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In this case, Garcia and Sanbonmatsu simulated the beta hairpin in
explicit solvent using the 1994 version of the AMBER force field. They
observed an energy landscape with little or no barrier to folding, but
also found nonnative trapped states where the peptide adopted an
alpha-helical conformation. A subsequent study by Zhou et al. also
used replica exchange in explicit solvent but made use of a more recent
OPLS force field [43]. No helical intermediates were observed in
that case. Further thermodynamic studies have concentrated on more
detailed force field or solvent model comparisons (especially compar-
ing implicit and explicit solvent results), though the current consensus
is that stable nonnative helical structures are likely to be an artifact of
the force fields used in early studies.
Attempts have also been made to simulate the kinetics of beta
hairpin folding. One attempt made use of a distributed computing
effort, where tens of thousands of independent short simulations of the
beta hairpin in implicit solvent were used. The rate at which individual
simulations reach the folded state could be observed, and correlated to
the experimentally observed folding time constant of 6
s. The kinetics
have also been studied using a simulation technique called transition
path sampling, which allows accurate estimations of the rates for
rare transitions between two well-defined end states. Bolhuis modeled
the folding process by two transitions—one from the unfolded mani-
fold to an intermediate with native hydrophobic contacts, and one
from that intermediate to the native state—and calculated a simulated
folding time constant of 5
µ
s [44]. Further work has concentrated on
the application of Markov chain-type models to this system, to produce
a more complete and detailed picture of the folding kinetics [45,46].
A key insight of later studies has been that the distinction between
folding mechanisms where hydrogen bonds form first and those where
hydrophobic interactions form first is largely semantic. The same
simulation can support either model depending on the exact defini-
tions used for the identification of hydrogen bonds and hydrophobic
contacts.
These extensive simulation efforts have prompted further experi-
mental studies to determine the mechanism of folding in this system.
Dyer and coworkers studied the kinetics of a series of insertion
mutants where the hairpin loop was moved progressively further
from the hydrophobic core and established that longer loops have
slower folding kinetics [47]. This suggests that searching for the correct
intrastrand contacts may be a diffusive, entropy-dominated process.
The stability of the wild-type hairpin has also been revisited by by a
comparison of earlier circular dichroism experiments with measure-
ments of chemical shifts as a function of temperature [48]. This analysis
indicated that the wild-type hairpin may be approximately 30% folded
in water at room temperature.
µ
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