迷向周期和方法在β-簮结构折褶模拟中的应用(英文)

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

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。

A newly developed method, the isotropic periodic sum （IPS） method, was applied to the study of theβ-hairpinfold mechanism of a 9-residue peptide. In a self-gulded Langevin dynamics simulation at the native condition, a 9-residuepeptide successfully folded into aβ-hairpin structure. Theβ-hairpin structure is very close to that observed in NMR experiment. The simulation revealed the mechanism ofβ-hairpin folding and unfolding in explicit water environment. Comparisonsimulations 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 simulationusing the IPS method, the peptide avoided this bias and visited the compact conformations more frequently, indicating theIPS method is more suitable for simulations with periodic boundary conditions.