An approach to understand the complexation of supramolecular dye Congo red with immunoglobulin L chain λ

Congo red, a dye of high self‐assembling tendency, has been found to form complexes with proteins by adhesion of the ribbon‐like supramolecular ligand to polypeptide chains of β‐conformation. Complexation is allowed by local or global protein instability, facilitating penetration of the dye to the locus of its binding. At elevated temperatures, L chain λ of myeloma origin was found to form two distinct complexes with Congo red, easily differentiated in electrophoresis as slow‐ and fast‐migrating fractions, bearing four‐ and eight‐dye‐molecule ligands, respectively, in the V domain of each individual chain. The slow‐migrating complex is formed after displacement of the N‐terminal polypeptide chain fragment (about 20 residues) from its packing locus, thereby exposing the entrance to the binding cavity. In this work the formation and stability of this complex was studied by molecular dynamics (MD) simulations. The effect of three‐ and five‐molecule ligands introduced to the site binding the dye was also analyzed in an attempt to understand the formation of fast‐migrating complexes. The wedging of the ligand containing five dye molecules, hence longer than established experimentally as the maximum for the slow‐migrating complex, was found to generate significant structural changes. These changes were assumed to represent the crossing of the threshold on the way to forming a fast‐migrating complex more capacious for dyes. They led to almost general destabilization of the V domain, making it susceptible to extra dye complexation. Theoretical studies were designed in close reference to experimental findings concerning the number of dye molecules in the ligand inserted to the site binding the dye, the location of the site in the domain, and the conditions of formation of the complexes. The results of the two kinds of studies appeared coherent. © 2005 Wiley Periodicals, Inc. Biopolymers, 2005