{"entity": "researcher", "timestamp": "2026-08-20T20:35:34.623Z", "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-affiliated.scilifelab.se/researcher/eae6fd83468f4ddfbbb7609d710dec6c.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/researcher/eae6fd83468f4ddfbbb7609d710dec6c"}}, "publications": [{"entity": "publication", "iuid": "ba215788484f4e7db1d69fe6ac73f074", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/ba215788484f4e7db1d69fe6ac73f074.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/ba215788484f4e7db1d69fe6ac73f074"}}, "title": "Insight into Malt1 activation mechanism through synergetic approach of AlphaFold, MD Simulation and NMR dynamic analyses.", "authors": [{"family": "Lesovoy", "given": "Dmitry", "initials": "D"}, {"family": "Agback", "given": "Tatiana", "initials": "T"}, {"family": "Roshchin", "given": "Konstantin", "initials": "K"}, {"family": "Sandalova", "given": "Tatyana", "initials": "T"}, {"family": "Achour", "given": "Adnane", "initials": "A"}, {"family": "Han", "given": "Xiao", "initials": "X"}, {"family": "Lomzov", "given": "Alexander", "initials": "A"}, {"family": "Orekhov", "given": "Vladislav", "initials": "V"}, {"family": "Agback", "given": "Peter", "initials": "P", "orcid": "0000-0003-2226-0746", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/eae6fd83468f4ddfbbb7609d710dec6c.json"}}], "type": "journal article", "published": "2025-12-19", "journal": {"title": "bioRxiv", "issn": "2692-8205", "issn-l": null}, "abstract": "Mucosa-associated lymphoid tissue lymphoma translocation protein 1 (MALT1) is a central regulator of immune signalling, yet the conformational dynamics governing its activation remain poorly defined. Building on our earlier solution-state analysis of apo MALT1(PCASP-Ig3)339-719, which revealed domain flexibility, dynamic autoinhibition, and sensitivity to physiological ionic conditions, we combine NMR relaxation, molecular dynamics simulations, and ensemble modelling to delineate how solution environment reshapes its conformational landscape. Because most structural information derives from dimeric or inhibitor-bound states, the behaviour of monomeric, ligand-free MALT1 in physiological solution has remained unclear. Here, MD simulations show that low-salt conditions drive all trajectories toward a unified inactive-like ensemble, marked by inward rotation of W580 and coordinated rearrangements of Loop 2 and Loop 3, indicating that the inactive state is energetically favoured and its reactivation kinetically suppressed. Physiological ionic strength partially restores access to active-like loop motions, aligning with NMR evidence that sodium modulates catalytic readiness. In contrast, high-salt conditions rigidify the PCASP-Ig3 module, suppressing loop fluctuations and preventing active-inactive transitions, thereby strongly enriching the active-state population. Importantly, the combined MD-NMR analysis demonstrates that the NMR-initiated ensembles provide the most faithful representation of backbone and loop dynamics under low-salt conditions, capturing substrate-independent loop rearrangements, stable hydrophobic-core behaviour, and the intrinsic transitions that shape MALT1's conformational equilibrium. Together, these findings identify ionic strength as a key regulator of MALT1 conformational equilibria,, highlighting how loop dynamics and domain flexibility tune its proteolytic competence and providing a dynamic framework for future structure-based modulation of MALT1 activity.", "doi": "10.64898/2025.12.17.694852", "pmid": "41446076", "labels": [], "xrefs": [{"db": "pmc", "key": "PMC12724407"}, {"db": "pii", "key": "2025.12.17.694852"}], "notes": [], "created": "2026-08-20T13:48:41.719Z", "modified": "2026-08-20T13:48:41.780Z"}, {"entity": "publication", "iuid": "ecf043c12388471b9ad9ffce190a577b", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/ecf043c12388471b9ad9ffce190a577b.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/ecf043c12388471b9ad9ffce190a577b"}}, "title": "Accurate Protein Dynamic Conformational Ensembles: Combining AlphaFold, MD, and Amide 15N(1H) NMR Relaxation.", "authors": [{"family": "Lesovoy", "given": "Dmitry", "initials": "D"}, {"family": "Roshchin", "given": "Konstantin", "initials": "K"}, {"family": "Sala", "given": "Benedetta Maria", "initials": "BM"}, {"family": "Sandalova", "given": "Tatyana", "initials": "T"}, {"family": "Achour", "given": "Adnane", "initials": "A", "orcid": "0000-0003-0432-710X", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/65fba324156a4fcbafbe636e642587a9.json"}}, {"family": "Agback", "given": "Tatiana", "initials": "T", "orcid": "0000-0003-1325-6024", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/45cf38c8b15946cda75b81cde94bbdfe.json"}}, {"family": "Agback", "given": "Peter", "initials": "P", "orcid": "0000-0003-2226-0746", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/eae6fd83468f4ddfbbb7609d710dec6c.json"}}, {"family": "Orekhov", "given": "Vladislav", "initials": "V"}], "type": "journal