(Georgia Institute of Technology, 1996)
Vieth, Michal; Kolinski, Andrzej; Brooks, C. L., III; Skolnick, Jeffrey
A hierarchical approach to protein folding is employed to examine the folding pathway and predict the quaternary structure of the GCN4 leucine zipper. Structures comparable in quality to experiment have been predicted. In addition, the equilibrium between dimers, trimers and tetramers of a number of GCN4 mutants has been examined. In five out of eight cases, the simulation results are in accordance with the experimental studies of Harbury, et al.
(Georgia Institute of Technology, 1986-01-30)
Kolinski, Andrzej; Skolnick, Jeffrey; Yaris, Robert
We present preliminary results of Monte Carlo studies on the dynamics of multichain diamond-lattice systems at considerably greater densities than those done previously. Chain dynamics were simulated by a random sequence of three or four bond kink motions. The single bead autocorrelation function exhibits "slow" mode relaxation behavior with a g(t)∝ tβ. There is a smooth crossover from Rouse-like dynamics, β=1/2, at low density to smaller values of β at higher density and β=0 at the glass transition density (φG≅0.92). The simulation provides a self-diffusion coefficient D ∝ n-2, with n the number of beads, in agreement with experiment. A phenomenological model, different from the widely accepted reptation picture, is proposed.