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1. Discrete analysis of camelid variable domains: sequences, structures, and in-silico structure prediction: Sequence-structure characteristics of VHH domains

Author

Melarkode Vattekatte, Akhila, Shinada, Nicolas Ken, Narwani, Tarun, Noël, Floriane, Bertrand, Olivier, Meyniel, Jean-Philippe, Malpertuy, Alain, Gelly, Jean-Christophe, Cadet, Frédéric, De Brevern, Alexandre, Université de La Réunion - Faculté des Sciences et Technologies (FST), Université de La Réunion (UR), Laboratoire d'Excellence : Biogenèse et pathologies du globule rouge (Labex Gr-Ex), Université Sorbonne Paris Cité (USPC)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Université de Paris (UP), Dynamique des Structures et Interactions des Macromolécules Biologiques - Pôle de La Réunion (DSIMB Réunion), Biologie Intégrée du Globule Rouge (BIGR (UMR_S_1134 / U1134)), Institut National de la Transfusion Sanguine [Paris] (INTS)-Université Paris Diderot - Paris 7 (UPD7)-Université de La Réunion (UR)-Université des Antilles (UA)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Institut National de la Transfusion Sanguine [Paris] (INTS)-Université Paris Diderot - Paris 7 (UPD7)-Université de La Réunion (UR)-Université des Antilles (UA)-Institut National de la Santé et de la Recherche Médicale (INSERM), Institut National de la Transfusion Sanguine [Paris] (INTS)-Université de La Réunion (UR)-Institut National de la Santé et de la Recherche Médicale (INSERM)-CHU Pointe-à-Pitre/Abymes [Guadeloupe] -Université des Antilles (UA)-Université de Paris (UP), Services and solutions for Research Informatics [Paris] (Discngine), Discngine S.A.S [Paris], Institut National de la Transfusion Sanguine [Paris] (INTS), Immunité et cancer (U932), Institut Curie [Paris]-Institut National de la Santé et de la Recherche Médicale (INSERM), ISoft, Atragene (Atragene), Atragene, GR-Ex, Laboratoire d'Excellence, GR-Ex, PEACCEL, Ministry of Research (France)., University Paris Diderot, Sorbonne, Paris Cité (France)., Discngine, Paris, France., ANRT, France., Conseil Régional de la Réunion., The European Social Fund EU (ESF)., French National Computing Centre CINES under grant no. A0010707621 by the GENCI (Grand Equipement National de Calcul Intensif)., French National Computing Centre CINES under grant no. A0040710426 by the GENCI (Grand Equipement National de Calcul Intensif)., University of La Réunion, Réunion Island (France)., National Institute for Blood Transfusion (INTS, France)., National Institute for Health and Medical Research (INSERM, France)., Indo-French Centre for the Promotion of Advanced Research/CEFIPRA: 5302-2., ANR-18-IDEX-0001,Université de Paris,Université de Paris(2018), and ANR-11-IDEX-0005,USPC,Université Sorbonne Paris Cité(2011)

Subjects
Frameworks, Structural alphabet, [SDV]Life Sciences [q-bio], complementarity determining regions, Bioinformatics Keywords Secondary structure, Sequence structure relationship, [SDV.BBM]Life Sciences [q-bio]/Biochemistry, Molecular Biology, secondary structure, Subjects Biochemistry, [SDV.BIBS]Life Sciences [q-bio]/Quantitative Methods [q-bio.QM], nanobodies, Antibodies
Abstract

