A Computational Study of the Role of Solvation Effects in Reverse Turn Formation in the Tetrapeptides APGD and APGN

Abstract

The tetrapeptides APGD and APGN are known by NMR analysis to adopt reverse turn conformations to a significant degree in aqueous solution. We have carried out a 7.7 ns molecular dynamics simulation of Ace-APGD-NHMe in explicit water, and have analyzed the energetics of snapshots from this simulation in terms of a molecular mechanics energy function, estimates of solvation free energy based on numerical solutions of the Poisson−Boltzmann equation (in which the solvent is treated as a high-dielectric continuum), and an estimate of chain entropy effects derived from a systematic search procedure. In the unconstrained trajectory, 17 transitions occur between turn and extended conformers, suggesting that the free energy profile is nearly flat and that the simulation is moderately-well-equilibrated with respect to this transition; the turn population found is within the experimental range. The potential of mean force, constructed as the sum of solute force-field energies, continuum solvation, and hard-sphere chain entropy, agrees with that computed directly from the simulation to within 2 kcal/mol across the entire range of configurations sampled. The study has been extended to the tetrapeptide APGN by repeating the energetic analysis with an Asn side chain replacing the Asp in the APGD snapshots. A comparison of energetics with Asp and Asn side chains shows a complex interplay among vacuum electrostatic terms, dielectric screening terms, and solvation free energy terms such that the net effect of side chain substitution on turn formation is very small. Prospects for application of this sort of analysis to other peptide and protein conformational problems are discussed.