcriptases of all domains of life, homodimeric RNA-silencing pathway RNAPs and atypical viral RNAPs. This finding bridges together, in non-viral world, DNA transcription and DNA replication within the same protein superfamily. This study documents further the complex evolutionary history of the DNA replication apparatus in different domains of life and proposes a classification of all extant DNAPs. The structures of many DNA polymerases is known, but PolD was a missing piece. Here, the authors report the crystal structure of this protein and use it to connect the DNA replication machinery with the transcription machinery in the same protein family.
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Affiliation(s)
- Ludovic Sauguet
- Unit of Structural Dynamics of Macromolecules, Pasteur Institute and CNRS UMR 3528, 75015 Paris, France
| | - Pierre Raia
- Unit of Structural Dynamics of Macromolecules, Pasteur Institute and CNRS UMR 3528, 75015 Paris, France.,Pierre and Marie Curie University, Paris 6, 75006 Paris, France
| | - Ghislaine Henneke
- Ifremer, UMR 6197, Laboratoire de Microbiologie des Environnements Extrêmes, 29280 Plouzané, France.,UBO, UMR 6197, Laboratoire de Microbiologie des Environnements Extrêmes, 29280 Plouzané, France.,CNRS, UMR 6197, Laboratoire de Microbiologie des Environnements Extrêmes, 29280 Plouzané, France
| | - Marc Delarue
- Unit of Structural Dynamics of Macromolecules, Pasteur Institute and CNRS UMR 3528, 75015 Paris, France
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46
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Loc'h J, Rosario S, Delarue M. Structural Basis for a New Templated Activity by Terminal Deoxynucleotidyl Transferase: Implications for V(D)J Recombination. Structure 2016; 24:1452-63. [PMID: 27499438 DOI: 10.1016/j.str.2016.06.014] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2016] [Revised: 06/13/2016] [Accepted: 06/13/2016] [Indexed: 12/20/2022]
Abstract
Eukaryotic DNA polymerase of the polX family, such as pol μ and terminal deoxynucleotidyl transferase (TdT), are key components of the non-homologous end-joining or V(D)J recombination machinery, respectively. The established role of TdT is to add random nucleotides during V(D)J recombination. Here we show that TdT also has a templated-polymerase activity, similar to pol μ, in the presence of higher concentrations of a downstream DNA duplex, and performs a micro-homology single base-pair search to align the DNA synapsis. To understand the molecular basis of this alignment, we solve crystal structures of TdT with four DNA strands and study the influence of the 3' protruding end. Two mutations in TdT inspired by sequence alignments with pol μ further improve the templated activity. We propose that both templated and untemplated activities of TdT are needed to explain the distributions of lengths of N regions observed experimentally in T cell receptors and antibodies.
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Affiliation(s)
- Jérôme Loc'h
- Unité de Dynamique Structurale des Macromolécules, Institut Pasteur, UMR 3528 du C.N.R.S., 25 rue du Dr Roux, 75015 Paris, France
| | - Sandrine Rosario
- Unité de Dynamique Structurale des Macromolécules, Institut Pasteur, UMR 3528 du C.N.R.S., 25 rue du Dr Roux, 75015 Paris, France
| | - Marc Delarue
- Unité de Dynamique Structurale des Macromolécules, Institut Pasteur, UMR 3528 du C.N.R.S., 25 rue du Dr Roux, 75015 Paris, France.
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47
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Abstract
We present a method aimed at sampling charge density fluctuations in Coulomb systems. The derivation follows from a functional integral representation of the partition function in terms of charge density fluctuations. Starting from the mean-field solution given by the Poisson-Boltzmann equation, an original approach is proposed to numerically sample fluctuations around it, through the propagation of a Langevin-like stochastic partial differential equation (SPDE). The diffusion tensor of the SPDE can be chosen so as to avoid the numerical complexity linked to long-range Coulomb interactions, effectively rendering the theory completely local. A finite-volume implementation of the SPDE is described, and the approach is illustrated with preliminary results on the study of a system made of two like-charge ions immersed in a bath of counterions.
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Affiliation(s)
- Frédéric Poitevin
- Institut de Physique Théorique, Université Paris Saclay, CEA, UMR3681 du CNRS, F-91191 Gif-sur-Yvette, France
| | - Marc Delarue
- Unit of Structural Dynamics of Macromolecules, UMR 3528 du CNRS, Institut Pasteur, 75015 Paris, France
| | - Henri Orland
- Institut de Physique Théorique, Université Paris Saclay, CEA, UMR3681 du CNRS, F-91191 Gif-sur-Yvette, France.,Beijing Computational Science Research Center, Haidian District, Beijing 100094, China
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48
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Laurent B, Murail S, Shahsavar A, Sauguet L, Delarue M, Baaden M. Sites of Anesthetic Inhibitory Action on a Cationic Ligand-Gated Ion Channel. Structure 2016; 24:595-605. [DOI: 10.1016/j.str.2016.02.014] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2015] [Revised: 02/12/2016] [Accepted: 02/22/2016] [Indexed: 01/09/2023]
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49
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Sauguet L, Fourati Z, Prangé T, Delarue M, Colloc'h N. Structural Basis for Xenon Inhibition in a Cationic Pentameric Ligand-Gated Ion Channel. PLoS One 2016; 11:e0149795. [PMID: 26910105 PMCID: PMC4765991 DOI: 10.1371/journal.pone.0149795] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2015] [Accepted: 02/04/2016] [Indexed: 12/15/2022] Open
Abstract
GLIC receptor is a bacterial pentameric ligand-gated ion channel whose action is inhibited by xenon. Xenon has been used in clinical practice as a potent gaseous anaesthetic for decades, but the molecular mechanism of interactions with its integral membrane receptor targets remains poorly understood. Here we characterize by X-ray crystallography the xenon-binding sites within both the open and "locally-closed" (inactive) conformations of GLIC. Major binding sites of xenon, which differ between the two conformations, were identified in three distinct regions that all belong to the trans-membrane domain of GLIC: 1) in an intra-subunit cavity, 2) at the interface between adjacent subunits, and 3) in the pore. The pore site is unique to the locally-closed form where the binding of xenon effectively seals the channel. A putative mechanism of the inhibition of GLIC by xenon is proposed, which might be extended to other pentameric cationic ligand-gated ion channels.
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Affiliation(s)
- Ludovic Sauguet
- Unité de Dynamique Structurale des Macromolécules (UMR 3528 CNRS) Institut Pasteur, Paris, France
| | - Zeineb Fourati
- Unité de Dynamique Structurale des Macromolécules (UMR 3528 CNRS) Institut Pasteur, Paris, France
| | - Thierry Prangé
- Laboratoire de cristallographie et RMN biologiques (UMR 8015 CNRS), Paris, France
| | - Marc Delarue
- Unité de Dynamique Structurale des Macromolécules (UMR 3528 CNRS) Institut Pasteur, Paris, France
- * E-mail:
| | - Nathalie Colloc'h
- CNRS, UMR 6301, ISTCT CERVOxy group, GIP Cyceron, Caen, France
- UNICAEN, Normandie Univ., UMR 6301 ISTCT, Caen, France
- CEA, DSV/I2BM, UMR 6301 ISTCT, Caen, France
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50
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Nemecz Á, Fourati Z, Hu H, Corringer PJ, Delarue M. Elucidating Proton Sensitivity and Activation in the Gloeobacter Violaceus Ligand-Gated Ion Channel. Biophys J 2016. [DOI: 10.1016/j.bpj.2015.11.2444] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022] Open
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