Formation of Amyloid-Like Conformational States of β-Structured Membrane Proteins on the Example of OMPF Porin from the Yersinia pseudotuberculosis Outer Membrane

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Olga D. Novikova^1,a, Tatyana V. Rybinskaya¹, Elena A. Zelepuga¹, Vladimir N. Uversky², Nataliya Yu. Kim¹, Ekaterina A. Chingizova¹, Ekaterina S. Menchinskaya¹, Valentina A. Khomenko¹, Dmitriy K. Chistyulin¹, Olga Yu. Portnyagina^1,b*

¹Elyakov Pacific Institute of Bioorganic Chemistry, Far Eastern Branch of the Russian Academy of Sciences, 690021 Vladivostok, Russia

²Department of Molecular Medicine, Morsani College of Medicine, University of South Florida, Tampa, FL 33620, USA

^* To whom correspondence should be addressed.

Received: October 26, 2023; Revised: March 14, 2024; Accepted: March 31, 2024

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The work presents results of the in vitro and in silico study of formation of amyloid-like structures under harsh denaturing conditions by non-specific OmpF porin of Yersinia pseudotuberculosis (YpOmpF), a membrane protein with β-barrel conformation. It has been shown that in order to obtain amyloid-like porin aggregates, preliminary destabilization of its structure in a buffer solution with acidic pH at elevated temperature followed by long-term incubation at room temperature is necessary. After heating at 95°C in a solution with pH 4.5, significant conformational rearrangements are observed in the porin molecule at the level of tertiary and secondary structure of the protein, which are accompanied by the increase in the content of total β-structure and sharp decrease in the value of characteristic viscosity of the protein solution. Subsequent long-term exposure of the resulting unstable intermediate YpOmpF at room temperature leads to formation of porin aggregates of various shapes and sizes that bind thioflavin T, a specific fluorescent dye for the detection of amyloid-like protein structures. Compared to the initial protein, early intermediates of the amyloidogenic porin pathway, oligomers, have been shown to have increased toxicity to the Neuro-2aCCL-131™ mouse neuroblastoma cells. The results of computer modeling and analysis of the changes in intrinsic fluorescence during protein aggregation suggest that during formation of amyloid-like aggregates, changes in the structure of YpOmpF affect not only the areas with an internally disordered structure corresponding to the external loops of the porin, but also main framework of the molecule, which has a rigid spatial structure inherent to β-barrel.

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KEY WORDS: OmpF porin, Yersinia pseudotuberculosis, membrane protein, amyloidogenesis, spatial structure, cytotoxic activity, computer modeling

DOI: 10.1134/S0006297924060087

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