User:Pakpoom Subsoontorn/Notebook/general reading/2008/10/22: Difference between revisions

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**** Modified Lennard-Jones potential
**** Modified Lennard-Jones potential
**** rapid computation
**** rapid computation
** Design outcomes
** Building new proteins
***  PCR mutagenesis
*** Design outcomes
** Testing Results:
** Testing Results:
***QSAR
*** binding affinities/selectivities
*** binding affinities/selectivities
*** Rewiring Pathways
*** Rewiring Pathways

Revision as of 11:37, 23 October 2008

Project name <html><img src="/images/9/94/Report.png" border="0" /></html> Main project page
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Computational design of receptor and sensor proteins with novel functions(BioE300a presentation)

Outline

  • Challenges in designing protein
    • Complexity of protein-ligand interaction, too many possibility
    • Two approaches
      • Rational Design
      • Directed Evolution
  • What's new here?
    • Specific goals: changes the specificity of receptors/sensor protein
      • Precursors/ligand (from E.coli PBP): GBP, RBP, ABP, QBP, HBP
      • Targeted ligands: TNT, Serotonin, L-lactate
    • Designing Algorithms
      • Identify amino acid sequences that can form a complementary surface between the protein and the target ligand
      • Dead-end elimination theorem (DEE)
        • Deterministically identifies the global minimum of a semi-empirical potential function of molecular interactions
        • Modified Lennard-Jones potential
        • rapid computation
    • Building new proteins
      • PCR mutagenesis
      • Design outcomes
    • Testing Results:
      • QSAR
      • binding affinities/selectivities
      • Rewiring Pathways
  • Summary/Critique
  • More recent papers



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