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PDF 01 Clambert These 26 0 Institutional Repository - Research Portal Dépôt Institutionnel - Portail de la Recherche University of Namurresearchportal.unamur.be THESIS / THÈSE DOCTEUR EN SCIENCES Développement d'une méthode automatique fiable de modélisation de la structure tridimensionnelle des protéines par homologie et application au protéome de Brucella Melitensis Author(s) - Auteur(s) : Lambert, Christophe Award date: 2003 SupervisorAwarding - institution:Co-Supervisor / Promoteur - Co-Promoteur : Universite de Namur Link to publication Publication date - Date de publication : Permanent link - Permalien : Rights / License - Licence de droit d’auteur : General rights Copyright and moral rights for the publications made accessible in the public portal are retained by the authors and/or other copyright owners and it is a condition of accessing publications that users recognise and abide by the legal requirements associated with these rights. • Users may download and print one copy of any publication from the public portal for the purpose of private study or research. • You may not further distribute the material or use it for any profit-making activity or commercial gain • You may freely distribute the URL identifying the publication in the public portal ? Take down policy If you believe that this document breaches copyright please contact us providing details, and we will remove access to the work immediately Bibliothèqueand investigate Universitaire your claim. Moretus Plantin Download date: 05. oct.. 2021 FACULTES UNIVERSITAIRES NOTRE-DAME DE LA PAIX NAMUR FACULTE DES SCIENCES DEPARTEMENT DE BIOLOGIE Développement d’une méthode automatique fiable de modélisation de la structure tridimensionnelle des protéines par homologie et application au protéome de Brucella melitensis Dissertation présentée par Christophe Lambert en vue de l’obtention du grade de Docteur en Sciences Composition du jury: Xavier De Bolle (FUNDP) Eric Depiereux (Promoteur, FUNDP) Martine Raes (FUNDP) Jean-Louis Ruelle (GlaxoSmithKline Biologicals, Rixensart) Jacques van Helden (SCMB, ULB, Bruxelles) 2003 © Presses universitaires de Namur & Christophe Lambert Rempart de la Vierge, 13 B - 5000 Namur (Belgique) Toute reproduction d'un extrait quelconque de ce livre, hors des limites restrictives prévues par la loi, par quelque procédé que ce soit, et notamment par photocopie ou scanner, est strictement interdite pour tous pays. Imprimé en Belgique ISBN: 2-87037-425-9 Dépôt légal: D / 2003 / 1881 / 37 Facultés Universitaires Notre-Dame de la Paix Faculté des Sciences Rue de Bruxelles, 61 B-5000 Namur, Belgique Développement d’une méthode automatique fiable de modélisation de la structure tridimensionnelle des protéines par homologie et application au protéome de Brucella melitensis Par Christophe Lambert La connaissance de la structure tridimensionnelle (3D) des protéines est une information capitale. Néanmoins, le nombre de protéines dont la structure 3D a été déterminée expérimentalement est cent fois plus faible que le nombre de protéines connues aujourd'hui. Cet écart ne pourra pas être comblé, car les techniques expérimentales de détermination de structure (diffraction de rayons X et résonance magnétique nucléaire) sont coûteuses et lentes (un an de travail en moyenne pour une seule protéine). Un moyen d'obtenir plus rapidement la structure 3D de protéines est de la prédire par des moyens bioinformatiques. La technique de prédiction la plus précise actuellement est la modélisation par homologie. Celle-ci est basée sur la similitude de structure entre deux protéines de séquences similaires. L'étape critique de cette méthode est l'étape d'alignement entre la séquence à modéliser et une séquence similaire de structure connue. Notre travail a consisté tout d'abord en la conception d'une nouvelle méthode d'alignement pairé très fiable. Cette méthode a ensuite été incluse dans un système automatique de modélisation par homologie: la bonne qualité des structures prédites par le système trouve en partie son origine dans le programme d'alignement utilisé. Enfin, nous avons appliqué notre système de modélisation automatique à la modélisation de toutes les protéines déduites du génome d'une bactérie pathogène étudiée dans notre unité de recherche: Brucella melitensis. Cela nous a conduit à créer une banque de données structurales et fonctionnelles consacrée au génome de cette bactérie. Cette banque de données est devenue un outil de travail indispensable pour plusieurs équipes de recherche européennes qui étudient Brucella melitensis. Facultés Universitaires Notre-Dame de la Paix Faculté des Sciences Rue de Bruxelles, 61 B-5000 Namur, Belgium Developing a reliable automatic method to predict the three-dimensional structure of proteins by homology modeling and application to the Brucella melitensis proteome by Christophe Lambert The three-dimensional (3D) structure of proteins is an important information. Nevertheless, the number of proteins for which the 3D structure has been determined experimentally is hundred times smaller than the number of currently known proteins. This gap will never been filled because the experimental techniques to determine protein structure (X-ray diffraction and nuclear magnetic resonance) are expensive and slow (one year of work on average for only one protein). One way to obtain the 3D structure of proteins faster is to predict it using bioinformatics tools. The most accurate technique is currently homology modelling. It is based on the structural similarity between two proteins having similar sequences. The critical step of this technique is the alignment step between the target sequence and a similar sequence of known structure, used as template. Our work has consisted primarily to design a new reliable pairwise alignment method. This method has been included in an automatic homology modelling system: the high quality of structures predicted by the system comes partly from the alignment program used. Finally, we have applied our automatic modelling system to the modelling of all proteins deduced from the genome of a pathogenic bacteria studied in our research unit: Brucella melitensis. This has lead us to create a structural and functional databank focused on Brucella's genome. This databank has become an essential tool for European research teams that study Brucella melitensis. Table des matières INDEX DES FIGURES...................................................................................... XIII INDEX DES TABLEAUX ..................................................................................XIX REMERCIEMENTS......................................................................................... XXV ABRÉVIATIONS .............................................................................................XXIX AVANT-PROPOS .........................................................................................XXXIII I. INTRODUCTION.................................................................................................1 I.1. STRUCTURE DES PROTÉINES..............................................................................2 I.1.1. Structure primaire des protéines ..............................................................2 I.1.1.1. Définition .......................................................................................................2 I.1.1.2. La liaison peptidique ......................................................................................3 I.1.1.3. Les angles de torsion ......................................................................................4 I.1.2. Structure secondaire des protéines...........................................................5 I.1.2.1. Définition .......................................................................................................5 I.1.2.2. Hélice ..........................................................................................................6 ,3ODQ ..............................................................................................................6 I.1.2.4. Autres conformations régulières.....................................................................8 I.1.2.5. Conformations irrégulières.............................................................................9 I.1.3. Structure tertiaire des protéines ...............................................................9 I.1.4. Structure quaternaire des protéines .......................................................10 I.2. MÉTHODES D’ALIGNEMENT DE SÉQUENCES PROTÉIQUES................................11 I.2.1. Introduction ............................................................................................11 I.2.2. Définition................................................................................................12 I.2.3. Alignement de deux séquences................................................................13 I.2.3.1. Matrices de scores ........................................................................................13 I.2.3.1.1. Matrices de Dayhoff (Mutation Data Matrix, MDM) ...........................14 I.2.3.1.2. Les matrices BLOSUM ........................................................................16 I.2.3.2. Algorithme de Needleman-Wunsch..............................................................16 I.2.3.3. Algorithme de Smith-Waterman...................................................................17 I.2.3.4. Autres programmes d’alignement pairé de séquences..................................18 I.2.4. Alignement multiple de séquences..........................................................19
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