International audience; Antigen binding by antibodies requires precise orientation of the complementarity- determining region (CDR) loops in the variable domain to establish the correct contact surface. Members of the family Camelidae have a modified form of immunoglobulin gamma (IgG) with only heavy chains, called Heavy Chain only Antibodies (HCAb). Antigen binding in HCAbs is mediated by only 3 CDR loops from the single variable domain (VHH) at the N-terminus of each heavy chain. This feature of the VHH, along with other important features, e.g. easy expression, small size, thermo-stability and hydrophilicity, made them promising candidates for therapeutics and diagnostics. Thus, to design better VHH domains, it is important to thoroughly understand their sequence and structure characteristics and relationships. In this study sequence, characteristics of VHH have been analysed in depth, along with their structural features using innovative approaches, namely a structural alphabet. An elaborate summary of various studies proposing structural models of VHHs showed diversity in the algorithms used. Finally, a case study to elucidate the differences in structural models from single and multiple templates is presented. In this case study, along with the above-mentioned aspects of VHH, an exciting view of various factors in structure prediction of VHH, like template framework selection, is also discussed.

Published
2020
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2. Discrete analysis of camelid variable domains: sequences, structures, and in-silico structure prediction

Author

Melarkode Vattekatte, Akhila, Shinada, Nicolas Ken, Narwani, Tarun, Noël, Floriane, Bertrand, Olivier, Meyniel, Jean-Philippe, Malpertuy, Alain, Gelly, Jean-Christophe, Cadet, Frédéric, de Brevern, Alexandre, de Brevern, Alexandre G., Université de Paris - - Université de Paris2018 - ANR-18-IDEX-0001 - IDEX - VALID, Université Sorbonne Paris Cité - - USPC2011 - ANR-11-IDEX-0005 - IDEX - VALID, Université de La Réunion - Faculté des Sciences et Technologies (FST), Université de La Réunion (UR), Laboratoire d'Excellence : Biogenèse et pathologies du globule rouge (Labex Gr-Ex), Université Sorbonne Paris Cité (USPC)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Université Paris Cité (UPCité), Dynamique des Structures et Interactions des Macromolécules Biologiques - Pôle de La Réunion (DSIMB Réunion), Biologie Intégrée du Globule Rouge (BIGR (UMR_S_1134 / U1134)), Institut National de la Transfusion Sanguine [Paris] (INTS)-Université Paris Diderot - Paris 7 (UPD7)-Université de La Réunion (UR)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Université des Antilles (UA)-Institut National de la Transfusion Sanguine [Paris] (INTS)-Université Paris Diderot - Paris 7 (UPD7)-Université de La Réunion (UR)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Université des Antilles (UA), Institut National de la Transfusion Sanguine [Paris] (INTS)-Université de La Réunion (UR)-Institut National de la Santé et de la Recherche Médicale (INSERM)-CHU Pointe-à-Pitre/Abymes [Guadeloupe] -Université des Antilles (UA)-Université Paris Cité (UPCité), Services and solutions for Research Informatics [Paris] (Discngine), Discngine S.A.S [Paris], Institut National de la Transfusion Sanguine [Paris] (INTS), Immunité et cancer (U932), Institut Curie [Paris]-Institut National de la Santé et de la Recherche Médicale (INSERM), ISoft, Atragene (Atragene), Atragene, GR-Ex, Laboratoire d'Excellence, GR-Ex, PEACCEL, Ministry of Research (France)., University Paris Diderot, Sorbonne, Paris Cité (France)., Discngine, Paris, France., ANRT, France., Conseil Régional de la Réunion., The European Social Fund EU (ESF)., French National Computing Centre CINES under grant no. A0010707621 by the GENCI (Grand Equipement National de Calcul Intensif)., French National Computing Centre CINES under grant no. A0040710426 by the GENCI (Grand Equipement National de Calcul Intensif)., University of La Réunion, Réunion Island (France)., National Institute for Blood Transfusion (INTS, France)., National Institute for Health and Medical Research (INSERM, France)., Indo-French Centre for the Promotion of Advanced Research/CEFIPRA: 5302-2., ANR-18-IDEX-0001,Université de Paris,Université de Paris(2018), and ANR-11-IDEX-0005,USPC,Université Sorbonne Paris Cité(2011)