article", "published": "2025-09-12", "journal": {"title": "Int J Mol Sci", "issn": "1422-0067", "volume": "26", "issue": "18", "issn-l": null}, "abstract": "Conformational heterogeneity is essential for protein function, yet validating theoretical molecular dynamics (MD) ensembles remains a significant challenge. In this study, we present an approach that integrates free MD simulations, starting from an AlphaFold-generated structure, with refined experimental NMR-relaxation data to identify biologically relevant holistic time-resolved 4D conformational ensembles. Specifically, we select trajectory segments (RMSD plateaus) consistent with experimental observables. For the extracellular region of Streptococcus pneumoniae PsrSp, we found that only specific segments of the long MD trajectory aligned well with experimental data. The resulting ensembles revealed two regions with increased flexibility, both of which play important functional roles.", "doi": "10.3390/ijms26188917", "pmid": "41009484", "labels": [], "xrefs": [{"db": "pmc", "key": "PMC12469643"}, {"db": "pii", "key": "ijms26188917"}], "notes": [], "created": "2026-08-20T13:42:02.285Z", "modified": "2026-08-20T13:42:02.369Z"}, {"entity": "publication", "iuid": "bcb0138859b24f8987019deddced517f", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/bcb0138859b24f8987019deddced517f.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/bcb0138859b24f8987019deddced517f"}}, "title": "Accurate Protein Dynamic Conformational Ensembles: Combining AlphaFold, MD and Amide 15 N( 1 H) NMR Relaxation", "authors": [{"family": "Lesovoy", "given": "Dmitry", "initials": "D"}, {"family": "Roshchin", "given": "Konstantin", "initials": "K"}, {"family": "Sala", "given": "Benedetta Maria", "initials": "BM"}, {"family": "Sandalova", "given": "Tatyana", "initials": "T"}, {"family": "Achour", "given": "Adnane", "initials": "A"}, {"family": "Agback", "given": "Tatiana", "initials": "T"}, {"family": "Orekhov", "given": "Vladislav", "initials": "V"}, {"family": "Agback", "given": "Peter", "initials": "P", "orcid": "0000-0003-2226-0746", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/eae6fd83468f4ddfbbb7609d710dec6c.json"}}], "type": "posted-content", "published": "2025-02-07", "journal": {"issn-l": null}, "abstract": null, "doi": "10.1101/2025.02.07.637034", "pmid": null, "labels": [], "xrefs": [], "notes": [], "created": "2026-08-20T11:00:47.649Z", "modified": "2026-08-20T11:00:47.698Z"}, {"entity": "publication", "iuid": "6827909de85a489e824ef89cfb1f3ad3", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/6827909de85a489e824ef89cfb1f3ad3.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/6827909de85a489e824ef89cfb1f3ad3"}}, "title": "Crystallographic and NMR Study of Streptococcus pneumonia LCP Protein PsrSp Indicate the Importance of Dynamics in Four Long Loops for Ligand Specificity", "authors": [{"family": "Sandalova", "given": "Tatyana", "initials": "T"}, {"family": "Sala", "given": "Benedetta Maria", "initials": "BM"}, {"family": "Moche", "given": "Martin", "initials": "M", "orcid": "0000-0002-4834-7076", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/34394d4441c548fba9faad777b1252be.json"}}, {"family": "Ljunggren", "given": "Hans Gustaf", "initials": "HG"}, {"family": "Alici", "given": "Evren", "initials": "E"}, {"family": "Henriques-Normark", "given": "Birgitta", "initials": "B"}, {"family": "Agback", "given": "Tatiana", "initials": "T"}, {"family": "Lesovoy", "given": "Dmitry", "initials": "D"}, {"family": "Agback", "given": "Peter", "initials": "P", "orcid": "0000-0003-2226-0746", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/eae6fd83468f4ddfbbb7609d710dec6c.json"}}, {"family": "Achour", "given": "Adnane", "initials": "A", "orcid": "0000-0003-0432-710X", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/65fba324156a4fcbafbe636e642587a9.json"}}], "type": "journal-article", "published": "2024-12-19", "journal": {"title": "Crystals", "issn": "2073-4352", "volume": "14", "issue": "12", "pages": "1094", "issn-l": null}, "abstract": null, "doi": "10.3390/cryst14121094", "pmid": null, "labels": [], "xrefs": [], "notes": [], "created": "2026-08-20T13:40:26.238Z", "modified": "2026-08-20T13:40:26.329Z"}, {"entity": "publication", "iuid": "0102d2378dc1467b93cf164440fd96fc", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/0102d2378dc1467b93cf164440fd96fc.