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Tools and techniques for:

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.

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Tools and techniques for:

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  1. 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.

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

  3. Tools and techniques for: • Analize • Save • Visualize • Predict • Compare • Evaluate • ESTRUCTURE OF PROTEINS

  4. 1-GLSDGEWQLV LNVWGKVEAD IPGHGQEVLI RLFKGHPETL EKFDKFKHLK SEDEMKASED LKKHGATVLT ALGGILKKKG HHEAEIKPLA QSHATKHKIP VKYLEFISEC IIQVLQSKHP GDFGADAQGA MNKALELFRK DM ASNYKELG FQG-153

  5. -Ala-Ser-Ile-Met-Arg- Función Aminoacid sequence determines one significative form. 3D form of the protein determines its function

  6. Complexity levels: Hierarchics Primary: so far Secundary: α-helix 35% of residues ß - sheet, 25% of residues ß turns, Ω turns, 3/10 helix Total: 65-75% Rest: inclasificable subestructures, hazard forms (ramdom coils)

  7. Tertiary Structure • Simple Clasification: • All alfa (>50% helix; <10% ß) • All ß (>30% beta; <5% heix) • Mixture • Refined Clasification • Topologies, motifs, domains • Foldings . Most of the proteins will be classified in one or other way from about 1000 distinct basic foldings Quaternary structure

  8. X ray difraction

  9. NMR

  10. 3D structural Data Bank

  11. Protein data Bank Tour • Statistics • Look for the active form (closed • Conformation from human glucokinase) • Take a look to the file • Save archive

  12. PDB archives

  13. Molecular Visualization FIRST GLANCE JMOL JMOL web JMOL molecular visualization program Example of a tutorial on glucokinase

  14. Molecular Visualization Programs • Rasmol (1995) • Chime • Protein Explorer ( Chime interface, requieres Chime, problems with Chime) • Jmol (java) • Deep View • Others: “professionals” Pymol

  15. Tools for 3D structures analysis and comparison • Check structures • Looking for similars in structures. VAST • (1 mbn, whale myoglobin) • Structure alignment: servers and deepview • conserved surfaces (glucokinase)

  16. Structural alignment

  17. Structural alignment • Goal: Obtain best superposition from several structures • Dinamic program scoring from geometric characteristics • Matrices of intramolecular distances • Clustering in 3D • It is possible to classify proteins based on structural homology Servidor

  18. Derived Data bases and classification of proteins based on 3D structures • PDBsum • Clasification: SCOP, CATH

  19. PDBSUM

  20. CATH Hierarchy • C: 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)

  21. SCOP. Structural Classification of Proteins • Family. Clear evolutive relationship • Superfamily. Probably common evolutive origin • Folding. Strong structural homology

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