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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View Full DocumentAssuming 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 singlestep 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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 Spring '08
 LIM
 Physical chemistry, pH, Reaction, Atmosphere, Rate equation, RT ln, KU, steady state approximation

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