Figure 3. Molecular dynamics analysis of water density distribution and hydration motifs at the peptide interface. (IMAGE)
Caption
a Representative 3D visualization of the simulated peptide–water interfacial model system, shown together with xz and yz views overlaid on the underlying peptide assembly on the graphene lattice. b Simulated 2D xy slice showing the localized in-plane water O-density distribution over the peptide assembly at z = 6.65 nm (see Supplementary Figure 28a). c Experimental 2D xy Δf slice extracted from the 3D map (Fig. 4b, z = 0.55 nm), showing circular molecular hydration features at sub-nanometre resolution, similar to those observed in the simulated image in b. d,h 2D vertical xz Δf slice taken along the peptide rows at two different lateral positions. e,i 2D vertical density profile of water O-atoms above the peptide nanostructures, extracted along the x–x′ and y–y′ directions (white and yellow dashed lines) indicated in panel b, respectively. f,j Representative visualization generated from 100 MD snapshots, showing the spatial distribution of water around the peptide self-assembled structures. The color scale in panels f and j represents the normalized water oxygen density. The underlying peptide molecular assembly is indicated by yellow arrows in panels f and j. g,k Corresponding H-bonds formed between the peptide and surrounding water molecules shown in panels f and j, respectively. In panels g and k, color coding represents distinct water populations within the hydration layer: red denotes water molecules participating in hydrogen-bond networks at the peptide–water interface, while blue denotes other water molecules in the surrounding solvent region.
Credit
Yurtsever A., et al., Nat Commun (2026)
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