{"entity": "researcher", "timestamp": "2026-08-20T20:36:20.668Z", "family": "Odai", "given": "Roni", "initials": "R", "orcid": "0009-0002-2280-3915", "affiliations": ["Department of Experimental Medical Science, Lund University, 223 62 Lund, Sweden."], "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/researcher/604a6d6e3cdb468d8c6acfb6a2e45ff9.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/researcher/604a6d6e3cdb468d8c6acfb6a2e45ff9"}}, "publications": [{"entity": "publication", "iuid": "3aece26036754a8f89bfecad5f024849", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/3aece26036754a8f89bfecad5f024849.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/3aece26036754a8f89bfecad5f024849"}}, "title": "Evidence for a functional interaction between yeast Pol \u03b5 and PCNA in vivo.", "authors": [{"family": "Singh", "given": "Noopur", "initials": "N"}, {"family": "Odai", "given": "Roni", "initials": "R", "orcid": "0009-0002-2280-3915", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/604a6d6e3cdb468d8c6acfb6a2e45ff9.json"}}, {"family": "Persson", "given": "Ulf", "initials": "U"}, {"family": "Bylund", "given": "G\u00f6ran O", "initials": "GO"}, {"family": "Obi", "given": "Ikenna", "initials": "I"}, {"family": "Sabouri", "given": "Nasim", "initials": "N", "orcid": "0000-0002-4541-7702", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/8bbda597fa314881a10de1f7a6ad09ee.json"}}, {"family": "Atkinson", "given": "Gemma C", "initials": "GC", "orcid": "0000-0002-4861-4584", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/f1879e0a722045769cfca0dd00d611a8.json"}}, {"family": "Johansson", "given": "Erik", "initials": "E", "orcid": "0000-0002-8526-6224", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/2e8695cbe08e41e0a9ee097e2f38a37b.json"}}], "type": "journal article", "published": "2025-11-26", "journal": {"title": "Nucleic Acids Res.", "issn": "1362-4962", "volume": "53", "issue": "22", "issn-l": "0305-1048"}, "abstract": "DNA replication relies on precise coordination between proteins, including the sliding clamp proliferating cell nuclear antigen (PCNA), which encircles DNA to interact with key players in replication and repair. While biochemical studies have demonstrated interactions between PCNA and DNA polymerases \u03b4 and \u03b5 during DNA synthesis, the functional role of the Pol \u03b5-PCNA interaction in vivo, particularly during leading strand synthesis, remains to be elucidated. To address this question, we employed AlphaFold to model how PCNA interact with four-subunit yeast Pol \u03b5. Our models revealed two distinct points of interaction between Pol \u03b5 and PCNA: one at the P-domain and another at a PIP-box, a classical PCNA interaction motif. To validate these findings, we generated mutants that disrupted the Pol \u03b5-PCNA interaction interface. Biochemical assays demonstrated that the PIP-box is critical for this interaction, with the P-domain serving as a secondary contact point. Notably, introducing these mutants into yeast, caused no phenotype in a wild-type background. However, when fewer origins are firing, resulting in longer stretches of leading strand synthesis before forks converge, strains expressing a Pol \u03b5 mutant lacking interaction with PCNA showed slower growth. These findings suggest that PCNA enhances the processivity of Pol \u03b5 both in vitro and in vivo.", "doi": "10.1093/nar/gkaf1339", "pmid": "41404803", "labels": [], "xrefs": [{"db": "pmc", "key": "PMC12709181"}, {"db": "pii", "key": "8382373"}], "notes": [], "created": "2026-08-20T09:50:15.101Z", "modified": "2026-08-20T09:50:15.248Z"}, {"entity": "publication", "iuid": "d5dd1820f3d64bba98b64bc4c1396191", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/d5dd1820f3d64bba98b64bc4c1396191.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/d5dd1820f3d64bba98b64bc4c1396191"}}, "title": "The Viral AlphaFold Database of monomers and homodimers reveals conserved protein folds in viruses of bacteria, archaea, and eukaryotes.", "authors": [{"family": "Odai", "given": "Roni", "initials": "R", "orcid": "0009-0002-2280-3915", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/604a6d6e3cdb468d8c6acfb6a2e45ff9.json"}}, {"family": "Leemann", "given": "Mich\u00e8le", "initials": "M", "orcid": "0009-0008-9641-8837", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/124f42d408ce4e23aa91f3d82ab73f22.json"}}, {"family": "Al-Murad", "given": "Tamim", "initials": "T", "orcid": "0009-0009-9450-6734", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/09af3a6db1304f58ba96542af779c538.json"}}, {"family": "Abdullah", "given": "Minhal", "initials": "M", "orcid": "0000-0002-6018-314X", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/1c8fb279f2df41d2a5d86e7afbab9592.json"}}, {"family": "Shyrokova", "given": "Lena", "initials": "L", "orcid": "0000-0002-0361-6359", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/f9e14037d4da48408ecfa16d12742d1f.json"}}, {"family": "Tenson", "given": "Tanel", "initials": "T", "orcid": "0000-0002-0260-3601", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/44fd1d5f2b4f43c0a2067d75306c85ed.json"}}, {"family": "Hauryliuk", "given": "Vasili", "initials": "V", "orcid": "0000-0003-2389-5057", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/1884d638ebd34b34bcabc105ca2f4092.json"}}, {"family": "Durairaj", "given": "Janani", "initials": "J", "orcid": "0000-0002-1698-4556", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/bbc37e3024a34e18b93c50bd7ce6c3a7.json"}}, {"family": "Pereira", "given": "Joana", "initials": "J", "orcid": "0000-0002-5588-6588", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/18123de080c84f7fba8ca71f1f294773.json"}}, {"family": "Atkinson", "given": "Gemma C", "initials": "GC", "orcid": "0000-0002-4861-4584", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/f1879e0a722045769cfca0dd00d611a8.json"}}], "type": "journal article", "published": "2025-10-03", "journal": {"title": "Sci Adv", "issn": "2375-2548", "volume": "11", "issue": "40", "pages": "eadz8560", "issn-l": "2375-2548"}, "abstract": "Viruses are the most abundant and genetically diverse entities on Earth, yet the functions and evolution of most viral proteins remain poorly understood. Their rapid evolution often obscures evolutionary relationships, limiting the ability to assign functions using sequence-based methods. Although the conservation of protein fold can reveal deep homologies, viral proteins remain underrepresented in structural databases. We address this by clustering viral sequences from RefSeq and predicting the structures of ~27,000 representative proteins using AlphaFold2 to create the Viral AlphaFold Database (VAD). We uncover conserved folds in diverse viruses infecting bacteria, archaea, and eukaryotes. We predict homodimers and make comparisons to the Protein Data Bank, providing data on oligomerization potential. We reveal considerable functional darkness in the viral protein universe and report the discovery and validation of an uncharacterized toxin-antitoxin system. The VAD provides a foundation for exploring viral structure-function relationships, including ancient folds shaping viral interactions across all life.", "doi": "10.1126/sciadv.adz8560", "pmid": "41032608", "labels": [], "xrefs": [{"db": "pmc", "key": "PMC12487901"}], "notes": [], "created": "2026-08-20T11:59:12.908Z", "modified": "2026-08-20T11:59:13.115Z"}]}