Molecular dynamics study of protein folding: Potentials and mechanisms

This paper is concerned with the investigations of the protein folding problem by molecular dynamics simulations performed with minimal protein models. We briefly review some of the recently presented off-lattice protein models. In detail description is given for a particular model which uses spherical beads placed at the positions of Cas to represent amino acid residues. Then we turn to discussing some of the algorithms available presently for efficient simulations of protein models. In particular we concentrate on the non-iterative multicanonical algorithm. Finally we demonstrate the usage of the models and computational methods by investigating thermodynamics and kinetics of a short P-sheet protein motif From thermodynamical point of view we determine the temperatures of three basic phase transitions that take place in the present model: collapse, folding and glass transition. Kinetically we show that folding reaction of the employed model is well described by a diffusion-equation formula.