Subjects
[SDV.BIBS] Life Sciences [q-bio]/Quantitative Methods [q-bio.QM], [SDV]Life Sciences [q-bio], complementarity determining regions, Bioinformatics Keywords Secondary structure, secondary structure, Subjects Biochemistry, [SDV.BIBS]Life Sciences [q-bio]/Quantitative Methods [q-bio.QM], nanobodies, [SDV] Life Sciences [q-bio], frameworks, [SDV.BBM] Life Sciences [q-bio]/Biochemistry, Molecular Biology, antibodies, structural alphabet, [SDV.BBM]Life Sciences [q-bio]/Biochemistry, Molecular Biology, sequence structure relationship
Abstract

International audience; Antigen binding by antibodies requires precise orientation of the complementarity- determining region (CDR) loops in the variable domain to establish the correct contact surface. Members of the family Camelidae have a modified form of immunoglobulin gamma (IgG) with only heavy chains, called Heavy Chain only Antibodies (HCAb). Antigen binding in HCAbs is mediated by only 3 CDR loops from the single variable domain (VHH) at the N-terminus of each heavy chain. This feature of the VHH, along with other important features, e.g. easy expression, small size, thermo-stability and hydrophilicity, made them promising candidates for therapeutics and diagnostics. Thus, to design better VHH domains, it is important to thoroughly understand their sequence and structure characteristics and relationships. In this study sequence, characteristics of VHH have been analysed in depth, along with their structural features using innovative approaches, namely a structural alphabet. An elaborate summary of various studies proposing structural models of VHHs showed diversity in the algorithms used. Finally, a case study to elucidate the differences in structural models from single and multiple templates is presented. In this case study, along with the above-mentioned aspects of VHH, an exciting view of various factors in structure prediction of VHH, like template framework selection, is also discussed.

Published
2020
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3. Trends in IT Innovation to Build a Next Generation Bioinformatics Solution to Manage and Analyse Biological Big Data Produced by NGS Technologies

Author

de Brevern, Alexandre G., Meyniel, Jean-Philippe, Fairhead, Cecile, Neuvéglise, Cécile, Malpertuy, Alain, Université Paris Diderot - Paris 7 (UPD7), ISoft, Institut de génétique et microbiologie [Orsay] (IGM), Université Paris-Sud - Paris 11 (UP11)-Centre National de la Recherche Scientifique (CNRS), MICrobiologie de l'ALImentation au Service de la Santé (MICALIS), Institut National de la Recherche Agronomique (INRA)-AgroParisTech, Atragene, Ministry of Research (France), University Paris Diderot, Sorbonne, Paris Cite (France), National Institute for Blood Transfusion (INTS, France), National Institute for Health and Medical Research (INSERM, France), labex GR-Ex, University Paris Sud, CNRS, INRA, AgroParisTech, ISOFT, ATRAGENE, and program 'Investissements d'avenir' of the French National Research Agency [11-LABX-0051, ANR-11-IDEX-0005-02]

Subjects
Databases, Factual, [SDV]Life Sciences [q-bio], lcsh:R, lcsh:Medicine, Computational Biology, High-Throughput Nucleotide Sequencing, Humans, Review Article, Genomics, Software
Abstract

International audience; Sequencing the human genome began in 1994, and 10 years of work were necessary in order to provide a nearly complete sequence. Nowadays, NGS technologies allow sequencing of a whole human genome in a few days. This deluge of data challenges scientists in many ways, as they are faced with data management issues and analysis and visualization drawbacks due to the limitations of current bioinformatics tools. In this paper, we describe how the NGS Big Data revolution changes the way of managing and analysing data. We present how biologists are confronted with abundance of methods, tools, and data formats. To overcome these problems, focus on Big Data Information Technology innovations from web and business intelligence. We underline the interest of NoSQL databases, which are much more efficient than relational databases. Since Big Data leads to the loss of interactivity with data during analysis due to high processing time, we describe solutions from the Business Intelligence that allow one to regain interactivity whatever the volume of data is. We illustrate this point with a focus on the Amadea platform. Finally, we discuss visualization challenges posed by Big Data and present the latest innovations with JavaScript graphic libraries.

