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Homework 6 solutions_F

Homework 6 solutions_F - CH353M Homework assignment 6(due...

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CH353M Homework assignment 6 ( due Mon Nov. 28) 1(10). For the reaction k unfolding Arc-(G) n -Arc R U k folding from Problem 5 HW5, what is the dependence of the folding and unfolding rate constants on the linker length n ? Explain your answer (It is sufficient to give a qualitative answer, not a formula). If the two monomers are far apart, it should take longer for them to find each other to initiate folding. So k folding should decrease with increasing n. There is no reason why k unfolding would depend on n (assuming that the linker does not affect the enthalpy of folding). From HW5, we have 3/2 / ufolding folding kk K n =∝ or folding kn (the exact answer of course depends on which physical model you used for the equilibrium constant) 2. Experiments show that folding of protein L is well described by the first order mechanism shown below: Mechanism 1 Here U labels the denatured (unfolded) state, F the native (folded) state. The folding rate under standard conditions is k f = 60 s -1 , the unfolding rate k f = 0.011 s -1 . A. (5) Calculate G 0 .

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Assuming T = 298.15K, 0 ln ln( / ) 21330 J/mol fu GR T K R T k k ∆= = = B. (5) It is hard to imagine that protein folding would be a single-step process without any intermediates. To see whether the existence of intermediates would affect the observed time dependence of the concentrations of the folded and the unfolded proteins, [U] and [F], consider the following reaction mechanism: Mechanism 2 where k 1 = 120.5 s -1 , k -1 = 103109 s -1 , k 2 = 103109 s -1 . Assuming that 0 G for the overall U F process is the same as for Mechanism 1, calculate k -2 .
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Homework 6 solutions_F - CH353M Homework assignment 6(due...

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