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Membrane Protein Structure Prediction and Visualization

Membrane Protein Structure Prediction and Visualization. Chuck Staben Jerzy Jaromczyk. Genbank Growth. Genomic View. Genome. Transcriptome. Protein. Structures Processes. Cell. Environment. Hypothesis. Bioinformatics-what is it?. DATA. Acquisition, curation, and analysis of

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Membrane Protein Structure Prediction and Visualization

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  1. Membrane ProteinStructure Prediction and Visualization Chuck Staben Jerzy Jaromczyk

  2. Genbank Growth

  3. Genomic View Genome Transcriptome Protein Structures Processes Cell Environment

  4. Hypothesis Bioinformatics-what is it? DATA Acquisition, curation, and analysis of biological data INFORMATION KNOWLEDGE

  5. Typical Cell • ~10% proteins membrane bound • Up to 90% cell’s energy involved in transport • Receptors, transporters, adhesion • Basic and applied

  6. Protein Structure • Rasmol image • 3D structure (tertiary) • Secondary structure • Alpha helix • Beta sheet • PRIMARY STRUCTURE  3D Structure

  7. Primary Structure • 20 amino acids • Unique chemical properties • 100-1000’s (400 typical)

  8. Structure Prediction • Quantum models • Molecular dynamics • Comparative--“Threading” • Simple predictive • Eg. Chou-Fasman

  9. Chou-Fasman, 1978 • 8 proteins (ALL soluble), determine relative tendencies of amino acids • Palpha, Pbeta… • “Rules” for prediction • Does this sample represent proteins well? • Prediction success compared to “newly solved”

  10. Overall Success • ~60% correct • Membrane proteins • ~30% correct!!!! Redo CF for Membrane Proteins

  11. Membrane Protein Sample • ~60 structures of “membrane” proteins • Some were soluble-only parts of larger ones • Redundancy/similarity • ~20 DISTINCT proteins • Vary in membrane localization • DIFFERENT P-factors!!! • Statistically evaluated differences

  12. Algorithm • Adopt, essentially without reconsideration • Code (several versions) • Up to 50% CORRECT readily

  13. Visualization • “Simple” problem • No obvious good solution • Start simple • “beads on a string” • modular • Interactive • collaborative

  14. Visualization • Beads on a string • Insertion

  15. Interpretation Critical?

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