In order to study of the structural features of water cluster structures (WCS), discovered during studies of the self-organization of diphenylalanine (FF) peptide nanotubes (L- and D-chiralities) inside their cavities, was performed 3D-modeling of D-FF nanotubes containing water in the channel cavity was performed. The simulation indicated the optimal number of water cluster molecules per unit cell (two turns of the spiral section), equal to 21 water molecules. To better understand the nature of structural rearrangements of the WCS that occur in the internal cavity of the D-FF channel during optimization, we developed a method of visual-differential analysis of conformational changes in biological macromolecules. Identifying (ID) and “hypsometric” projections were obtained: the outer surface of the water cluster structures located inside the D-FF PNT, the projections of the inner surface of the D-FF PNT channel. Analysis of the ID projections of water clusters in the initial and optimized states revealed a slight change (+0.568%) in the available surface of oxygen atoms and hydrogen atoms (-0.68%). A visual analysis of the ID projections revealed significant structural changes in the structure of the water cluster. To describe them, three “hypsometric maps” were used to compose complex “topographic maps” and hybrid (2D/3D) models, showing the regions most likely involved in the formation of stable hydrogen bonds and the nature of changes in the structure of the water cluster.
peptide nanotubes, PNT, diphenylalanine, FF-NT, visual differential, 3D, projection, hypsometric, model, Blender, PhotoReactor, G’MIC
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