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Tema 14. Bases of protein structure and structural prediction. Structural data bank. Protein Data Bank. Molecular Visualization Tools for 3D. Prediction based on sequence. Folding prediction. 3D structural prediction by homology. Quality criteria. - PowerPoint PPT Presentation

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  • Tema 14. Bases of protein structure and structural prediction. Structural data bank. Protein Data Bank. Molecular Visualization Tools for 3D. Prediction based on sequence. Folding prediction. 3D structural prediction by homology. Quality criteria.

  • Structural Bioinformatics: analysisis of protein structures and their functions by informatic tools

  • Tools and techniques for:AnalizeSaveVisualizePredictCompareEvaluateESTRUCTURE OF PROTEINS

  • 1-GLSDGEWQLV LNVWGKVEAD IPGHGQEVLI RLFKGHPETL EKFDKFKHLK SEDEMKASED LKKHGATVLT ALGGILKKKG HHEAEIKPLA QSHATKHKIP VKYLEFISEC IIQVLQSKHP GDFGADAQGA MNKALELFRK DMASNYKELG FQG-153

  • -Ala-Ser-Ile-Met-Arg-FuncinAminoacid sequence determines one significative form.3D form of the protein determines its function

  • Complexity levels: Hierarchics

    Primary: so far

    Secundary: -helix 35% of residues - sheet, 25% of residues turns, turns, 3/10 helix Total: 65-75%Rest: inclasificable subestructures, hazard forms (ramdom coils)

  • Tertiary StructureSimple Clasification:All alfa (>50% helix; 30% beta;
  • X ray difraction

  • NMR

  • 3D structural Data Bank

  • Protein data Bank TourStatisticsLook for the active form (closed Conformation from human glucokinase)Take a look to the fileSave archive

  • PDB archives

  • Molecular VisualizationJMOL webJMOL molecular visualization programFIRST GLANCE JMOLExample of a tutorial on glucokinase

  • Molecular Visualization ProgramsRasmol (1995)ChimeProtein Explorer ( Chime interface, requieres Chime, problems with Chime)Jmol (java)

    Deep ViewOthers: professionals Pymol

  • Tools for 3D structures analysis and comparisonCheck structuresLooking for similars in structures. VAST(1 mbn, whale myoglobin)Structure alignment: servers and deepviewconserved surfaces (glucokinase)

  • Structural alignment

  • Structural alignmentGoal: Obtain best superposition from several structuresDinamic program scoring from geometric characteristics Matrices of intramolecular distancesClustering in 3D

    It is possible to classify proteins based on structural homologyServidor

  • Derived Data bases and classification of proteins based on 3D structuresPDBsum

    Clasification: SCOP, CATH

  • PDBSUM

  • CATH HierarchyC: Class (secondary structure content)A: Architecture (disposition of the secondary structure elements)T: Topology (disposition of the connexions between elements)H: Homology (Structural homology)S: Sequence (Sequence homology)

  • SCOP. Structural Classification of ProteinsFamily. Clear evolutive relationship

    Superfamily. Probably common evolutive origin

    Folding. Strong structural homology