{"entity": "researcher", "timestamp": "2026-07-17T08:58:08.291Z", "family": "Agback", "given": "Tatiana", "initials": "T", "orcid": "0000-0003-1325-6024", "affiliations": ["Department of Molecular Sciences, Swedish University of Agricultural Sciences, Box 7015, Uppsala, 75007, Sweden."], "links": {"self": {"href": "https://publications.scilifelab.se/researcher/8ded0891ca3d4bdda4082ffa347ca37a.json"}, "display": {"href": "https://publications.scilifelab.se/researcher/8ded0891ca3d4bdda4082ffa347ca37a"}}, "publications": [{"entity": "publication", "iuid": "89a9d81b95104d2ead4db6caebd4990c", "links": {"self": {"href": "https://publications.scilifelab.se/publication/89a9d81b95104d2ead4db6caebd4990c.json"}, "display": {"href": "https://publications.scilifelab.se/publication/89a9d81b95104d2ead4db6caebd4990c"}}, "title": "Scalable deep learning reconstruction for accelerated multidimensional nuclear magnetic resonance spectroscopy of proteins", "authors": [{"family": "Huang", "given": "Yihui", "initials": "Y", "orcid": "0000-0002-5035-7687", "researcher": {"href": "https://publications.scilifelab.se/researcher/773bedbe71644bb3adab46fba3477c24.json"}}, {"family": "Gao", "given": "Yuncheng", "initials": "Y", "orcid": "0009-0005-8549-1789", "researcher": {"href": "https://publications.scilifelab.se/researcher/b568fae51f86472487896e51029f0c6f.json"}}, {"family": "Tu", "given": "Zhangren", "initials": "Z", "orcid": "0000-0002-0863-2454", "researcher": {"href": "https://publications.scilifelab.se/researcher/e450c06cfb6d4ff3847e5d98dc818d2b.json"}}, {"family": "Agback", "given": "Tatiana", "initials": "T", "orcid": "0000-0003-1325-6024", "researcher": {"href": "https://publications.scilifelab.se/researcher/8ded0891ca3d4bdda4082ffa347ca37a.json"}}, {"family": "Orekhov", "given": "Vladislav", "initials": "V", "orcid": "0000-0002-7892-6896", "researcher": {"href": "https://publications.scilifelab.se/researcher/77382c412de04fa08ff7c3bc7087b77e.json"}}, {"family": "Hyberts", "given": "Sven G", "initials": "SG", "orcid": "0000-0002-3169-4709", "researcher": {"href": "https://publications.scilifelab.se/researcher/5a0d5dc0f7b040f1b979312bf59a5daf.json"}}, {"family": "Wagner", "given": "Gerhard", "initials": "G", "orcid": "0000-0002-2063-4401", "researcher": {"href": "https://publications.scilifelab.se/researcher/ab6dec04566246c28cfd076fb667f929.json"}}, {"family": "Lin", "given": "Yanqin", "initials": "Y", "orcid": "0000-0003-0596-0740", "researcher": {"href": "https://publications.scilifelab.se/researcher/92d8757206c6419c97d3e6699cc1a8d0.json"}}, {"family": "Chen", "given": "Zhong", "initials": "Z", "orcid": "0000-0002-1473-2224", "researcher": {"href": "https://publications.scilifelab.se/researcher/c95d3606af9b4826a6a298c5ddcdc01e.json"}}, {"family": "Guo", "given": "Di", "initials": "D", "orcid": "0000-0002-9910-5720", "researcher": {"href": "https://publications.scilifelab.se/researcher/0450ec43a296466d8a31387fa3bd9ea6.json"}}, {"family": "Qu", "given": "Xiaobo", "initials": "X", "orcid": "0000-0002-8675-5820", "researcher": {"href": "https://publications.scilifelab.se/researcher/cd0bbb61a58d4218ac29f5ec08ed3520.json"}}], "type": "journal-article", "published": "2025-09-26", "journal": {"title": "Sci Adv", "issn": "2375-2548", "volume": "11", "issue": "39", "issn-l": "2375-2548"}, "abstract": null, "doi": "10.1126/sciadv.adw8122", "pmid": null, "labels": {"Swedish NMR Centre": "Collaborative"}, "xrefs": [], "notes": [], "created": "2025-11-27T08:02:33.748Z", "modified": "2025-11-27T08:02:34.801Z"}, {"entity": "publication", "iuid": "f6952d433d3d4a739c73bcfe7118c1ae", "links": {"self": {"href": "https://publications.scilifelab.se/publication/f6952d433d3d4a739c73bcfe7118c1ae.json"}, "display": {"href": "https://publications.scilifelab.se/publication/f6952d433d3d4a739c73bcfe7118c1ae"}}, "title": "Insights into mechanisms of MALT1 allostery from NMR and AlphaFold dynamic