迷向周期和方法在β-簮结构折褶模拟中的应用

采用新近提出的迷向周期和方法(IPS),结合自导Lang evin动态模拟,模拟研究9余肽折褶成β簮结构的情况,表明了该结构与NMR观察到的基本一致,而Ewald模拟由于是强烈的镜像相互作用会产生构型偏差,获得致密构型的几率增大,表明IPS方法更适合于周期边界条件的模拟.

Application of the isotropic periodic sum method in β-hairpin folding simulation

A newly developed method, the isotropic periodic sum (IPS) method, was applied to the study of the β-hairpin fold mechanism of a 9-residue peptide. In a self-guided Langevin dynamics simulation at the native condition, a 9-residue peptide successfully folded into a β-hairpin structure. The β-hairpin structure is very close to that observed in NMR experiment. The simulation revealed the mechanism of β-hairpin folding and unfolding in explicit water environment. Comparison simulations show that the structural and energetic properties from the IPS method are very close to that from Ewald summation. It is observed that Ewald summation creates a bias to conformations with strong imgae interactions. In the simulation using the IPS method, the peptide avoided this bias and visited the compact conformations more frequently, indicating the IPS method is more suitable for simulations with periodic boundary conditions.