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structure tri-dimensionnelle et fonction des protéines: principes et méthodes de prédiction

structure tri-dimensionnelle et fonction des protéines: principes et méthodes de prédiction. ENS, année académique 2002-2003 Shoshana Wodak, Shosh@ucmb.ulb.ac.be. Plan des leçons. 1. Introduction 2. Méthodes d ’analyse des structures 3D -Définition de domaines de structure

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structure tri-dimensionnelle et fonction des protéines: principes et méthodes de prédiction

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  1. structure tri-dimensionnelle et fonction des protéines: principes et méthodes de prédiction ENS, année académique 2002-2003 Shoshana Wodak, Shosh@ucmb.ulb.ac.be

  2. Plan des leçons 1. Introduction 2. Méthodes d ’analyse des structures 3D -Définition de domaines de structure -Comparaison de structures 3D 3. Différentes classifications des protéines 4. Prédiction de structure a partir de la séquence -structures secondaires -structures tertiaires -prédiction des interactions protéine-protéine

  3. Ouvrages et site de référence: -Introduction à la structure des protéines Branden & Tooze, Deboeck Université - Structural bioinformatics - site web: http://www.expasy.org/swissmod/course/course-index.htm

  4. Introduction -Propriétés conformantionnelles des acides aminés, relation avec la structure des protéines -Bref aperçu des structures locales (secondaires) -Panorama des motifs de structure; architectures et topologies des protéines -Bases de données et classifications de structures des protéines -Relation entre la structure 3D et la fonction

  5. al R The Ramachandran map Dipeptide unit

  6. The Ramachandran map & secondary structure http://www.expasy.org/swissmod/course/course-index.htm

  7. The Ramachandran map of a protein Ramachandran plot of a protein containing almost exclusively b-strands (yellow dots) And only 1 helix (red dots). http://www.expasy.org/swissmod/course/course-index.htm

  8. The alpha helix http://www.expasy.org/swissmod/course/course-index.htm

  9. The beta strand and beta sheets http://www.expasy.org/swissmod/course/course-index.htm

  10. beta sheets have a left handed twist ~25º http://www.expasy.org/swissmod/course/course-index.htm

  11. Chain turns http://www.expasy.org/swissmod/course/course-index.htm

  12. Supersecondary structures (1) http://www.expasy.org/swissmod/course/course-index.htm

  13. Supersecondary structures (2) Beta corner http://www.expasy.org/swissmod/course/course-index.htm

  14. Helix-turn-helix Supersecondary structures (3) http://www.expasy.org/swissmod/course/course-index.htm

  15. Supersecondary structures (4) http://www.expasy.org/swissmod/course/course-index.htm

  16. Cold shock protein Ribosomal binding factor Fab/Immunoglobulin Myoglobin Apolipoprotein E3 Triose Phosphate Isomerase dimer

  17. Protein structure classification Class Architecture Topology

  18. Protein folds of the “all alpha” class Single helix Helix-turn-helix http://www.expasy.org/swissmod/course/course-index.htm

  19. Four helix bundles with different topologies Myohemerythrin Ferritin http://www.expasy.org/swissmod/course/course-index.htm

  20. DNA binding proteins CRO repressor from 434 phage Homeodomain binding DNA http://www.expasy.org/swissmod/course/course-index.htm

  21. Helix/helix packing ~50º ~90º orthogonal packing ~Parallel packing

  22. Beta sandwiches http://www.expasy.org/swissmod/course/course-index.htm

  23. Beta barrels porin Gama crystallin

  24. Architectures & topologies of alpha/beta proteins (1) alpha/beta barrel http://www.expasy.org/swissmod/course/course-index.htm

  25. Architectures & topologies of alpha/beta proteins (2) Flavodoxine (FMN) http://www.expasy.org/swissmod/course/course-index.htm

  26. The quaternary structure of proteins (1) http://www.expasy.org/swissmod/course/course-index.htm

  27. The quaternary structure of proteins (2) http://www.expasy.org/swissmod/course/course-index.htm

  28. Proteins are made of domains Domain 1 Domain 2 6 phosphogluconate dehydrogenase Cathepsin D, Lysozomal aspartic protease

  29. Protein Databank: PDB: http://www.rcsb.org/pdb Current holding: ~18700 Structures (sep. 2002) Content growth

  30. Old folds New folds PDB : growth in the number of all folds and new folds (Sep. 2002)

  31. Intermolecular interactions Protein 2 Protein 1 protein-ligand protein-protein protein-DNA

  32. One protein, several functions

  33. P53, tumour suppresser protein P53 protein-DNA interactions The DNA-binding domainof P53

  34. Peptide-binding domain ATP-binding domain HSP-70 Protein-size cavity Ring 1 Ring 2 Prefoldin GroEL-GroES complex of the bacterium E. coli (HSP-60) GroES Cap

  35. GroEL-GroES

  36. Functions of membrane proteins

  37. Classifications of protein structures (domains) CATH: structural classification of proteins, [http://www.biochem.ucl.ac.uk/bsm/cath/] SCOP: Structural classification of proteins [http://scop.mrc-lmb.cam.ac.uk/scop/] FSSP:Fold classification based on structure alignments [http://www.sander.ebi.ac.uk/fssp/] HSSP: Homology derived secndary structure assignments [http://www.sander.ebi.ac.uk/hssp/] DALI:Classification of protein domains [http://www.ebi.ac.uk/dali/domain/] VAST: structural neighbours by direct 3D structure comparison [http://www.ncbi.nlm.nih.gov:80/Structure/VAST/vast.shtml] CE: Structure comparisons by Combinatorial Extension [http://cl.sdsc.edu/ce.html]

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