Next-generation sequencing of a combinatorial peptide phage library screened against ubiquitin identifies peptide aptamers that can inhibit the in vitro ubiquitin transfer cascade.

Autor:	Lisowska M; International Centre for Cancer Vaccine Science, University of Gdańsk, Gdańsk, Poland., Lickiss F; International Centre for Cancer Vaccine Science, University of Gdańsk, Gdańsk, Poland., Gil-Mir M; University of Edinburgh, Institute of Genetics and Molecular Medicine, Edinburgh, United Kingdom., Huart AS; University of Edinburgh, Institute of Genetics and Molecular Medicine, Edinburgh, United Kingdom., Trybala Z; International Centre for Cancer Vaccine Science, University of Gdańsk, Gdańsk, Poland., Way L; University of Edinburgh, Institute of Genetics and Molecular Medicine, Edinburgh, United Kingdom., Hernychova L; Research Centre for Applied Molecular Oncology, Masaryk Memorial Cancer Institute, Brno, Czechia., Krejci A; Research Centre for Applied Molecular Oncology, Masaryk Memorial Cancer Institute, Brno, Czechia., Muller P; Research Centre for Applied Molecular Oncology, Masaryk Memorial Cancer Institute, Brno, Czechia., Krejcir R; Research Centre for Applied Molecular Oncology, Masaryk Memorial Cancer Institute, Brno, Czechia., Zhukow I; Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Warsaw, Poland., Jurczak P; Faculty of Chemistry, University of Gdańsk, Gdańsk, Poland., Rodziewicz-Motowidło S; Faculty of Chemistry, University of Gdańsk, Gdańsk, Poland., Ball K; University of Edinburgh, Institute of Genetics and Molecular Medicine, Edinburgh, United Kingdom., Vojtesek B; Research Centre for Applied Molecular Oncology, Masaryk Memorial Cancer Institute, Brno, Czechia., Hupp T; University of Edinburgh, Institute of Genetics and Molecular Medicine, Edinburgh, United Kingdom., Kalathiya U; International Centre for Cancer Vaccine Science, University of Gdańsk, Gdańsk, Poland.
Jazyk:	angličtina
Zdroj:	Frontiers in microbiology [Front Microbiol] 2022 Dec 02; Vol. 13, pp. 875556. Date of Electronic Publication: 2022 Dec 02 (Print Publication: 2022).
DOI:	10.3389/fmicb.2022.875556
Abstrakt:	Defining dynamic protein-protein interactions in the ubiquitin conjugation reaction is a challenging research area. Generating peptide aptamers that target components such as ubiquitin itself, E1, E2, or E3 could provide tools to dissect novel features of the enzymatic cascade. Next-generation deep sequencing platforms were used to identify peptide sequences isolated from phage-peptide libraries screened against Ubiquitin and its ortholog NEDD8. In over three rounds of selection under differing wash criteria, over 13,000 peptides were acquired targeting ubiquitin, while over 10,000 peptides were selected against NEDD8. The overlap in peptides against these two proteins was less than 5% suggesting a high degree in specificity of Ubiquitin or NEDD8 toward linear peptide motifs. Two of these ubiquitin-binding peptides were identified that inhibit both E3 ubiquitin ligases MDM2 and CHIP. NMR analysis highlighted distinct modes of binding of the two different peptide aptamers. These data highlight the utility of using next-generation sequencing of combinatorial phage-peptide libraries to isolate peptide aptamers toward a protein target that can be used as a chemical tool in a complex multi-enzyme reaction. Competing Interests: The authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest. (Copyright © 2022 Lisowska, Lickiss, Gil-Mir, Huart, Trybala, Way, Hernychova, Krejci, Muller, Krejcir, Zhukow, Jurczak, Rodziewicz-Motowidło, Ball, Vojtesek, Hupp and Kalathiya.)
Databáze:	MEDLINE
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