Length dependent folding kinetics of phenylacetylene oligomers:
Structural characterization of a kinetic trap
JOURNAL OF CHEMICAL PHYSICS, (March 2005)Length dependent folding kinetics of phenylacetylene oligomers: Structural characterization of a kinetic trap.Preview By: Elmer, Sidney P.; Pande, Vijay S.. Journal of Chemical Physics, 3/22/2005, Vol. 122 Issue 12, pN.PAG, 9p, 2 diagrams, 3 graphs; DOI: 10.1063/1.1867375; (AN 16669506).DOI: {10.1063/1.1867375}
Abstract
Using simulation to study the folding kinetics of 20-mer
poly-phenylacetylene (pPA) oligomers, we find a long time scale trapped
kinetic phase in the cumulative folding time distribution. This is
demonstrated using molecular dynamics to simulate an ensemble of over
100 folding trajectories. The simulation data are fit to a four-state
kinetic model which includes the typical folded and unfolded states,
along with an intermediate state, and most surprisingly, a kinetically
trapped state. Topologically diverse conformations reminiscent of alpha
helices, beta turns, and sheets in proteins are observed, along with
unique structures in the form of knots. The nonhelical conformations
are implicated, on the basis of structural correlations to kinetic
parameters, to contribute to the trapped kinetic behavior. The strong
solvophobic forces which mediate the folding process and produce a
stable helical folded state also serve to overstabilize the nonhelical
conformations, ultimately trapping them. From our simulations, the
folding time is predicted to be on the order of 2.5-12.5 mu s in the
presence of the trapped kinetic phase. The folding mechanism for these
20-mer chains is compared with the previously reported folding
mechanism for the pPA 12-mer chains. A linear scaling relationship
between the chain length and the mean first passage time is predicted
in the absence of the trapped kinetic phase. We discuss the major
implications of this discovery in the design of self-assembling
nanostructures.