{"entity": "researcher", "timestamp": "2026-08-20T20:37:31.595Z", "family": "Petzold", "given": "Katja", "initials": "K", "orcid": "0000-0001-9470-0347", "affiliations": ["Biomedicinskt centrum (BMC)  Husargatan 3 752 37 Uppsala Sweden", "Centre of Excellence for the Chemical Mechanisms of Life Uppsala University  Husargatan 3 75237 Uppsala Sweden", "Science for Life Laboratory Uppsala Biomedical Centre Uppsala University  Husargatan 3 75237 Uppsala Sweden"], "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/researcher/c62bcc3f6a1e4616ab9f842a98885f72.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/researcher/c62bcc3f6a1e4616ab9f842a98885f72"}}, "publications": [{"entity": "publication", "iuid": "68701601de1d4f49a1396ae5f3c8303a", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/68701601de1d4f49a1396ae5f3c8303a.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/68701601de1d4f49a1396ae5f3c8303a"}}, "title": "Sequence, structure, and affinity of miR-34a binding sites determine repression efficacy.", "authors": [{"family": "Sweetapple", "given": "Lara", "initials": "L"}, {"family": "Kosek", "given": "David M", "initials": "DM", "orcid": "0000-0002-0192-4761", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/67257ad840e3425ca7e29400ef8347b5.json"}}, {"family": "Banijamali", "given": "Elnaz", "initials": "E", "orcid": "0000-0003-4718-9720", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/aad5c1b791324f20bdf0f789254ac50d.json"}}, {"family": "Becker", "given": "Walter", "initials": "W"}, {"family": "M\u00fcller", "given": "Juliane", "initials": "J"}, {"family": "Karadiakos", "given": "Christina", "initials": "C"}, {"family": "Baronti", "given": "Lorenzo", "initials": "L"}, {"family": "Guzzetti", "given": "Ileana", "initials": "I"}, {"family": "Schritt", "given": "Dimitri", "initials": "D"}, {"family": "Chen", "given": "Alan", "initials": "A", "orcid": "0000-0001-8246-2935", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/bd3f186534784ea3af0ceab6e47df62c.json"}}, {"family": "Andersson", "given": "Emma R", "initials": "ER", "orcid": "0000-0002-8608-625X", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/91ddadc74058484aafc0f9efc90e0ad9.json"}}, {"family": "Petzold", "given": "Katja", "initials": "K", "orcid": "0000-0001-9470-0347", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/c62bcc3f6a1e4616ab9f842a98885f72.json"}}], "type": "journal article", "published": "2025-07-08", "journal": {"title": "Nucleic Acids Res.", "issn": "1362-4962", "volume": "53", "issue": "13", "issn-l": "0305-1048"}, "abstract": "MicroRNAs (miRs) regulate gene expression post-transcriptionally by guiding Argonaute (AGO) proteins to target mRNAs. Efficiently predicting the repressive effects of miRNAs remains limited largely due to an incomplete understanding of how mRNA:miR structure affects function. Using EMSAs, structural probing, luciferase reporter assays, and transcriptome analysis, we investigated the structural, biophysical, and functional interaction between the human tumour suppressor miR-34a and 12 mRNA targets. Comparison of isolated mRNA:miRNA duplexes and those bound within functional AGO2 revealed that while the binary duplex largely predicts AGO2-associated affinity and structure, AGO2 bidirectionally modulates binding by attenuating strong interactions and stabilising weaker ones. Furthermore, we show that the impact of supplementary pairing is more pronounced in targets with shorter seeds compared to those with full-length seeds and confirm this effect in a transcriptome-wide analysis. Finally, we identified three structural groups of mRNA:miR-34a-AGO2 complexes, adopting either a symmetrical structure, or a bulge on the mRNA or miR side. miR-bulged complex repression was strongly linked to mRNA:miR affinity, whereas mRNA-bulged complexes showed no such correlation. Our results thus identify structural and biophysical characteristics of mRNA:miR duplexes that contribute to repression efficacy, revealing a hierarchy of seed type, structure, and affinity that determine repression efficiency.", "doi": "10.1093/nar/gkaf633", "pmid": "40671527", "labels": [], "xrefs": [{"db": "pmc", "key": "PMC12266142"}, {"db": "pii", "key": "8203466"}], "notes": [], "created": "2026-08-20T09:50:17.272Z", "modified": "2026-08-20T09:50:17.494Z"}, {"entity": "publication", "iuid": "592fae3b422940e484cac829aaf477f5", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/592fae3b422940e484cac829aaf477f5.