BACKGROUND: The complexing of Congo red in two different ligand forms -unimolecular and supramolecular (seven molecules in a micelle) - with eight deca-peptides organized ina b-sheet was tested by computational analysis to identify its dye-binding preferences. Polyphenylananineand polylysine peptides were selected to represent the specific side chain interactions expected to ensureparticularly the stabilization of the dye-protein complex. Polyalanine was used to verify the participationof non-specific backbone-derived interactions.
MATERIAL AND METHODS: The initial complexes for calculationwere constructed by intercalating the dye between the peptides in the middle of the beta-sheet. The longaxis of the dye molecule (in the case of unimolecular systems) or the long axis of the ribbon-like micelle(in the case of the supramolecular dye form) was oriented parallel to the peptide backbone. This positioningmaximally reduced the exposure of the hydrophobic diphenyl (central dye fragment) to water. In generalthe complexes of supramolecular Congo red ligands appeared more stable than those formed by individualdye molecules. Specific interactions (electrostatic and/or ring stacking) dominated as binding forcesin the case of the single molecule, while non-specific surface adsorption seemed decisive in complexingwith the supramolecular ligand.
RESULTS: Both the unimolecular and supramolecular versions of the dyeligand were found to be likely to form complexes of sufficient stability with peptides. The low stabilityof the protein and the gap accessible to penetration in the peptide sheet seem sufficient for supramolecularligand binding, but the presence of positively charged or hydrophobic amino acids may strengthen bindingsignificantly.
CONCLUSIONS: The need for specific interaction makes single-molecule Congo red bindingrather unusual as a general amyloid protein ligand. The structural feature of Congo red, which enablesspecific and common interaction with amyloid proteins, probably derives from the ribbon-like self-assembledform of the dye.

Keywords: Amyloidosis, Congo Red, beta-structure, supramolecular systems, dynamics simulation