Several short peptide sequences are known to self-assemble into supramolecular nanostructures with interesting properties. In this study, coarse-grained molecular dynamics is employed to rapidly screen all 400 dipeptide combinations and predict their ability to aggregate as a potential precursor to their self-assembly. The simulation protocol and scoring method proposed allows a rapid determination of whether a given peptide sequence is likely to aggregate (an indicator for the ability to self-assemble) under aqueous conditions. Systems that show strong aggregation tendencies in the initial screening are selected for longer simulations, which result in good agreement with the known self-assembly or aggregation of dipeptides reported in the literature. Our extended simulations of the diphenylalanine system show that the coarse-grain model is able to reproduce salient features of nanoscale systems and provide insight into the self-assembly process for this system.
- peptide self-assembly
- TIC - Bionanotechnology
Frederix, P., Ulijn, R. V., Hunt, N., & Tuttle, T. (2011). Virtual screening for dipeptide aggregation: toward predictive tools for peptide self-assembly. Journal of Physical Chemistry Letters, 2(19), 2380-2384. https://doi.org/10.1021/jz2010573