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/592fae3b422940e484cac829aaf477f5"}}, "title": "Investigating Interaction Dynamics of an Enantioselective Peptide-Catalyzed Acylation Reaction.", "authors": [{"family": "Brauser", "given": "Matthias", "initials": "M", "orcid": "0000-0002-0047-1481", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/fb25c86744d9418e91bd8d4a3c2c4312.json"}}, {"family": "Petzold", "given": "Katja", "initials": "K", "orcid": "0000-0001-9470-0347", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/c62bcc3f6a1e4616ab9f842a98885f72.json"}}, {"family": "Thiele", "given": "Christina M", "initials": "CM", "orcid": "0000-0001-7876-536X", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/e90f0248271f4d9285bad02127226b52.json"}}], "type": "journal article", "published": "2025-03-03", "journal": {"title": "Angew. Chem. Int. Ed. Engl.", "issn": "1521-3773", "volume": "64", "issue": "10", "pages": "e202421062", "issn-l": "1433-7851"}, "abstract": "Modern nuclear magnetic resonance (NMR) methods like carbon relaxation dispersion in the rotating frame (13C-R1\u03c1) and proton chemical exchange saturation transfer (1H-CEST) are key methods to investigate molecular recognition in biomacromolecules and to detect molecular motions on the \u03bcs to s timescale, revealing transient conformational states. Changes in kinetics can be linked to binding, folding, or catalytic events. Here, we investigated whether these methods allow detection of changes in the dynamics of a small, highly selective peptide catalyst during recognition of its enantiomeric substrates. The flexible tetrapeptide Boc-l-(\u03c0-Me)-His-AGly-l-Cha-l-Phe-OMe, used for the monoacetylation of cycloalkane-diols, is probed at natural abundance using 13C-R1\u03c1 and 1H-CEST. Indeed, we detected differences in dynamics of the peptide upon interaction with the diol. Importantly, these differ depending on the enantiomer of the substrate used. These enantiospecific influences of the substrates on the dynamics of the peptide are rationalized using computational techniques. We find that even though one enantiomer reacts faster, as confirmed by reaction monitoring, the other is more tightly bound in DCM (as confirmed by 1H-saturation transfer difference (STD) measurements). These findings provide insights into the recognition of the substrates and explain the selectivity differences observed between the solvents toluene and DCM.", "doi": "10.1002/anie.202421062", "pmid": "39621941", "labels": [], "xrefs": [], "notes": [], "created": "2026-08-20T06:30:02.137Z", "modified": "2026-08-20T06:30:02.218Z"}, {"entity": "publication", "iuid": "65fd26b33adc49cc8094675e39222b22", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/65fd26b33adc49cc8094675e39222b22.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/65fd26b33adc49cc8094675e39222b22"}}, "title": "Investigating Interaction Dynamics of an Enantioselective Peptide\u2010Catalyzed Acylation Reaction", "authors": [{"family": "Brauser", "given": "Matthias", "initials": "M", "orcid": "0000-0002-0047-1481", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/fb25c86744d9418e91bd8d4a3c2c4312.json"}}, {"family": "Petzold", "given": "Katja", "initials": "K", "orcid": "0000-0001-9470-0347", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/c62bcc3f6a1e4616ab9f842a98885f72.json"}}, {"family": "Thiele", "given": "Christina M", "initials": "CM", "orcid": "0000-0001-7876-536X", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/e90f0248271f4d9285bad02127226b52.json"}}], "type": "journal-article", "published": "2025-03-03", "journal": {"title": "Angewandte Chemie", "issn": "0044-8249", "volume": "137", "issue": "10", "issn-l": null}, "abstract": null, "doi": "10.1002/ange.202421062", "pmid": null, "labels": [], "xrefs": [], "notes": [], "created": "2026-08-20T06:29:51.825Z", "modified": "2026-08-20T06:29:51.992Z"}]}