Characterization of hydrogen bonding in a continuum solvent model

A simple approach for calculating hydrogen bonding (H-bonding) effects in molecular mechanics simulations of peptides and proteins is presented for use in the framework of the continuum solvent model described in the previous paper. In this approach, the solvated macromolecule is treated as a three-component dielectric system consisting of the solvent, bulk protein, and proton acceptor media. The hydrogen bond (H-bond) interaction is identified from the interpenetration of the van der Waals spheres of the polar hydrogen and the proton acceptor. The H-bond geometry is characterized by the ideal orientation of the electron lone pairs in the acceptor atom and the directionality of the proton donor bond, as observed in experimental and ab initio studies, and classified according to the hybridization state of the acceptor atom. The algorithm was implemented into CHARMM using the PAR22 force field. By introducing the concept of a Born radius of a polar hydrogen immersed in an acceptor environment, the stabilization of H-bond energies can be introduced by means of a simple fitting procedure. This H-bonding description is easily implemented in standard force fields, with virtually no additional computing time requirements. Monte Carlo simulations were carried out on two peptides with this H-bonding treatment and the continuum solvent model. The results clearly demonstrate the need for an explicit treatment of H-bonding with the proposed continuum model, and its reliability to predict peptide structures from the primary sequence that are in agreement with experimental results.