Helical formation of a 17-residue peptide by molecular dynamics simulations

Hiroki Kimoto, Takuzo Kurotsu

Abstract

A molecular dynamics simulation of a 17-residue peptide AcYKA4KAGAAKA4KNH2 was carried out using ff03 force field. 1000- ns MD simulations were performed with 2 fs time step. The helical content dynamically fluctuated between 0 and 90 % in all regions of simulation time and it did not converge to any definite value because of the large flexibility of 17-residue peptide. The time-averaged helical contents were calculated by using our simulation data and were in good agreement with the experimental data. Moreover, we proposed the possible pathway of helical formation of the 17-residue peptide.