analyses.", "authors": [{"family": "Wallerstein", "given": "Johan", "initials": "J"}, {"family": "Han", "given": "Xiao", "initials": "X"}, {"family": "Levkovets", "given": "Maria", "initials": "M", "orcid": "0000-0002-1805-9057", "researcher": {"href": "https://publications.scilifelab.se/researcher/cf8cc61d91474483ab51728701d2f75a.json"}}, {"family": "Lesovoy", "given": "Dmitry", "initials": "D"}, {"family": "Malmodin", "given": "Daniel", "initials": "D"}, {"family": "Mirabello", "given": "Claudio", "initials": "C", "orcid": "0000-0001-7868-034X", "researcher": {"href": "https://publications.scilifelab.se/researcher/00052b54a3d24fd4a6e648f987d15e5f.json"}}, {"family": "Wallner", "given": "Bj\u00f6rn", "initials": "B", "orcid": "0000-0002-3772-8279", "researcher": {"href": "https://publications.scilifelab.se/researcher/108086b7b06e4247b332ff4a119b97a5.json"}}, {"family": "Sun", "given": "Renhua", "initials": "R", "orcid": "0000-0002-8203-4946", "researcher": {"href": "https://publications.scilifelab.se/researcher/f639c1a9dca647c0b583ce74ab398f02.json"}}, {"family": "Sandalova", "given": "Tatyana", "initials": "T", "orcid": "0000-0002-7694-6420", "researcher": {"href": "https://publications.scilifelab.se/researcher/8adca17a49fc47b696cb2b2795f83e6f.json"}}, {"family": "Agback", "given": "Peter", "initials": "P", "orcid": "0000-0003-2226-0746", "researcher": {"href": "https://publications.scilifelab.se/researcher/84e8e871e8224c9898ad1cfa71481399.json"}}, {"family": "Karlsson", "given": "G\u00f6ran", "initials": "G", "orcid": "0000-0002-1821-4715", "researcher": {"href": "https://publications.scilifelab.se/researcher/2c6463abd05b415696c52be577ca2be6.json"}}, {"family": "Achour", "given": "Adnane", "initials": "A", "orcid": "0000-0003-0432-710X", "researcher": {"href": "https://publications.scilifelab.se/researcher/39682601d1a24f5ba1d103bf74c9acbd.json"}}, {"family": "Agback", "given": "Tatiana", "initials": "T", "orcid": "0000-0003-1325-6024", "researcher": {"href": "https://publications.scilifelab.se/researcher/8ded0891ca3d4bdda4082ffa347ca37a.json"}}, {"family": "Orekhov", "given": "Vladislav", "initials": "V", "orcid": "0000-0002-7892-6896", "researcher": {"href": "https://publications.scilifelab.se/researcher/77382c412de04fa08ff7c3bc7087b77e.json"}}], "type": "journal article", "published": "2024-07-16", "journal": {"title": "Commun Biol", "issn": "2399-3642", "volume": "7", "issue": "1", "pages": "868", "issn-l": "2399-3642"}, "abstract": "Mucosa-associated lymphoid tissue lymphoma-translocation protein 1 (MALT1) is an attractive target for the development of modulatory compounds in the treatment of lymphoma and other cancers. While the three-dimensional structure of MALT1 has been previously determined through X-ray analysis, its dynamic behaviour in solution has remained unexplored. We present here dynamic analyses of the apo MALT1 form along with the E549A mutation. This investigation used NMR 15N relaxation and NOE measurements between side-chain methyl groups. Our findings confirm that MALT1 exists as a monomer in solution, and demonstrate that the domains display semi-independent movements in relation to each other. Our dynamic study, covering multiple time scales, along with the assessment of conformational populations by Molecular Dynamic simulations, Alpha Fold modelling and PCA analysis, put the side chain of residue W580 in an inward position, shedding light at potential mechanisms underlying the allosteric regulation of this enzyme.", "doi": "10.1038/s42003-024-06558-y", "pmid": "39014105", "labels": {"Bioinformatics Support, Infrastructure and Training": "Technology development", "Bioinformatics (NBIS)": "Technology development", "Swedish NMR Centre": "Technology development"}, "xrefs": [{"db": "pmc", "key": "PMC11252132"}, {"db": "pii", "key": "10.1038/s42003-024-06558-y"}], "notes": [], "created": "2024-08-06T09:19:26.577Z", "modified": "2025-10-17T13:03:52.905Z"}, {"entity": "publication", "iuid": "05ed7f33d6124a1a9894b922310b7fe9", "links": {"self": {"href": "https://publications.scilifelab.se/publication/05ed7f33d6124a1a9894b922310b7fe9.json"}, "display": {"href": "https://publications.scilifelab.se/publication/05ed7f33d6124a1a9894b922310b7fe9"}}, "title": "Combined