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

摘要

A series of seven off-lattice protein model is analyzed that spans a range of chain geometry from a simple, low-resolution homopolymer model to an intermediate-resolution model that accounts for the presence of side chains, the varied character of the individual amino acids. the rigid nature of protein backbone angles, and the length scales that characterize real protein bead sizes and bond lengths. Discontinuous molecular dynamics is used to study the transition temperatures and physical structures resulting from simulations with each protein model. Our results show that each protein model undertgoes multiple thermodynamic transitions that roughly correlate wth protein transitions during folding the the native state. Other realisteic protein behaviork such as burial of hydrophobic side chanis and hindered motion due to backbone rigidity, is observed with the more -detailed models. The results suirggest that, despite their simplicity when compared with all-atom protein models, the models presented here display a significant amount of protein charater and, when coupled with the efficient discontinuous molecular dynamics algorthm, may enable simulation of multiprotein systems over long times