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/0102d2378dc1467b93cf164440fd96fc"}}, "title": "Crystallographic and NMR studies of Streptococcus pneumonia LCP protein Psr Sp indicate the importance of dynamics in four long loops for ligand specificity", "authors": [{"family": "Sandalova", "given": "Tatyana", "initials": "T", "orcid": "0000-0002-7694-6420", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/d2ea3d2ec9e94fe3876f88bd0786c24b.json"}}, {"family": "Sala", "given": "Benedetta Maria", "initials": "BM", "orcid": "0000-0002-1592-0817", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/f03e2bb1aeba4436a2f1571f50335b87.json"}}, {"family": "Moche", "given": "Martin", "initials": "M", "orcid": "0000-0002-4834-7076", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/34394d4441c548fba9faad777b1252be.json"}}, {"family": "Ljunggren", "given": "Hans Gustaf", "initials": "HG", "orcid": "0000-0003-0908-7387", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/0a134515bf6242818aad27e86a8da06a.json"}}, {"family": "Alici", "given": "Evren", "initials": "E", "orcid": "0000-0001-5307-6648", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/1b15e3ead7914feb86af38946f373dfb.json"}}, {"family": "Henriques-Normark", "given": "Birgitta", "initials": "B", "orcid": "0000-0002-5429-4759", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/40da20f498284552b13443f9109b7e32.json"}}, {"family": "Agback", "given": "Tatiana", "initials": "T", "orcid": "0000-0003-1325-6024", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/45cf38c8b15946cda75b81cde94bbdfe.json"}}, {"family": "Lesovoy", "given": "Dmitry", "initials": "D", "orcid": "0000-0002-9130-715X", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/706f3a39328e4e17823901ccc52b27c1.json"}}, {"family": "Agback", "given": "Peter", "initials": "P", "orcid": "0000-0003-2226-0746", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/eae6fd83468f4ddfbbb7609d710dec6c.json"}}, {"family": "Achour", "given": "Adnane", "initials": "A", "orcid": "0000-0003-0432-710X", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/65fba324156a4fcbafbe636e642587a9.json"}}], "type": "posted-content", "published": "2024-10-21", "journal": {"issn-l": null}, "abstract": null, "doi": "10.1101/2024.10.21.619401", "pmid": null, "labels": [], "xrefs": [], "notes": [], "created": "2026-08-20T10:58:53.965Z", "modified": "2026-08-20T10:58:54.223Z"}, {"entity": "publication", "iuid": "6491d310ed614b32a81d9061a74a3503", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/6491d310ed614b32a81d9061a74a3503.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/6491d310ed614b32a81d9061a74a3503"}}, "title": "Assigned NMR backbone resonances of the ligand-binding region domain of the pneumococcal serine-rich repeat protein (PsrP-BR) reveal a rigid monomer in solution.", "authors": [{"family": "Schulte", "given": "Tim", "initials": "T"}, {"family": "Sala", "given": "Benedetta Maria", "initials": "BM"}, {"family": "Nilvebrant", "given": "Johan", "initials": "J"}, {"family": "Nygren", "given": "Per-\u00c5ke", "initials": "P\u00c5"}, {"family": "Achour", "given": "Adnane", "initials": "A"}, {"family": "Shernyukov", "given": "Andrey", "initials": "A"}, {"family": "Agback", "given": "Tatiana", "initials": "T"}, {"family": "Agback", "given": "Peter", "initials": "P", "orcid": "0000-0003-2226-0746", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/eae6fd83468f4ddfbbb7609d710dec6c.json"}}], "type": "journal article", "published": "2020-10-00", "journal": {"title": "Biomol NMR Assign", "issn": "1874-270X", "volume": "14", "issue": "2", "pages": "195-200", "issn-l": null}, "abstract": "The pneumococcal serine rich repeat protein (PsrP) is displayed on the surface of Streptococcus pneumoniae with a suggested role in colonization in the human upper respiratory tract. Full-length PsrP is a 4000 residue-long multi-domain protein comprising a positively charged functional binding region (BR) domain for interaction with keratin and extracellular DNA during pneumococcal adhesion and biofilm formation, respectively. The previously determined crystal structure of the BR domain revealed a flat compressed barrel comprising two sides with an extended \u03b2-sheet on one side, and another \u03b2-sheet that is distorted by loops and \u03b2-turns on the other side. Crystallographic B-factors indicated a relatively high mobility of loop regions that were hypothesized to be important for binding. Furthermore, the crystal structure revealed an inter-molecular \u03b2-sheet formed between edge strands of two symmetry-related molecules, which could promote bacterial aggregation during biofilm formation. Here we report the near complete 15N/13C/1H backbone resonance assignment of the BR domain of PsrP, revealing a secondary structure profile that is almost identical to the X-ray structure. Dynamic 15N-T1, T2 and NOE data suggest a monomeric and rigid structure of BR with disordered residues only at the N- and C-termini. The presented peak assignment will allow us to identify BR residues that are crucial for ligand binding.", "doi": "10.1007/s12104-020-09944-9", "pmid": "32314099", "labels": [], "xrefs": [{"db": "pmc", "key": "PMC7462905"}, {"db": "pii", "key": "10.1007/s12104-020-09944-9"}], "notes": [], "created": "2026-08-20T06:40:33.601Z", "modified": "2026-08-20T06:40:33.695Z"}]}