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Amyloid fibrils formation accompanies many serious diseases such as Alzheimer’s, Parkinson’s disease and others. Recent studies showed that the structure of fibrils formed from various proteins is not identical and the differences in the fibrils structure can be related with the variety of their pathogenicity (cytotoxicity). Therefore, investigation of amyloid fibrils structure is an actual problem. Fluorescence dye thioflavin T (ThT) is a widely used probe for amyloid fibrils. We showed that ThT can be used for examination of amyloid fibrils structure if the samples are prepared by equilibrium microdialysis. Using this approach the structure of amyloid fibrils formed from lysozyme, insulin, Sup35p, alfa-synuclein and beta-2-microglobulin were studied. For these samples various number of ThT–fibrils binding modes with different affinity and stoichometry as well as different properties of bound to fibrils ThT were shown. These data in combination with the results of other methods (transmission electron microscopy and CD spectroscopy of amyloid fibrils, ThT fluorescence lifetime measurements) allowed concluding the polymorphism of tested amyloid fibrils and possibility of using of the proposed approach for this aim.