Structural and dynamical characteristics of peptoid oligomers with achiral aliphatic side chains studied by molecular dynamics simulation.

ABSTRACT: All-atom molecular dynamics simulations of N-substituted glycine peptoid oligomers with methyl and methoxyethyl side chains have been carried out for chain lengths of 5, 10, 20, and 50 residues in aqueous phase at room temperature. The (ϕ, ψ) backbone dihedral angle distributions in the Ramachandran plots show that helical structures, similar to polyproline type I and type II helices, are the most favorable conformations in most peptoid oligomers studied. The left-handed helical structures are shown to be increasingly favored as the oligomer chain length grows. A significant population of cis amide bond configurations has been identified in the peptoid oligomers. By combining the analysis of ϕ and ω backbone dihedral angles, we determined the relative composition of the four major conforma

SUBMITTER: Park SH 

PROVIDER: S-EPMC3177600 | biostudies-literature | 2011 Sep

REPOSITORIES: biostudies-literature