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Biochemistry 412 2004 23 March Lecture Protein-Protein Interactions II

Biochemistry 412 2004 23 March Lecture Protein-Protein Interactions II. Today’s topics: • isothermal titration calorimetry • phage display. First, to review some of the stuff from last time…. Mutant ovomucoid third domains binding to serine proteases

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Biochemistry 412 2004 23 March Lecture Protein-Protein Interactions II

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  1. Biochemistry 412 2004 23 March Lecture Protein-Protein Interactions II

  2. Today’s topics: • isothermal titration calorimetry • phage display

  3. First, to review some of the stuff from last time…. Mutant ovomucoid third domains binding to serine proteases Q: how is this related to drug discovery?

  4. Reference Molecule: Turkey Ovomucoid Third Domain (a Serine Protease Inhibitor) • All nineteen possible amino acid substitutions were made for each of the residues shown in blue (total = 190). • For each inhibitor, binding constants were measured precisely for each of six different serine proteases. • X-ray structures were performed on a subset of the mutant complexes.

  5. Structure of the complex to TKY-OM3D P1 Pro with Streptomyces griseus Protease B Bateman et al (2001) J. Mol. Biol.305, 839.

  6. Qasim et al (2003) Biochemistry42, 6460.

  7. …and the theorists are now beginning to mine this data to refine their docking programs. “Good” prediction “Bad” prediction Lorber et al (2002) Protein Sci.11, 1393.

  8. If you want to be “hard core” and really understand protein-protein interactions, you need to know more than just the free energies of association. You (ultimately) will need to know something about enthalpies, entropies, and heat capacities, too.

  9. Makarov et al (1998) Biopolymers45, 469.

  10. Makarov et al (2000) Biophys. J.76, 2966.

  11. Makarov et al (2002) Acc. Chem. Res.35, 376.

  12. When two proteins form a complex, solvent must be displaced from the interfacial regions and the conformational freedom (configurational entropy) of the main chain and side chain atoms will change also.

  13. Jelesarov and Bosshard (1999) J. Molec. Recognition12, 3.

  14. Jelesarov and Bosshard (1999) J. Molec. Recognition12, 3.

  15. Isothermal Titration Calorimetry Yields DH of Binding

  16. …and when you have DH and DG (= -RTlnKa), you can calculate DS.

  17. Some examples of experimentally-measured thermodynamic quantities for interacting proteins, measured using isothermal titration calorimetry: Note: isothermal titration calorimetry also directly yields n, the stoichiometry of binding. Weber and Salemme (2003) Curr. Opin. Struct. Biol.13, 115.

  18. Phage Display G. P. Smith (1985) “Filamentous fusion phage: novel expression vectors that display cloned antigens on a virion surface” Science 228, 315.

  19. Bass et al (1990) Proteins8, 309 (as referenced in Sidhu (2000) Curr. Opin. Biotechnol.11, 610).

  20. Sidhu et al (2003) ChemBiochem4, 14.

  21. Sidhu (2001) Biomolec. Eng.18, 57.

  22. Sidhu (2001) Biomolec. Eng.18, 57.

  23. Rodi et al (2002) Curr. Opin. Chem. Biol.6, 92.

  24. Other interesting (and related) topics: • antibody engineering • yeast “two-hybrid” technology

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