Partial proteolysis improves the identification of the extracellular segments of transmembrane proteins by surface biotinylation

Abstract Transmembrane proteins (TMP) play a crucial role in several physiological processes. Despite their importance and diversity, only a few TMP structures have been determined by high-resolution protein structure characterization methods so far. Due to the low number of determined TMP structure...

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Autores principales:	Tamás Langó, Zoltán Gergő Pataki, Lilla Turiák, András Ács, Julia Kornélia Varga, György Várady, Nóra Kucsma, László Drahos, Gábor E. Tusnády
Formato:	article
Lenguaje:	EN
Publicado:	Nature Portfolio 2020
Materias:	Medicine R Science Q
Acceso en línea:	https://doaj.org/article/59f84953b9054598b7843cb7e89e568f
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spelling	oai:doaj.org-article:59f84953b9054598b7843cb7e89e568f2021-12-02T15:02:24ZPartial proteolysis improves the identification of the extracellular segments of transmembrane proteins by surface biotinylation10.1038/s41598-020-65831-22045-2322https://doaj.org/article/59f84953b9054598b7843cb7e89e568f2020-06-01T00:00:00Zhttps://doi.org/10.1038/s41598-020-65831-2https://doaj.org/toc/2045-2322Abstract Transmembrane proteins (TMP) play a crucial role in several physiological processes. Despite their importance and diversity, only a few TMP structures have been determined by high-resolution protein structure characterization methods so far. Due to the low number of determined TMP structures, the parallel development of various bioinformatics and experimental methods was necessary for their topological characterization. The combination of these methods is a powerful approach in the determination of TMP topology as in the Constrained Consensus TOPology prediction. To support the prediction, we previously developed a high-throughput topology characterization method based on primary amino group-labelling that is still limited in identifying all TMPs and their extracellular segments on the surface of a particular cell type. In order to generate more topology information, a new step, a partial proteolysis of the cell surface has been introduced to our method. This step results in new primary amino groups in the proteins that can be biotinylated with a membrane-impermeable agent while the cells still remain intact. Pre-digestion also promotes the emergence of modified peptides that are more suitable for MS/MS analysis. The modified sites can be utilized as extracellular constraints in topology predictions and may contribute to the refined topology of these proteins.Tamás LangóZoltán Gergő PatakiLilla TuriákAndrás ÁcsJulia Kornélia VargaGyörgy VáradyNóra KucsmaLászló DrahosGábor E. TusnádyNature PortfolioarticleMedicineRScienceQENScientific Reports, Vol 10, Iss 1, Pp 1-11 (2020)
institution	DOAJ
collection	DOAJ
language	EN
topic	Medicine R Science Q
spellingShingle	Medicine R Science Q Tamás Langó Zoltán Gergő Pataki Lilla Turiák András Ács Julia Kornélia Varga György Várady Nóra Kucsma László Drahos Gábor E. Tusnády Partial proteolysis improves the identification of the extracellular segments of transmembrane proteins by surface biotinylation
description	Abstract Transmembrane proteins (TMP) play a crucial role in several physiological processes. Despite their importance and diversity, only a few TMP structures have been determined by high-resolution protein structure characterization methods so far. Due to the low number of determined TMP structures, the parallel development of various bioinformatics and experimental methods was necessary for their topological characterization. The combination of these methods is a powerful approach in the determination of TMP topology as in the Constrained Consensus TOPology prediction. To support the prediction, we previously developed a high-throughput topology characterization method based on primary amino group-labelling that is still limited in identifying all TMPs and their extracellular segments on the surface of a particular cell type. In order to generate more topology information, a new step, a partial proteolysis of the cell surface has been introduced to our method. This step results in new primary amino groups in the proteins that can be biotinylated with a membrane-impermeable agent while the cells still remain intact. Pre-digestion also promotes the emergence of modified peptides that are more suitable for MS/MS analysis. The modified sites can be utilized as extracellular constraints in topology predictions and may contribute to the refined topology of these proteins.
format	article
author	Tamás Langó Zoltán Gergő Pataki Lilla Turiák András Ács Julia Kornélia Varga György Várady Nóra Kucsma László Drahos Gábor E. Tusnády
author_facet	Tamás Langó Zoltán Gergő Pataki Lilla Turiák András Ács Julia Kornélia Varga György Várady Nóra Kucsma László Drahos Gábor E. Tusnády
author_sort	Tamás Langó
title	Partial proteolysis improves the identification of the extracellular segments of transmembrane proteins by surface biotinylation
title_short	Partial proteolysis improves the identification of the extracellular segments of transmembrane proteins by surface biotinylation
title_full	Partial proteolysis improves the identification of the extracellular segments of transmembrane proteins by surface biotinylation
title_fullStr	Partial proteolysis improves the identification of the extracellular segments of transmembrane proteins by surface biotinylation
title_full_unstemmed	Partial proteolysis improves the identification of the extracellular segments of transmembrane proteins by surface biotinylation
title_sort	partial proteolysis improves the identification of the extracellular segments of transmembrane proteins by surface biotinylation
publisher	Nature Portfolio
publishDate	2020
url	https://doaj.org/article/59f84953b9054598b7843cb7e89e568f
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Partial proteolysis improves the identification of the extracellular segments of transmembrane proteins by surface biotinylation

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