Statistical properties and kinetics of end-end contact formation of unfolded polypeptides: A systematic molecular dynamics study

Abstract

The authors have systematically examined the statistical properties of the unfolded states of series of polypeptides and the kinetics of their end-to-end contact (ring closure) formation by molecular dynamics simulations. The formation of an end-to-end contact follows a single-exponential decay as measured by the first-passage time. It is shown that the shifted Gaussian chain model can be applied to describe the dimensions of glycine-rich polypeptides at high temperature. However, notable deviation from the ideal Gaussian chain model was observed at lower temperatures particularly for those polypeptides without glycines, due to the tendency to form local structures. © 2007 American Institute of Physics.