We have investigated the supramolecular structure of helical ribbons formed during self-assembly of a beta-sheet peptide using computer simulation. We tested a wide range of molecular packing geometries consistent with the experimental dimensions to identify the most stable structure, and then systematically changed the helical geometry to investigate its energy landscape. The effect of pH was incorporated by scaling the amount of charge on the side chains based on the electrostatic double layer theory. Our results suggest that these left-handed helical ribbons are comprised of a double beta-sheet and that the experimentally measured dimensions correspond to a local energy minimum. Side chain interactions are found to be critical in determining the stability and curvature of the helix. Our approach has general applicability of the study of self-assembled nanostructures from beta-sheet peptides where high resolution data are not yet available.
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