HTS topology analyses
Although theoretical protein topology prediction methods have high accuracy, they can predict the topology correctly for only 70-80% of the proteome. Unfortunately molecular biology experimental techniques applied in the verification of the predicted transmembrane protein topology (e. g. epitope insertion, examination of glycosylation state) are very slow and expensive. Furthermore, if modification happens at an inadequate site (functional sites, membrane-embedded regions, etc.) experimental results may prove difficult to interpret or may even be misleading. However, incorporating the results of well performed experiments as constraints into the hidden Markov model based topology prediction methods will make our prediction notably more accurate. This prediction then may be utilized during the design of further experiments.
Related publications
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Tálas A, Huszár K, Kulcsár PI, Varga JK, Varga É, Tóth E, Welker Zs, Erdős G, Pach PF, Welker Á, Györgypál Z, Tusnády GE and Welker E (2021) A method for characterizing Cas9 variants via a one-million target sequence library of self-targeting sgRNAs Nucleic Acids Res 49, e31.
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Langó T, Pataki ZG, Turiák L, Ács A, Varga JK, Várady, G, Kucsma, N, Drahos, L and Tusnády GE (2020) Partial Proteolysis Improves the Identification of the Extracellular Segments of Transmembrane Proteins by Surface Biotinylation Scientific Reports 10, 8880.
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Muller, A, Lango, T, Turiak, L, Acs, A, Varady, G, Kucsma, N, Drahos, L and Tusnady, GE (2019) Covalently modified carboxyl side chains on cell surface leads to a novel method toward topology analysis of transmembrane proteins Scientific Reports 9, 15729.
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Lango T, Rona G, Hunyadi-Gulyas E, Turiak L, Varga J, Dobson L, Varady Gy, Drahos L, Vertessy BG, Medzihradszky FK, Szakacs G and Tusnady GE (2017) Identification of extracellular segments by mass spectrometry improves topology prediction of transmembrane proteins Scientific Reports 7, 42610.
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Dobson L, Lango T, Remenyi I and Tusnady GE (2015) Expediting topology data gathering for the TOPDB database. Nucleic Acids Res 43, D283-9.