NMR and molecular dynamics conformational filter identifies unambiguously dynamic ensembles of Dengue protease NS2B/NS3pro.", "authors": [{"family": "Agback", "given": "Tatiana", "initials": "T", "orcid": "0000-0003-1325-6024", "researcher": {"href": "https://publications.scilifelab.se/researcher/8ded0891ca3d4bdda4082ffa347ca37a.json"}}, {"family": "Lesovoy", "given": "Dmitry", "initials": "D"}, {"family": "Han", "given": "Xiao", "initials": "X"}, {"family": "Lomzov", "given": "Alexander", "initials": "A", "orcid": "0000-0003-3889-9464", "researcher": {"href": "https://publications.scilifelab.se/researcher/4883dd36bfcf43f0a93f1f4c3137e2c8.json"}}, {"family": "Sun", "given": "Renhua", "initials": "R", "orcid": "0000-0002-8203-4946", "researcher": {"href": "https://publications.scilifelab.se/researcher/f639c1a9dca647c0b583ce74ab398f02.json"}}, {"family": "Sandalova", "given": "Tatyana", "initials": "T", "orcid": "0000-0002-7694-6420", "researcher": {"href": "https://publications.scilifelab.se/researcher/8adca17a49fc47b696cb2b2795f83e6f.json"}}, {"family": "Orekhov", "given": "Vladislav Yu", "initials": "VY"}, {"family": "Achour", "given": "Adnane", "initials": "A", "orcid": "0000-0003-0432-710X", "researcher": {"href": "https://publications.scilifelab.se/researcher/39682601d1a24f5ba1d103bf74c9acbd.json"}}, {"family": "Agback", "given": "Peter", "initials": "P", "orcid": "0000-0003-2226-0746", "researcher": {"href": "https://publications.scilifelab.se/researcher/84e8e871e8224c9898ad1cfa71481399.json"}}], "type": "journal article", "published": "2023-11-24", "journal": {"title": "Commun Biol", "issn": "2399-3642", "volume": "6", "issue": "1", "pages": "1193", "issn-l": "2399-3642"}, "abstract": "The dengue protease NS2B/NS3pro has been reported to adopt either an 'open' or a 'closed' conformation. We have developed a conformational filter that combines NMR with MD simulations to identify conformational ensembles that dominate in solution. Experimental values derived from relaxation parameters for the backbone and methyl side chains were compared with the corresponding back-calculated relaxation parameters of different conformational ensembles obtained from free MD simulations. Our results demonstrate a high prevalence for the 'closed' conformational ensemble while the 'open' conformation is absent, indicating that the latter conformation is most probably due to crystal contacts. Conversely, conformational ensembles in which the positioning of the co-factor NS2B results in a 'partially' open conformation, previously described in both MD simulations and X-ray studies, were identified by our conformational filter. Altogether, we believe that our approach allows for unambiguous identification of true conformational ensembles, an essential step for reliable drug discovery.", "doi": "10.1038/s42003-023-05584-6", "pmid": "38001280", "labels": {"Swedish NMR Centre": "Collaborative"}, "xrefs": [{"db": "pmc", "key": "PMC10673835"}, {"db": "pii", "key": "10.1038/s42003-023-05584-6"}], "notes": [], "created": "2023-12-04T09:35:34.802Z", "modified": "2025-10-17T13:03:53.330Z"}, {"entity": "publication", "iuid": "2d0ca3bc4bb74317b4b1fd76a9ca3a0c", "links": {"self": {"href": "https://publications.scilifelab.se/publication/2d0ca3bc4bb74317b4b1fd76a9ca3a0c.json"}, "display": {"href": "https://publications.scilifelab.se/publication/2d0ca3bc4bb74317b4b1fd76a9ca3a0c"}}, "title": "Resolution enhancement of NMR by decoupling with the low-rank Hankel