protein folding biochemistry 412 february 18, 2005
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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) - PowerPoint PPT PresentationTRANSCRIPT
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Protein Folding
Biochemistry 412
February 18, 2005
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Fersht & Daggett (2002) Cell 108, 573.
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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
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Dobson (2003) Nature 426, 884.
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Two-State BehaviorEnergetic and Kinetic Formalisms
At equilibrium kfold[U] = kunfold[N]
Let U signify the unfolded state and N signify the native state:
U NKeq
So Keq = [N]/[U] = kfold/kunfold
And likewise, the stabilization free energy can be expressed as
G° = GN° - GU° = -RTlnKeq
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CreightonProteinsW. H. Freeman1984, p. 288
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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.
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Dobson (2003) Nature 426, 884.
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Note that the transition state (TS) energy,G‡, can be indirectly measured based on itsDifference with the unfolded and nativeState free energies.
Thus,
GTS-U = G‡ - GU° and GN-TS = GN° - G‡
And
GTS-U = -RTlnkfold and GN-TS = RTlnkunfold
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Now….
Protein engineering rears its head!
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Denaturation Data for Barnase Mutants
Matouschek et al (1989) Nature 340, 122.
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Matouschek et al (1989) Nature 340, 122.
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Fersht & Daggett (2002) Cell 108, 573.
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-Value Analysis
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Baker (2000) Nature 405, 39.
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Vendruscolo & Paci (2003) Curr. Opin. Struct. Biol. 13, 82.
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Vendruscolo et al (2001) Nature 409, 641.
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Vendruscolo et al (2001) Nature 409, 641.
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Protein Folding In Vivo
Molecular Chaperones
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Hartl & Hayer-Hartl (2002) Science 295, 1852.
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Hartl & Hayer-Hartl (2002) Science 295, 1852.
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Hartl & Hayer-Hartl (2002) Science 295, 1852.
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Protein Folding and Disease
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Dobson (2003) Nature 426, 884.
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Computational Protein Folding
How are the theorists doing lately?
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Baker (2000) Nature 405, 39.
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