{"entity": "researcher", "timestamp": "2026-07-20T12:21:12.754Z", "family": "Agback", "given": "Peter", "initials": "P", "orcid": "0000-0003-2226-0746", "affiliations": ["Department of Molecular Sciences, Swedish University of Agricultural Sciences, PO Box 7015, 750 07, Uppsala, Sweden. peter.agback@slu.se."], "links": {"self": {"href": "https://publications.scilifelab.se/researcher/84e8e871e8224c9898ad1cfa71481399.json"}, "display": {"href": "https://publications.scilifelab.se/researcher/84e8e871e8224c9898ad1cfa71481399"}}, "publications": [{"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": "ce7e13f6941043b1b468b12bb1cbc675", "links": {"self": {"href": "https://publications.scilifelab.se/publication/ce7e13f6941043b1b468b12bb1cbc675.json"}, "display": {"href": "https://publications.scilifelab.se/publication/ce7e13f6941043b1b468b12bb1cbc675"}}, "title": "1H, 13C and 15N resonance assignment of backbone and IVL-methyl side chain of the S135A mutant NS3pro/NS2B protein of Dengue II virus reveals unique secondary structure features in solution.", "authors": [{"family": "Agback", "given": "Peter", "initials": "P", "orcid": "0000-0003-2226-0746", "researcher": {"href": "https://publications.scilifelab.se/researcher/84e8e871e8224c9898ad1cfa71481399.json"}}, {"family": "Lesovoy", "given": "Dmitry M", "initials": "DM"}, {"family": "Han", "given": "Xiao", "initials": "X"}, {"family": "Sun", "given": "Renhua", "initials": "R"}, {"family": "Sandalova", "given": "Tatyana", "initials": "T"}, {"family": "Agback", "given": "Tatiana", "initials": "T"}, {"family": "Achour", "given": "Adnane", "initials": "A"}, {"family": "Orekhov", "given": "Vladislav Yu", "initials": "VY"}], "type": "journal article", "published": "2022-04-00", "journal": {"title": "Biomol NMR Assign", "issn": "1874-270X", "volume": "16", "issue": "1", "pages": "135-145", "issn-l": null}, "abstract": "The serotype II Dengue (DENV 2) virus is the most prevalent of all four known serotypes. Herein, we present nearly complete 1H, 15N, and 13C backbone and 1H, 13C isoleucine, valine, and leucine methyl resonance assignment of the apo S135A catalytically inactive variant of the DENV 2 protease enzyme folded as a tandem formed between the serine protease domain NS3pro and the cofactor NS2B, as well as the secondary structure prediction of this complex based on the assigned chemical shifts using the TALOS-N software. Our results provide a solid ground for future elucidation of the structure and dynamic of the apo NS3pro/NS2B complex, key for adequate development of inhibitors, and a thorough molecular understanding of their function(s).", "doi": "10.1007/s12104-022-10071-w", "pmid": "35149939", "labels": {"Swedish NMR Centre": "Collaborative"}, "xrefs": [{"db": "pmc", "key": "PMC9068680"}, {"db": "pii", "key": "10.1007/s12104-022-10071-w"}], "notes": [], "created": "2022-04-25T12:31:04.004Z", "modified": "2025-10-17T13:03:54.872Z"}, {"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"}]}