A Molecular Dynamics Study on Controlling the Self-Assembly of -Sheet Peptides with Designer Nanorings

Recently, a rational approach for constructing -barrel protein mimics by the self-assembly of peptide-based building blocks has been demonstrated. We performed molecular dynamics simulations of nanoring formation by means of the self-assembly of designed -sheet-forming peptides. Several factors contributing to the stability of the nanoring structures with respect to size were investigated. Our simulations predicted that an optimal nanoring size may be achieved by minimizing repulsions due to steric hindrance between bulky groups while maintaining favorable hydrogen-bond interactions between neighboring -sheet chains. It was shown that mutations in a test peptide, in which all or half of the tryptophan residues were replaced by phenylalanine, could enable the assembly of stable nanoring structures with smaller pore sizes. Insights into the fundamental factors driving the formation of peptide-based nanostructures are expected to facilitate the design of novel functional bionanostructures.