Brownian dynamics simulations of protein folding

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Abstract
The torsional angle space macromolecular conformational dynamics treatment presented in the preceding paper is used to study the mechanism and kinetics of protein folding by using continuum rigid chain molecules. The main purpose is to test the treatment using simple macromolecular systems. It is found that the torsional angle space approach is much faster and more reliable than similar approaches in atomic coordinate space. The simulation results also suggest that the short-ranged Lennard-Jones binary interactions alone are not sufficient to fold the chain molecules, and that hydrophobic collapse is essential for the folding processes. In our simplified protein folding model, the hydrophobic collapse is achieved by introducing global dipole interactions. The collapse of the chain molecule induced by dipole interactions significantly reduces the folding time. The chain collapse processes effectively bring the atoms into the (short) range of Lennard-Jones attractions, which then, in turn, are able to play their role in the folding processes; without such collapse the folding processes are highly frustrated.