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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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Presentation Transcript
genomic view
Genomic View

Genome

Transcriptome

Protein

Structures

Processes

Cell

Environment

bioinformatics what is it

Hypothesis

Bioinformatics-what is it?

DATA

Acquisition, curation, and analysis of

biological data

INFORMATION

KNOWLEDGE

typical cell
Typical Cell
  • ~10% proteins membrane bound
  • Up to 90% cell’s energy involved in transport
  • Receptors, transporters, adhesion
  • Basic and applied
protein structure
Protein Structure
  • Rasmol image
  • 3D structure (tertiary)
    • Secondary structure
      • Alpha helix
      • Beta sheet
  • PRIMARY STRUCTURE  3D Structure
primary structure
Primary Structure
  • 20 amino acids
    • Unique chemical properties
  • 100-1000’s (400 typical)
structure prediction
Structure Prediction
  • Quantum models
  • Molecular dynamics
  • Comparative--“Threading”
  • Simple predictive
    • Eg. Chou-Fasman
chou fasman 1978
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”
overall success
Overall Success
  • ~60% correct
  • Membrane proteins
    • ~30% correct!!!!

Redo CF for Membrane Proteins

membrane protein sample
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
algorithm
Algorithm
  • Adopt, essentially without reconsideration
  • Code (several versions)
    • Up to 50% CORRECT readily
visualization
Visualization
  • “Simple” problem
    • No obvious good solution
  • Start simple
    • “beads on a string”
    • modular
    • Interactive
    • collaborative
visualization14
Visualization
  • Beads on a string
  • Insertion