On the energy of bifurcated hydrogen bonds for protein structure prediction

Abstract

Although hydrogen bonds are known to form cooperative networks, most protein structure prediction methods still model individual hydrogen bonds independently for computational efficiency. We are developing ways to identify and score networks of bonds, but need to determine the energies from such networks. In this paper we perform quantum calculations to compare energy profiles of individual hydrogen bonds to those of the simplest dependent interaction, bifurcated hydrogen bonds. When there are two lone pairs available for an acceptor to bond with two donors, then there is very little difference between the energies of two independent bonds and a bifurcated bond, but for one donor to bond to two acceptors is much harder. These results suggest that lone pair positions may be a better basis for hydrogen bond parameterization than atom positions.