Refolding molecular dynamics simulations of small- and middle-sized proteins in an explicit solvent

Abstract

In order to elucidate the protein folding problem, we performed molecular dynamics simulations for small- and middle-sized two unfolding and six refolding proteins in an explicit solvent. Histidine-containing phosphocarrier protein and small designed protein were chosen for the simulations. We found that the protein folding process of these proteins was divided into three phases: an α -helix formation phase, a packing phase and a β -sheet formation phase. In the α -helix formation phase, an α -helix was developed from a β -turn structure through a 310-helix state. In the packing phase, proteins became compact, and tertiary structures (α / α or pre- β / β packing) were formed. Formation of a hydrophobic nucleus occurred concomitant with the α -helix formation and packing phase. Finally, in the β -sheet formation phase, a β -sheet was developed owing to the sequential formation of hydrogen bonds between two neighbouring strands, just like a "closing zipper".