Force Response of Polypeptide Chains from Water-Explicit MD Simulations

Abstract

Using molecular dynamics simulations in explicit water, the force–extension relations for the five homopeptides polyglycine, polyalanine, polyasparagine, poly(glutamic acid), and polylysine are investigated. From simulations in the low-force regime the Kuhn length is determined, from simulations in the high-force regime the equilibrium contour length and the linear and nonlinear stretching moduli, which agree well with quantum-chemical density-functional theory calculations, are determined. All these parameters vary considerably between the different polypeptides. The augmented inhomogeneous partially freely rotating chain (iPFRC) model, which accounts for side-chain interactions and restricted dihedral rotation, is demonstrated to describe the simulated force–extension relations very well. We present a quantitative comparison between published experimental single-molecule force–extension curves for different polypeptides with simulation and model predictions. The thermodynamic stretching properties of polypeptides are investigated by decomposition of the stretching free energy into energetic and entropic contributions.