Effects of the fixed end in single-molecule imaging techniques: A replica-exchange molecular dynamics simulation study

A peptide with the sequence Ac-YGKAAAAKAAAAKAAAAKC-amide is studied with replica-exchange molecular dynamics simulations. We performed two different simulations in this study: one with no constraint and the other with one end fixed. The latter condition was introduced in order to understand the effects of fixing one end in single-molecule imaging techniques. We analyzed our simulation results utilizing principal component analysis. The free-energy landscape showed that fixing one end of the peptide limits the motion of the peptide backbone.