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 of fundamental interest in the context of protein folding research and studies of protein–peptide interactions. To date, no detailed quantitative data from experimental studies have been reported; only nuclear magnetic resonance parameters such as chemical shifts and J coupling constants have been reported. These experimental nuclear magnetic resonance data represent averages over multiple conformations, and hence they do not provide unique structural information. I have performed relatively long (2.5 ns) molecular dynamics simulations of Gly-X-Gly tripeptides, surrounded by explicit water molecules, where X represents eight different amino acids with long side chains. From the trajectories one can calculate time averaged backbone chemical shifts and 3JNHα coupling constants and compare these with experimental data. These calculated quantities are quite close to the experimental values for most amino acids, suggesting that these simulations are a good model for the random coil state of the tripeptides. On the basis of my simulations I predict 3Jαβ coupling constants and present dihedral distributions for the Φ, Ψ, as well as χ1 and χ2 angles. Finally, I present correlation plots for these dihedral angles.Key words: molecular dynamics (MD), nuclear magnetic resonance (NMR) spectroscopy, J-coupling, chemical shift, dihedral probability distribution.