PNNL

Abstract

Using Born-Oppenheimer molecular dynamics within the density functional framework, we calculated the effective force acting on water-mediated peptide-peptide interaction between antiparallel ?-sheets in an aqueous environment and also in the vicinity of a hydrophobic surface. From the magnitude of the effective force (corresponding to the slope of the free energy as a function of the inter-peptide distance) and its sign (a negative value indicating an effective attraction whereas a positive value an effective repulsion) we can elucidate the fundamental differences of the water-mediated peptide-peptide interactions in those two environments. The computed effective forces indicate that the water-mediated interaction between peptides in an aqueous environment is attractive in the range of inter-peptide distance d=7-8 Å when hydrophobic surfaces are not nearby. Due to the stabilization of the water molecules bridging between the two beta-sheets, a free energy barrier exists between the direct and indirect (water-mediated) inter-peptide interactions. However, when the peptides are in the proximity of hydrophobic surfaces, this free energy barrier decreases because the hydrophobic surfaces enhance the inter-peptide attraction by the destabilization and ease-to-libration of the bridging water molecules between them. This work was supported by the Chemical Sciences, Geosciences and Biosciences Division, Office of Basic Energy Sciences, US Department of Energy. Battelle operates the Pacific Northwest National Laboratory for the U.S. Department of Energy.