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Linear discriminant analysis reveals hidden patterns in NMR chemical shifts of intrinsically disordered proteins

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dc.abstract.enNMR spectroscopy is key in the study of intrinsically disordered proteins (IDPs). Yet, even the first step in such an analysis—the assignment of observed resonances to particular nuclei—is often problematic due to low peak dispersion in the spectra of IDPs. We show that the assignment process can be aided by finding “hidden” chemical shift patterns specific to the amino acid residue types. We find such patterns in the training data from the Biological Magnetic Resonance Bank using linear discriminant analysis, and then use them to classify spin systems in an α-synuclein sample prepared by us. We describe two situations in which the procedure can greatly facilitate the analysis of NMR spectra. The first involves the mapping of spin systems chains onto the protein sequence, which is part of the assignment procedure—a prerequisite for any NMR-based protein analysis. In the second, the method supports assignment transfer between similar samples. We conducted experiments to demonstrate these cases, and both times the majority of spin systems could be unambiguously assigned to the correct residue types.
dc.affiliationUniwersytet Warszawski
dc.contributor.authorZawadzka-Kazimierczuk, Anna
dc.contributor.authorKazimierczuk, Krzysztof
dc.contributor.authorUrbańczyk, Mateusz
dc.contributor.authorPutko, Paulina
dc.contributor.authorRomero, Javier
dc.date.accessioned2024-01-25T05:11:35Z
dc.date.available2024-01-25T05:11:35Z
dc.date.copyright2022-10-06
dc.date.issued2022
dc.description.accesstimeAT_PUBLICATION
dc.description.financeŚrodki finansowe, o których mowa w art. 365 pkt. 2 ustawy
dc.description.number10
dc.description.versionFINAL_PUBLISHED
dc.description.volume18
dc.identifier.doi10.1371/JOURNAL.PCBI.1010258
dc.identifier.issn1553-734X
dc.identifier.urihttps://repozytorium.uw.edu.pl//handle/item/111283
dc.identifier.weblinkhttps://dx.plos.org/10.1371/journal.pcbi.1010258
dc.languageeng
dc.pbn.affiliationchemical sciences
dc.relation.ispartofPLoS Computational Biology
dc.relation.pagese1010258
dc.rightsCC-BY
dc.sciencecloudnosend
dc.titleLinear discriminant analysis reveals hidden patterns in NMR chemical shifts of intrinsically disordered proteins
dc.typeJournalArticle
dspace.entity.typePublication