PROTEIN FOLDING DYNAMICS IN TORSIONAL ANGLE SPACE

Cornell University Ithaca, Ithaca NY

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Abstract

A Brownian dynamics treatment in torsional angle space was constructed for the simulation of conformational dynamics of macromolecules with fixed bond lengths and bond angles and with an arbitrary intramolecular potential energy function. The advantages of the torsional angle space treatment over similar treatments (Brownian dynamics or molecular dynamics) in atomic coordinate space are that the number of variables is reduced by roughly a factor of 10 and that the integration time step size is increased by three to four orders of magnitude. Consequently, the exploration of global conformational relaxation processes becomes computationally possible. The treatment is a general purpose one applicable to all macromolecular conformational relaxation processes (e.g., protein folding kinetics, drug/ligand docking on to target proteins, conformational multiple-minima problems, etc.). The torsional angle space Brownian dynamics treatment has been used to study the mechanism and kinetics of protein folding by using continuum rigid chain molecules (with unit bond lengths and tetrahedral bond angles). 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.