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Virtual screening for dipeptide aggregation : toward predictive tools for peptide self-assembly

Frederix, Pim and Ulijn, Rein Vincent and Hunt, Neil and Tuttle, Tell (2011) Virtual screening for dipeptide aggregation : toward predictive tools for peptide self-assembly. Journal of Physical Chemistry Letters, 2 (19). pp. 2380-2384.

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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.