Bridging the gap between homopolymer and protein models: A discontinuous molecular dynamics study

A series of seven off-lattice protein models is analyzed that spans a range of chain geometry from a simple, low-resolution homopolymer model to an in termediate-resolution model that accounts for the presence of side chains, the varied character of the individual amino acids, the rigid nature of pro tein backbone angles, and the length scales that characterize real protein bead sizes and bond lengths. Discontinuous molecular dynamics is used to st udy the transition temperatures and physical structures resulting from simu lations with each protein model. Our results show that each protein model u ndergoes multiple thermodynamic transitions that roughly correlate with pro tein transitions during folding to the native state. Other realistic protei n behavior, such as burial of hydrophobic side chains and hindered motion d ue to backbone rigidity, is observed with the more-detailed models. The res ults suggest that, despite their simplicity when compared with all-atom pro tein models, the models presented here display a significant amount of prot ein character and, when coupled with the efficient discontinuous molecular dynamics algorithm, may enable simulation of multiprotein systems over long times. (C) 2000 American Institute of Physics. [S0021-9606(00)51944-8].