model.", "authors": [{"family": "Qiu", "given": "Tianyu", "initials": "T", "orcid": "0000-0002-6102-8627", "researcher": {"href": "https://publications.scilifelab.se/researcher/c8230b09d4c0478f8deaed3a8b384b94.json"}}, {"family": "Jahangiri", "given": "Amir", "initials": "A", "orcid": "0000-0001-6051-3738", "researcher": {"href": "https://publications.scilifelab.se/researcher/e5925aa696864034a668230fb68d91bf.json"}}, {"family": "Han", "given": "Xiao", "initials": "X"}, {"family": "Lesovoy", "given": "Dmitry", "initials": "D"}, {"family": "Agback", "given": "Tatiana", "initials": "T", "orcid": "0000-0003-1325-6024", "researcher": {"href": "https://publications.scilifelab.se/researcher/8ded0891ca3d4bdda4082ffa347ca37a.json"}}, {"family": "Agback", "given": "Peter", "initials": "P"}, {"family": "Achour", "given": "Adnane", "initials": "A", "orcid": "0000-0003-0432-710X", "researcher": {"href": "https://publications.scilifelab.se/researcher/39682601d1a24f5ba1d103bf74c9acbd.json"}}, {"family": "Qu", "given": "Xiaobo", "initials": "X", "orcid": "0000-0002-0863-2454", "researcher": {"href": "https://publications.scilifelab.se/researcher/e450c06cfb6d4ff3847e5d98dc818d2b.json"}}, {"family": "Orekhov", "given": "Vladislav", "initials": "V", "orcid": "0000-0002-7892-6896", "researcher": {"href": "https://publications.scilifelab.se/researcher/77382c412de04fa08ff7c3bc7087b77e.json"}}], "type": "journal article", "published": "2023-05-02", "journal": {"title": "Chem. Commun. (Camb.)", "issn": "1364-548X", "issn-l": "1359-7345", "volume": "59", "issue": "36", "pages": "5475-5478"}, "abstract": "Nuclear magnetic resonance (NMR) spectroscopy has become a formidable tool for biochemistry and medicine. Although J-coupling carries essential structural information it may also limit the spectral resolution. Homonuclear decoupling remains a challenging problem. In this work, we introduce a new approach that uses a specific coupling value as prior knowledge, and the Hankel property of the exponential NMR signal to achieve broadband heteronuclear decoupling using the low-rank method. Our results on synthetic and realistic HMQC spectra demonstrate that the proposed method not only effectively enhances resolution by decoupling, but also maintains sensitivity and suppresses spectral artefacts. The approach can be combined with non-uniform sampling, which means that the resolution can be further improved without any extra acquisition time.", "doi": "10.1039/d2cc06682c", "pmid": "37070867", "labels": {"Swedish NMR Centre": "Technology development"}, "xrefs": [{"db": "pmc", "key": "PMC10152455"}], "notes": [], "created": "2023-05-31T16:37:33.329Z", "modified": "2025-10-17T13:03:53.921Z"}, {"entity": "publication", "iuid": "011d90ef2aa342389985def1f3047529", "links": {"self": {"href": "https://publications.scilifelab.se/publication/011d90ef2aa342389985def1f3047529.json"}, "display": {"href": "https://publications.scilifelab.se/publication/011d90ef2aa342389985def1f3047529"}}, "title": "Structural characterization and biological function of bivalent binding of CD2AP to intrinsically disordered domain of chikungunya virus nsP3 protein", "authors": [{"family": "Agback", "given": "Peter", "initials": "P", "orcid": "0000-0003-2226-0746", "researcher": {"href": "https://publications.scilifelab.se/researcher/84e8e871e8224c9898ad1cfa71481399.json"}}, {"family": "Dominguez", "given": "Francisco", "initials": "F"}, {"family": "Pustovalova", "given": "Yulia", "initials": "Y", "orcid": "0000-0003-3024-1764", "researcher": {"href": "https://publications.scilifelab.se/researcher/1b197bf375344485b02973e24d3e0826.json"}}, {"family": "Lukash", "given": "Tetyana", "initials": "T"}, {"family": "Shiliaev", "given": "Nikita", "initials": "N"}, {"family": "Orekhov", "given": "Vladislav Yu", "initials": "VY", "orcid": "0000-0002-7892-6896", "researcher": {"href": "https://publications.scilifelab.se/researcher/77382c412de04fa08ff7c3bc7087b77e.json"}}, {"family": "Frolov", "given": "Ilya", "initials": "I"}, {"family": "Agback", "given": "Tatiana", "initials": "T", "orcid": "0000-0003-1325-6024", "researcher": {"href": "https://publications.scilifelab.se/researcher/8ded0891ca3d4bdda4082ffa347ca37a.json"}}, {"family": "Frolova", "given": "Elena I", "initials": "EI"}], "type": "journal-article", "published": "2019-11-00", "journal": {"title": "Virology", "issn": "0042-6822", "volume": "537", "pages": "130-142", "issn-l": null}, "abstract": null, "doi": "10.1016/j.virol.2019.08.022", "pmid": "31493651", "labels": {"Swedish NMR Centre": "Collaborative"}, "xrefs": [], "notes": [], "created": "2023-05-31T16:50:30.491Z", "modified": "2025-10-17T13:03:57.403Z"}]}