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Protein Folding Biochemistry 412 February 18, 2005

Protein Folding Biochemistry 412 February 18, 2005. Fersht & Daggett (2002) Cell 108 , 573. Some folding-related facts about proteins:. • Many small, single domain proteins exhibit simple two-state folding behavior • Most proteins are only marginally stable (5 - 15 kcal/mol)

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Protein Folding Biochemistry 412 February 18, 2005

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  1. Protein Folding Biochemistry 412 February 18, 2005

  2. Fersht & Daggett (2002) Cell108, 573.

  3. Some folding-related facts about proteins: • Many small, single domain proteins exhibit simple two-state folding behavior • Most proteins are only marginally stable (5 - 15 kcal/mol) under physiological conditions • Small proteins generally fold very rapidly, often in less than a second • During folding, proteins sample only very few of the total number of possible conformations And... • It is assumed that a protein’s amino acid sequence uniquely determines its native 3D structure

  4. Dobson (2003) Nature426, 884.

  5. Two-State Behavior Energetic and Kinetic Formalisms Let U signify the unfolded state and N signify the native state: Keq U N At equilibrium kfold[U] = kunfold[N] So Keq = [N]/[U] = kfold/kunfold And likewise, the stabilization free energy can be expressed as DG° = GN° - GU° = -RTlnKeq

  6. Creighton Proteins W. H. Freeman 1984, p. 288

  7. Note that Keq is a function of the denaturant concentration, since denaturants by definition shift the equilibrium toward the unfolded state. In fact, lnKeq can be approximated as a linear function of the denaturant concentration, i. e., lnKeq = lnKeqH2O - c[denaturant] Where c is a constant for a given protein and set of conditions.

  8. Dobson (2003) Nature426, 884.

  9. Note that the transition state (TS) energy, G‡, can be indirectly measured based on its Difference with the unfolded and native State free energies. Thus, DGTS-U = G‡ - GU° and DGN-TS = GN° - G‡ And DGTS-U = -RTlnkfold and DGN-TS = RTlnkunfold

  10. Now…. Protein engineering rears its head!

  11. Denaturation Data for Barnase Mutants Matouschek et al (1989) Nature 340, 122.

  12. Matouschek et al (1989) Nature340, 122.

  13. Fersht & Daggett (2002) Cell108, 573.

  14. -Value Analysis

  15. Baker (2000) Nature405, 39.

  16. Vendruscolo & Paci (2003) Curr. Opin. Struct. Biol.13, 82.

  17. Vendruscolo et al (2001) Nature409, 641.

  18. Vendruscolo et al (2001) Nature409, 641.

  19. Protein Folding In Vivo Molecular Chaperones

  20. Hartl & Hayer-Hartl (2002) Science295, 1852.

  21. Hartl & Hayer-Hartl (2002) Science295, 1852.

  22. Hartl & Hayer-Hartl (2002) Science295, 1852.

  23. Protein Folding and Disease

  24. Dobson (2003) Nature426, 884.

  25. Computational Protein Folding How are the theorists doing lately?

  26. Baker (2000) Nature405, 39.

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