Replica-exchange molecular dynamics simulation of diffracted X-ray tracking

We examine the effects of the nanocrystal covalently bonded to one end, utilizing replica-exchange molecular dynamics simulation of a peptide with the sequence Ac-YGKAAAAKAAAAKAAAAKC-amide, to simulate the diffraction X-ray tracking (DXT) method. We performed three different simulations in this study. A simulation with no constraint, a simulation with one end fixed, and a simulation with one end fixed and also considering the effect of the nanocrystal by changing the mass of the sulfur atom in the C-terminus, which covalently bonded with the An nanocrystal in diffraction DXT method, was performed. The average configuration parameters of the three simulations are compared and discussed. We analyzed our simulation results utilizing principal component analysis. The obtained free-energy landscape indicated that the condition of the DXT technique will not affect the global-minimum state, however, it may affect the folding pathway.