The solution conformations of amino acids from molecular dynamics simulations of Gly-X-Gly peptides: comparison with NMR parameters

The conformations that amino acids can adopt in the random coil state are o f fundamental interest in the context of protein folding research and studi es of protein-peptide interactions. To date, no detailed quantitative data from experimental studies have been reported; only nuclear magnetic resonan ce parameters such as chemical shifts and J coupling constants have been re ported. These experimental nuclear magnetic resonance data represent averag es over multiple conformations, and hence they do not provide unique struct ural information. I have performed relatively long (2.5 ns) molecular dynam ics simulations of Gly-X-Cly tripeptides, surrounded by explicit water mole cules, where X represents eight different amino acids with long side chains . From the trajectories one can calculate time averaged backbone chemical s hifts and (3)J(NH alpha) coupling constants and compare these with experime ntal data. These calculated quantities are quite close to the experimental values for most amino acids, suggesting that these simulations are a good m odel for the random coil state of the tripeptides. On the basis of my simul ations I predict (3)J(alpha beta) coupling constants and present dihedral d istributions for the Phi, Psi, as well as chi(1) and chi(2) angles. Finally , I present correlation plots for these dihedral angles.