COMPUTER SIMULATION OF THE ROLE OF NON-NATIVE INTERACTIONS IN THE KINETIC PROCESS OF HELIX FORMATION FOR A HOMOPOLYPEPTIDE CHAIN
非天然相互作用对均聚多肽链螺旋形成动力学过程的影响的计算机模拟研究

The role of non-native hydrogen bonding on the kinetic process of helix formation for a homopolypeptide chain was explored based on a coarse-grained lattice model and dynamic Monte Carlo simulation.It was found that,though postponing the thermodynamic helix-coil transition,non-native hydrogen bonding can decrease the energy barrier of the folding kinetic process,and further increased the folding rate below a specific temperature.The distribution of folding trajectories indicated that the slow folding trajectories were reduced with the inclusion of non-native interactions,which can evidently influence the folding time.On the other hand,the evolution of chain conformation and the length of helix segment were investigated,and the non-native hydrogen bonding was found to delay the formation of native hydrogen bond and weaken the stabilization of the corresponding native conformation,thus speeding up its unfolding process.Our research indicated that the occurrence of non-native interaction can offer a potential means for frequently dynamical adjusting of protein conformation so as to perform biological functions.