A. E. Kokorev, V. M. Trusova, K. O. Vus, U. K. Tarabara, G. P. Gorbenko


Amyloid fibrils are highly ordered insoluble protein aggregates that are involved in molecular etiology of a number of severe disorders, including Alzheimer's, Parkinson’s and prion’s diseases, some types of systemic amyloidosis, etc. One of the most effective approaches to detecting the amyloid fibrils is based on monitoring the spectral behavior of specific fluorescent dye Thioflavin T (ThT). Using the molecular docking and molecular dynamics tools, such as PatchDock, FireDock, CreateFibril and GROMACS, the model of twisted K-peptide fibril that supposedly represent the core region of lysozyme amyloid fibrils, has been constructed and analyzed. The effect of fibril twisting angle on the binding characteristics of ThT has been evaluated. The results obtained strongly suggest that ThT specificity for the twisted ribbon fibril polymorphs is primarily determined by the curvature effects rather than amino acid composition of fibril grooveswhich accomodate ThT molecule.


amyloid fibrils; Thioflavin T; molecular docking; molecular dynamics; fibril twisting

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