Lattice Monte Carlo simulation of coil-helix transition

An improved self-avoiding lattice model was put forward to study coil-helix transition via dynamic Monte Carlo simulation. Each residue occupies eight simple lattices. By introducing a virtual-imino group and a virtual-carbonyl group, the helical period is not necessarily to be an integer. The Go-like restriction of hydrogen bonding interaction has also been partially released. The coil-helix transition was well reproduced and consistent with the Zimm-Bragg theory. Non-native hydrogen bonding interaction seems significant around transition temperature. In characterization of a statistically helical structure, a novel correlation function was put forward and verified

I. Introduction

The principles governing the formation of a-helix have been the subject of intensive investigation since the late 1950's. Compared to the all-atom model, the minimalist coarse-grained model can rapidly collect meaningful statistics with ensemble averaging, and lattice model is especially “economic” as computing time is concerned. Thus, lattice model was employed extensively in the field of protein folding.[l, 2] The most popular lattice models are based upon simple lattices and have been widely used to study coil-globule transition etc. However, a single-site lattice model is not easy to describe a helical structure compared to a globular one. So, a bond-fluctuation model originally to study polymers [3] has been extended to investigate coil-helix transition of polypeptide. This model, also called eight-site lattice model by us[4], contains much more permitted bond orientations and bond lengths than the conventional single-site lattice model, and can be considered a quasi-continuous or quasi-off-lattice model, while not evidently weaken the priority in efficiency for lattice model. Based upon this, a fine a-helix has been constructed and associated coil-helix transition has been easily reproduced on a PC.