On the Binding of Congo Red to Amyloid Fibrils. 2020

Alba Espargaró, and Salomé Llabrés, and Sven J Saupe, and Carles Curutchet, and F Javier Luque, and Raimon Sabaté
Department of Pharmacy and Pharmaceutical Technology and Physical-Chemistry, School of Pharmacy and Food Sciences, University of Barcelona, Joan XXIII, 27-31, 08028, Barcelona, Spain.

Amyloids are characterized by their capacity to bind Congo red (CR), one of the most used amyloid-specific dyes. The structural features of CR binding were unknown for years, mainly because of the lack of amyloid structures solved at high resolution. In the last few years, solid-state NMR spectroscopy enabled the determination of the structural features of amyloids, such as the HET-s prion forming domain (HET-s PFD), which also has recently been used to determine the amyloid-CR interface at atomic resolution. Herein, we combine spectroscopic data with molecular docking, molecular dynamics, and excitonic quantum/molecular mechanics calculations to examine and rationalize CR binding to amyloids. In contrast to a previous assumption on the binding mode, our results suggest that CR binding to the HET-s PFD involves a cooperative process entailing the formation of a complex with 1:1 stoichiometry. This provides a molecular basis to explain the bathochromic shift in the maximal absorbance wavelength when CR is bound to amyloids.

UI MeSH Term Description Entries
D007700 Kinetics The rate dynamics in chemical or physical systems.
D009682 Magnetic Resonance Spectroscopy Spectroscopic method of measuring the magnetic moment of elementary particles such as atomic nuclei, protons or electrons. It is employed in clinical applications such as NMR Tomography (MAGNETIC RESONANCE IMAGING). In Vivo NMR Spectroscopy,MR Spectroscopy,Magnetic Resonance,NMR Spectroscopy,NMR Spectroscopy, In Vivo,Nuclear Magnetic Resonance,Spectroscopy, Magnetic Resonance,Spectroscopy, NMR,Spectroscopy, Nuclear Magnetic Resonance,Magnetic Resonance Spectroscopies,Magnetic Resonance, Nuclear,NMR Spectroscopies,Resonance Spectroscopy, Magnetic,Resonance, Magnetic,Resonance, Nuclear Magnetic,Spectroscopies, NMR,Spectroscopy, MR
D011328 Prions Small proteinaceous infectious particles which resist inactivation by procedures that modify NUCLEIC ACIDS and contain an abnormal isoform of a cellular protein which is a major and necessary component. The abnormal (scrapie) isoform is PrPSc (PRPSC PROTEINS) and the cellular isoform PrPC (PRPC PROTEINS). The primary amino acid sequence of the two isoforms is identical. Human diseases caused by prions include CREUTZFELDT-JAKOB SYNDROME; GERSTMANN-STRAUSSLER SYNDROME; and INSOMNIA, FATAL FAMILIAL. Mink Encephalopathy Virus,Prion,Encephalopathy Virus, Mink
D011485 Protein Binding The process in which substances, either endogenous or exogenous, bind to proteins, peptides, enzymes, protein precursors, or allied compounds. Specific protein-binding measures are often used as assays in diagnostic assessments. Plasma Protein Binding Capacity,Binding, Protein
D003224 Congo Red An acid dye used in testing for hydrochloric acid in gastric contents. It is also used histologically to test for AMYLOIDOSIS. Red, Congo
D000077318 Density Functional Theory A theory that is used to describe the electronic ground state properties of matter. It forms the basis of methods in obtaining a solution to the Schrodinger equation for a many-body system, and to investigate the structural, magnetic, and electronic properties of molecules and materials. Density Functional Calculations,Density Functional Computations,Density Functional Theory Calculations,Density Functional Theory Computations,Td-DFT,Td-DFT Calculations,Td-DFT Computations,Time-Dependent Density Functional Theory,Time-Dependent Density Functional Theory Calculations,Time-Dependent Density Functional Theory Computations,DFT Calculations,KS-DFT,Kohn-Sham Density Functional Theory,Calculation, Density Functional,Calculation, Td-DFT,Computation, Density Functional,Computation, Td-DFT,DFT Calculation,Density Functional Calculation,Density Functional Computation,Density Functional Theories,Functional Calculation, Density,Functional Calculations, Density,Functional Computation, Density,Kohn Sham Density Functional Theory,Td DFT Calculations,Td DFT Computations,Td-DFT Calculation,Td-DFT Computation,Time Dependent Density Functional Theory,Time Dependent Density Functional Theory Calculations,Time Dependent Density Functional Theory Computations
D000682 Amyloid A fibrous protein complex that consists of proteins folded into a specific cross beta-pleated sheet structure. This fibrillar structure has been found as an alternative folding pattern for a variety of functional proteins. Deposits of amyloid in the form of AMYLOID PLAQUES are associated with a variety of degenerative diseases. The amyloid structure has also been found in a number of functional proteins that are unrelated to disease. Amyloid Fibril,Amyloid Fibrils,Amyloid Substance,Fibril, Amyloid,Fibrils, Amyloid,Substance, Amyloid
D001665 Binding Sites The parts of a macromolecule that directly participate in its specific combination with another molecule. Combining Site,Binding Site,Combining Sites,Site, Binding,Site, Combining,Sites, Binding,Sites, Combining
D062105 Molecular Docking Simulation A computer simulation technique that is used to model the interaction between two molecules. Typically the docking simulation measures the interactions of a small molecule or ligand with a part of a larger molecule such as a protein. Molecular Docking,Molecular Docking Simulations,Molecular Docking Analysis,Analysis, Molecular Docking,Docking Analysis, Molecular,Docking Simulation, Molecular,Docking, Molecular,Molecular Docking Analyses,Molecular Dockings,Simulation, Molecular Docking

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