Published
2015
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4. Global analysis of VHHs framework regions with a structural alphabet

Author

Noël, Floriane, Malpertuy, Alain, De Brevern, Alexandre, Biologie Intégrée du Globule Rouge (BIGR (UMR_S_1134 / U1134)), Institut National de la Transfusion Sanguine [Paris] (INTS)-Université Paris Diderot - Paris 7 (UPD7)-Université de La Réunion (UR)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Université des Antilles (UA), Atragene Informatics, and This work was supported by grants from the French Ministry of Research, University Paris Diderot, Sorbonne Paris Cité, French National Institute for Blood Transfusion (INTS), French Institute for Health and Medical Research (INSERM). AdB also acknowledges the Indo-French Centre for the Promotion of Advanced Research / CEFIPRA for collaborative grants (numbers 5302-2). This study was supported by grants from the Laboratory of Excellence GR-Ex, reference ANR-11-LABX-0051. The labex GR-Ex is funded by the programme 'Investissements d’avenir' of the French National Research Agency, reference ANR-11-IDEX-0005-02. Calculations were performed on an SGI cluster granted by Conseil Régional Ile de France and INTS (SESAME Grant).

Subjects
[SDV.IMM]Life Sciences [q-bio]/Immunology, [SDV.BBM]Life Sciences [q-bio]/Biochemistry, Molecular Biology, MESH: secondary structure, sequence structure relationship, structural alphabet, antibodies, frameworks, VHHs, nanobodies, [SDV.BIBS]Life Sciences [q-bio]/Quantitative Methods [q-bio.QM]
Abstract

International audience; The VHHs are antigen-binding region/domain of camelid heavy chain antibodies (HCAb). They have many interesting biotechnological and biomedical properties due to their small size, high solubility and stability, and high affinity and specificity for their antigens. HCAb and classical IgGs are evolutionary related and share a common fold. VHHs are composed of regions considered as constant, called the frameworks (FRs) connected by Complementarity Determining Regions (CDRs), a highly variable region that provide interaction with the epitope. Actually, no systematic structural analyses had been performed on VHH structures despite a significant number of structures. This work is the first study to analyse the structural diversity of FRs of VHHs. Using a structural alphabet that allows approximating the local conformation, we show that each of the four FRs do not have a unique structure but exhibit many structural variant patterns. Moreover, no direct simple link between the local conformational change and amino acid composition can be detected. These results indicate that long-range interactions affect the local conformation of FRs and impact the building of structural models.

Published
2016
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5. Global analysis of VHHs framework regions with a structural alphabet

Author

Noël, Floriane, Malpertuy, Alain, de Brevern, Alexandre, de Brevern, Alexandre G., Biologie Intégrée du Globule Rouge (BIGR (UMR_S_1134 / U1134)), Institut National de la Transfusion Sanguine [Paris] (INTS)-Université Paris Diderot - Paris 7 (UPD7)-Université de La Réunion (UR)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Université des Antilles (UA), Atragene Informatics, and This work was supported by grants from the French Ministry of Research, University Paris Diderot, Sorbonne Paris Cité, French National Institute for Blood Transfusion (INTS), French Institute for Health and Medical Research (INSERM). AdB also acknowledges the Indo-French Centre for the Promotion of Advanced Research / CEFIPRA for collaborative grants (numbers 5302-2). This study was supported by grants from the Laboratory of Excellence GR-Ex, reference ANR-11-LABX-0051. The labex GR-Ex is funded by the programme 'Investissements d’avenir' of the French National Research Agency, reference ANR-11-IDEX-0005-02. Calculations were performed on an SGI cluster granted by Conseil Régional Ile de France and INTS (SESAME Grant).

