{"entity": "researcher", "timestamp": "2026-08-20T20:43:09.086Z", "family": "Delarue", "given": "Marc", "initials": "M", "orcid": "0000-0003-0723-8102", "affiliations": [], "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/researcher/ee0e290455aa46c5a3a7d9f0ce226dcf.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/researcher/ee0e290455aa46c5a3a7d9f0ce226dcf"}}, "publications": [{"entity": "publication", "iuid": "38f6eb0690144d35b1585e0d75b478b1", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/38f6eb0690144d35b1585e0d75b478b1.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/38f6eb0690144d35b1585e0d75b478b1"}}, "title": "Discovering cryptic pocket opening and binding of a stimulant derivative in a vestibular site of the 5-HT3A receptor.", "authors": [{"family": "Haloi", "given": "Nandan", "initials": "N", "orcid": "0000-0003-3542-333X", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/a499486a86ba4df7a27d26dad6222b47.json"}}, {"family": "Karlsson", "given": "Emelia", "initials": "E", "orcid": "0009-0005-4878-964X", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/08a1be310cbe486895961fd1c757404d.json"}}, {"family": "Delarue", "given": "Marc", "initials": "M", "orcid": "0000-0003-0723-8102", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/ee0e290455aa46c5a3a7d9f0ce226dcf.json"}}, {"family": "Howard", "given": "Rebecca J", "initials": "RJ", "orcid": "0000-0003-2049-3378", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/5ce04593b5b24aaa8978fda1447dd0bf.json"}}, {"family": "Lindahl", "given": "Erik", "initials": "E", "orcid": "0000-0002-2734-2794", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/9eb30fa60f9b4b95842ac9d9f3a0eaa9.json"}}], "type": "journal article", "published": "2025-04-11", "journal": {"title": "Sci Adv", "issn": "2375-2548", "volume": "11", "issue": "15", "pages": "eadr0797", "issn-l": "2375-2548"}, "abstract": "A diverse set of modulators, including stimulants and anesthetics, regulates ion channel function in our nervous system. However, structures of ligand-bound complexes can be difficult to capture by experimental methods, particularly when binding is dynamic. Here, we used computational methods and electrophysiology to identify a possible bound state of a modulatory stimulant derivative in a cryptic vestibular pocket of a mammalian serotonin-3 receptor. We first applied a molecular dynamics simulation-based goal-oriented adaptive sampling method to identify possible open-pocket conformations, followed by Boltzmann docking that combines traditional docking with Markov state modeling. Clustering and analysis of stability and accessibility of docked poses supported a preferred binding site; we further validated this site by mutagenesis and electrophysiology, suggesting a mechanism of potentiation by stabilizing intersubunit contacts. Given the pharmaceutical relevance of serotonin-3 receptors in emesis, psychiatric, and gastrointestinal diseases, characterizing relatively unexplored modulatory sites such as these could open valuable avenues to understanding conformational cycling and designing state-dependent drugs.", "doi": "10.1126/sciadv.adr0797", "pmid": "40215320", "labels": [], "xrefs": [{"db": "pmc", "key": "PMC11988449"}], "notes": [], "created": "2026-08-20T11:58:57.705Z", "modified": "2026-08-20T11:58:57.859Z"}, {"entity": "publication", "iuid": "3d88996e69924c3e9569ca368c16309c", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/3d88996e69924c3e9569ca368c16309c.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/3d88996e69924c3e9569ca368c16309c"}}, "title": "Structure and dynamics of a multidomain ligand-gated ion channel revealed under acidic conditions", "authors": [{"family": "And\u00e9n", "given": "Olivia", "initials": "O", "orcid": "0009-0002-4816-5691", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/6e5867d3d6bb48bb935cf2c28642c9a3.json"}}, {"family": "Rov\u0161nik", "given": "Ur\u0161ka", "initials": "U", "orcid": "0000-0001-5889-6899", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/f0ab87a8712f4ad886da61c1edcf679f.json"}}, {"family": "Lycksell", "given": "Marie", "initials": "M", "orcid": "0000-0003-3271-7973", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/0833a696c9ec497bae99bbe631af624f.json"}}, {"family": "Delarue", "given": "Marc", "initials": "M", "orcid": "0000-0003-0723-8102", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/ee0e290455aa46c5a3a7d9f0ce226dcf.json"}}, {"family": "Howard", "given": "Rebecca J", "initials": "RJ", "orcid": "0000-0003-2049-3378", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/5ce04593b5b24aaa8978fda1447dd0bf.json"}}, {"family": "Lindahl", "given": "Erik", "initials": "E", "orcid": "0000-0002-2734-2794", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/9eb30fa60f9b4b95842ac9d9f3a0eaa9.json"}}], "type": "posted-content", "published": "2025-02-27", "journal": {"issn-l": null}, "abstract": null, "doi": "10.1101/2025.02.27.640520", "pmid": null, "labels": [], "xrefs": [], "notes": [], "created": "2026-08-20T11:01:20.993Z", "modified": "2026-08-20T11:01:21.080Z"}, {"entity": "publication", "iuid": "9bd6efd7c222488cad615f064e0d3b12", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/9bd6efd7c222488cad615f064e0d3b12.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/9bd6efd7c222488cad615f064e0d3b12"}}, "title": "Structural basis for the increased processivity of D-family DNA polymerases in complex with PCNA", "authors": [{"family": "Madru", "given": "Cl\u00e9ment", "initials": "C", "orcid": "0000-0002-5412-8822", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/f44a96b044984968bcc43d86899d5be3.json"}}, {"family": "Raia", "given": "Pierre", "initials": "P", "orcid": "0000-0003-3469-1922", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/6ef78cfd1dfd48828ccad074180c75ed.json"}}, {"family": "Hugonneau-Beaufet", "given": "In\u00e8s", "initials": "I"}, {"family": "Pehau-Arnaudet", "given": "G\u00e9rard", "initials": "G"}, {"family": "England", "given": "Patrick", "initials": "P"}, {"family": "Lindahl", "given": "Erik", "initials": "E", "orcid": "0000-0002-2734-2794", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/9eb30fa60f9b4b95842ac9d9f3a0eaa9.json"}}, {"family": "Delarue", "given": "Marc", "initials": "M", "orcid": "0000-0003-0723-8102", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/ee0e290455aa46c5a3a7d9f0ce226dcf.json"}}, {"family": "Carroni", "given": "Marta", "initials": "M", "orcid": "0000-0002-7697-6427", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/55fa4ba347a34d7ca80d214e8d718e44.json"}}, {"family": "Sauguet", "given": "Ludovic", "initials": "L", "orcid": "0000-0002-1259-6601", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/f352b1cc2fcb434a8b63923413b2ef4a.json"}}], "type": "posted-content", "published": "2020-01-30", "journal": {"issn-l": null}, "abstract": null, "doi": "10.1101/2020.01.29.925263", "pmid": null, "labels": [], "xrefs": [], "notes": [], "created": "2026-08-20T09:55:40.979Z", "modified": "2026-08-20T09:55:41.216Z"}]}