“Crawling” on the self-assembly system: A molecular simulation of peptide position adjusting over self-assembly block

¹ Beihang University, Beijing, China
² The National Centre for Nanoscience and Technology, Beijing, China

^* Corresponding author : shixh@nanoctr.cn

Abstract

By combining non-equilibrium molecular dynamics(NEMD), umbrella sampling, and weighted histogram analysis method(WHAM), we calculated the potential of mean force of histidine peptide moving over a self-assembly structure. The reaction coordinate is along the main chain direction of the histidine peptide in the self-assembly structure. It is found that the energy needed for the histidine peptide with 3 and 5 residues while moving along the reaction coordinate is around -2.2 kCal/mol and -7.4 kCal/mol, respectively. And the histidine peptide crawls along the reaction coordinate, performing a snake-like movement. This result could illustrate how histidine peptide adjusts its position during self-assembly process.