Subjects
[SDV.BIBS] Life Sciences [q-bio]/Quantitative Methods [q-bio.QM], [SDV.IMM] Life Sciences [q-bio]/Immunology, [SDV.BBM] Life Sciences [q-bio]/Biochemistry, Molecular Biology, [SDV.IMM]Life Sciences [q-bio]/Immunology, [SDV.BBM]Life Sciences [q-bio]/Biochemistry, Molecular Biology, MESH: secondary structure, sequence structure relationship, structural alphabet, antibodies, frameworks, VHHs, nanobodies, [SDV.BIBS]Life Sciences [q-bio]/Quantitative Methods [q-bio.QM]
Abstract

International audience; The VHHs are antigen-binding region/domain of camelid heavy chain antibodies (HCAb). They have many interesting biotechnological and biomedical properties due to their small size, high solubility and stability, and high affinity and specificity for their antigens. HCAb and classical IgGs are evolutionary related and share a common fold. VHHs are composed of regions considered as constant, called the frameworks (FRs) connected by Complementarity Determining Regions (CDRs), a highly variable region that provide interaction with the epitope. Actually, no systematic structural analyses had been performed on VHH structures despite a significant number of structures. This work is the first study to analyse the structural diversity of FRs of VHHs. Using a structural alphabet that allows approximating the local conformation, we show that each of the four FRs do not have a unique structure but exhibit many structural variant patterns. Moreover, no direct simple link between the local conformational change and amino acid composition can be detected. These results indicate that long-range interactions affect the local conformation of FRs and impact the building of structural models.

Published
2016
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6. Le cahier de laboratoire électronique (CLE)

Author

Amiard, Anabelle, Baczynski, Céline, Blanchet, Christophe, de Brevern, Alexandre, Dorlanne-Messiaen, Emmanuelle, Grognard, Eric, Kisselova, Galina, Malpertuy, Alain, Menez Jamet, Jeanne, Racle, Ivan, Rouger, Céline, de Brevern, Alexandre G., Sanofi, Fovea Pharmaceuticals/Vision Institute, SANOFI Recherche, Novo Nordisk Production SAS, Novo Nordisk, Agilent Technologies France, DSIMB, U 665, Dynamique des Structures et Interactions des Macromolécules Biologiques (DSIMB), Institut National de la Transfusion Sanguine [Paris] (INTS)-Université Paris Diderot - Paris 7 (UPD7)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Institut National de la Transfusion Sanguine [Paris] (INTS)-Université Paris Diderot - Paris 7 (UPD7)-Institut National de la Santé et de la Recherche Médicale (INSERM), ProductLife (ProductLife), ProductLife, Cambridgesoft, Ipsen, IPSEN, Atragene Informatics, Vaxon Biotech, I. Racle, Bayer Santé familiale SAS, Bayer HealthCare SAS, and Laboratoires Expanscience

Subjects
[SPI.OTHER]Engineering Sciences [physics]/Other, Information sharing, Intellectual property, Electronic signature, Archives, [SPI.OTHER] Engineering Sciences [physics]/Other, GLP, [INFO.INFO-SE] Computer Science [cs]/Software Engineering [cs.SE], [INFO.INFO-SE]Computer Science [cs]/Software Engineering [cs.SE], Regulatory, Electronic laboratory notebook (eLN), [SDV.BBM] Life Sciences [q-bio]/Biochemistry, Molecular Biology, [SDV.BBM]Life Sciences [q-bio]/Biochemistry, Molecular Biology, LIMS, Patent, Legal, Law, 21CFR Part 11
Abstract

International audience; The laboratory notebook is an essential tool in the company and in the laboratory. It allows durable follow-up of experiments; it is also an essential legal tool. Its electronic versions have become increasingly efficient over recent years, providing new functions, more rapid access to data and aid to decision-making, but they also raise new questions concerning their ease of use and their possible limitations. This article is designed to summarize the specificities and advantages of the electronic laboratory notebook as well as its current limitations.

Published
2011

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