Structure and Dynamics of the Homologous Series of Alanine Peptides: A Joint Molecular Dynamics/NMR Study

摘要

The φ,ψ backbone angle distribution of small homopolymeric model peptides is investigated by a joint molecular dynamics (MD) simulation and heteronuclear NMR study. Combining the accuracy of the measured scalar coupling constants and the atomistic detail of the all-atom MD simulations with explicit solvent, the thermal populations of the peptide conformational states are determined with an uncertainty of < 5 %. Trialanine samples mainly (～90%) a poly-L-proline Ⅱ helix-like structure, some (～10%) β extended structure, but no α_R helical conformations. No significant change in the distribution of conformers is observed with increasing chain length (Ala_3 to Ala_7). Trivaline samples all three major conformations significantly. Tryglycine samples the four corner regions of the Ramachandran space and exists in a slow conformational equilibrium between the cis and trans conformation of peptide bonds. The backbone angle distribution was also studied for the segment Ala_3 surrounded by either three or eight amino acids on both N- and C-termini from a sequence derived from the protein hen egg white lysozyme. While the conformational distribution of the central three alanine residues in the 9mer is similar to that for the small peptides Ala_3-Ala_7, major differences are found for the 19mer, which significantly (30-40%) samples α_R helical stuctures.