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Different charge treatment approaches are examined for cyclotide-induced plasma membrane disruption by lipid extraction studied with dissipative particle dynamics. A pure Coulomb approach with truncated forces tuned to avoid individual strong ion pairing still reveals hidden statistical pairing effects that may lead to artificial membrane stabilization or distortion of cyclotide activity depending on the cyclotide’s charge state. While qualitative behavior is not affected in an apparent manner, more sensitive quantitative evaluations can be systematically biased. The findings suggest a charge smearing of point charges by an adequate charge distribution. For large mesoscopic simulation boxes, approximations for the Ewald sum to account for mirror charges due to periodic boundary conditions are of negligible influence.
Description and Analysis of Glycosidic Residues in the Largest Open Natural Products Database
(2021)
Geometries, stabilities, electronic properties and NMR-shielding of cucurbit[6]uril–spermine host-ligand complexes are investigated with DFT calculations and compared to experimental results. Cucurbit[6]uril and spermine can form complexes with two different minimum energy geometries and corresponding characteristic differences in NMR shielding. The energetically preferred complex geometry has a perfect inversion symmetry and its proton NMR shielding agrees very well with experimental results. The cucurbit[6]uril host molecule shows a distinct geometrical flexibility in ligand binding which allows an induced fit of the spermine ligand. The energetic barrier for the rotation of spermine in the favourable complex is approximated to be in the order of a few kilocalories per mole.