Roterman I, KrUl M, Nowak M, Konieczny L, Rybarska J, Stopa B, Piekarska B, Zemanek G
Department of Biostatistics and Medical Informatics, Collegium Medicum, Jagiellonian University, Cracow, Poland.
Med Sci Monit. 2001 Jul-Aug;7(4):771-84.
The complexing of Congo red in two different ligand forms - unimolecular and supramolecular (seven molecules in a micelle) - with eight deca-peptides organized in a b-sheet was tested by computational analysis to identify its dye-binding preferences. Polyphenylananine and polylysine peptides were selected to represent the specific side chain interactions expected to ensure particularly the stabilization of the dye-protein complex. Polyalanine was used to verify the participation of non-specific backbone-derived interactions.
The initial complexes for calculation were constructed by intercalating the dye between the peptides in the middle of the beta-sheet. The long axis 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 positioning maximally reduced the exposure of the hydrophobic diphenyl (central dye fragment) to water. In general the complexes of supramolecular Congo red ligands appeared more stable than those formed by individual dye molecules. Specific interactions (electrostatic and/or ring stacking) dominated as binding forces in the case of the single molecule, while non-specific surface adsorption seemed decisive in complexing with the supramolecular ligand.
Both the unimolecular and supramolecular versions of the dye ligand were found to be likely to form complexes of sufficient stability with peptides. The low stability of the protein and the gap accessible to penetration in the peptide sheet seem sufficient for supramolecular ligand binding, but the presence of positively charged or hydrophobic amino acids may strengthen binding significantly.
The need for specific interaction makes single-molecule Congo red binding rather unusual as a general amyloid protein ligand. The structural feature of Congo red, which enables specific and common interaction with amyloid proteins, probably derives from the ribbon-like self-assembled form of the dye.
通过计算分析测试了刚果红以两种不同配体形式——单分子形式和超分子形式（胶束中有七个分子）与八个以β-折叠形式排列的十肽的络合情况，以确定其染料结合偏好。选择聚苯丙氨酸和聚赖氨酸肽来代表预期能确保染料 - 蛋白质复合物稳定的特定侧链相互作用。使用聚丙氨酸来验证非特异性主链衍生相互作用的参与情况。
计算的初始复合物通过将染料插入β-折叠中间的肽之间构建。染料分子的长轴（在单分子体系中）或带状胶束的长轴（在超分子染料形式中）与肽主链平行排列。这种定位最大程度地减少了疏水性二苯基（染料中心片段）与水的接触。一般来说，超分子刚果红配体的复合物比单个染料分子形成的复合物更稳定。在单分子情况下，特异性相互作用（静电和/或环堆积）作为结合力起主导作用，而在与超分子配体络合时，非特异性表面吸附似乎起决定性作用。
发现染料配体的单分子和超分子形式都可能与肽形成具有足够稳定性的复合物。蛋白质的低稳定性以及肽片中可穿透的间隙似乎足以实现超分子配体结合，但带正电荷或疏水性氨基酸的存在可能会显著增强结合。
作为一般的淀粉样蛋白配体，单分子刚果红结合因需要特异性相互作用而相当罕见。刚果红能够与淀粉样蛋白发生特异性和普遍相互作用的结构特征，可能源于染料的带状自组装形式。
