Monte Carlo calculations on polypeptide chains. 10. A study of the kinetics of the helix--coli transition

A stochastic model of the kinetics of the helix--coil transition based on the equilibrium statistical mechanical theory of Lifson and Roig is presented. A Monte Carlo simulation of the kinetics based on the stochastic model was used to study the kinetics of the helix--coil transition. Kinetics simulations were conducted from several initial values of the fractional hydrogen bonding parameter theta to each equilibrium value of theta. A spectrum of relaxation times and characteristic weighting constants is reported for each kinetics simulation. The chain lengths used in this study were 15, 34, and 85 residues. It was found that at each chain length the relaxation times depend only on the equilibrium value of 0 while the characteristic weighting constants depend on both the initial and equilibrium values of theta. The mean relaxation time was calculated for several relaxations at chain lengths 15, 34, and 85. It was found that the mean relaxation time does not reflect the correct order of magnitude of the slowest relaxation process. In addition, it was found that pure random coil species do not survive long enough to be measured by nmr spectroscopy and therefore values of t greater than or equal to 10(-1)s do not reflect a relaxation time of the helix--coil transition.