{"entity": "researcher", "timestamp": "2026-08-20T20:57:18.318Z", "family": "Bergh", "given": "Cathrine", "initials": "C", "orcid": "0000-0001-7540-5887", "affiliations": ["Department of Applied Physics, Science for Life Laboratory, KTH Royal Institute of Technology, 10044 Stockholm, Sweden."], "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/researcher/5c8a3efa976b41edb6ace4efae952125.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/researcher/5c8a3efa976b41edb6ace4efae952125"}}, "publications": [{"entity": "publication", "iuid": "91bd850059504c96939f313b9df5c5ff", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/91bd850059504c96939f313b9df5c5ff.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/91bd850059504c96939f313b9df5c5ff"}}, "title": "Discovery of lipid binding sites in a ligand-gated ion channel by integrating simulations and cryo-EM.", "authors": [{"family": "Bergh", "given": "Cathrine", "initials": "C", "orcid": "0000-0001-7540-5887", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/5c8a3efa976b41edb6ace4efae952125.json"}}, {"family": "Rov\u0161nik", "given": "Ur\u0161ka", "initials": "U"}, {"family": "Howard", "given": "Rebecca", "initials": "R"}, {"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": "2024-01-30", "journal": {"title": "Elife", "issn": "2050-084X", "volume": "12", "issn-l": "2050-084X"}, "abstract": "Ligand-gated ion channels transduce electrochemical signals in neurons and other excitable cells. Aside from canonical ligands, phospholipids are thought to bind specifically to the transmembrane domain of several ion channels. However, structural details of such lipid contacts remain elusive, partly due to limited resolution of these regions in experimental structures. Here, we discovered multiple lipid interactions in the channel GLIC by integrating cryo-electron microscopy and large-scale molecular simulations. We identified 25 bound lipids in the GLIC closed state, a conformation where none, to our knowledge, were previously known. Three lipids were associated with each subunit in the inner leaflet, including a buried interaction disrupted in mutant simulations. In the outer leaflet, two intrasubunit sites were evident in both closed and open states, while a putative intersubunit site was preferred in open-state simulations. This work offers molecular details of GLIC-lipid contacts particularly in the ill-characterized closed state, testable hypotheses for state-dependent binding, and a multidisciplinary strategy for modeling protein-lipid interactions.", "doi": "10.7554/eLife.86016", "pmid": "38289224", "labels": [], "xrefs": [{"db": "pmc", "key": "PMC10945520"}, {"db": "pii", "key": "86016"}], "notes": [], "created": "2026-08-20T13:55:07.648Z", "modified": "2026-08-20T13:55:07.736Z"}, {"entity": "publication", "iuid": "064fff0e468f4626b916e89be85f1939", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/064fff0e468f4626b916e89be85f1939.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/064fff0e468f4626b916e89be85f1939"}}, "title": "Author Response: Discovery of lipid binding sites in a ligand-gated ion channel by integrating simulations and cryo-EM", "authors": [{"family": "Bergh", "given": "Cathrine", "initials": "C", "orcid": "0000-0001-7540-5887", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/5c8a3efa976b41edb6ace4efae952125.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": "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": "peer-review", "published": "2024-01-05", "journal": {"issn-l": null}, "abstract": null, "doi": "10.7554/elife.86016.2.sa3", "pmid": null, "labels": [], "xrefs": [], "notes": [], "created": "2026-08-20T13:55:16.256Z", "modified": "2026-08-20T13:55:16.328Z"}, {"entity": "publication", "iuid": "45e69bee67dd45279fae7065d80dc422", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/45e69bee67dd45279fae7065d80dc422.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/45e69bee67dd45279fae7065d80dc422"}}, "title": "Discovery of lipid binding sites in a ligand-gated ion channel by integrating simulations and cryo-EM", "authors": [{"family": "Bergh", "given": "Cathrine", "initials": "C", "orcid": "0000-0001-7540-5887", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/5c8a3efa976b41edb6ace4efae952125.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": "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": "2024-01-05", "journal": {"issn-l": null}, "abstract": null, "doi": "10.7554/elife.86016.2", "pmid": null, "labels": [], "xrefs": [], "notes": [], "created": "2026-08-20T13:55:14.480Z", "modified": "2026-08-20T13:55:14.516Z"}, {"entity": "publication", "iuid": "2abe43f0c77f44e4a8c6439332f372e4", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/2abe43f0c77f44e4a8c6439332f372e4.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/2abe43f0c77f44e4a8c6439332f372e4"}}, "title": "Discovery of lipid binding sites in a ligand-gated ion channel by integrating simulations and cryo-EM", "authors": [{"family": "Bergh", "given": "Cathrine", "initials": "C", "orcid": "0000-0001-7540-5887", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/5c8a3efa976b41edb6ace4efae952125.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": "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": "2023-04-25", "journal": {"issn-l": null}, "abstract": null, "doi": "10.7554/elife.86016.1", "pmid": null, "labels": [], "xrefs": [], "notes": [], "created": "2026-08-20T13:55:09.480Z", "modified": "2026-08-20T13:55:09.552Z"}, {"entity": "publication", "iuid": "6ab19d76884941fa87ad367efa67b789", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/6ab19d76884941fa87ad367efa67b789.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/6ab19d76884941fa87ad367efa67b789"}}, "title": "Discovery of lipid binding sites in a ligand-gated ion channel by integrating simulations and cryo-EM", "authors": [{"family": "Bergh", "given": "Cathrine", "initials": "C", "orcid": "0000-0001-7540-5887", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/5c8a3efa976b41edb6ace4efae952125.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": "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": "2023-01-06", "journal": {"issn-l": null}, "abstract": null, "doi": "10.1101/2023.01.06.523006", "pmid": null, "labels": [], "xrefs": [], "notes": [], "created": "2026-08-20T10:43:16.244Z", "modified": "2026-08-20T10:43:16.316Z"}, {"entity": "publication", "iuid": "93fd95c94ec94e2eba303f9e4212c4c9", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/93fd95c94ec94e2eba303f9e4212c4c9.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/93fd95c94ec94e2eba303f9e4212c4c9"}}, "title": "Markov state models of proton- and pore-dependent activation in a pentameric ligand-gated ion channel.", "authors": [{"family": "Bergh", "given": "Cathrine", "initials": "C", "orcid": "0000-0001-7540-5887", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/5c8a3efa976b41edb6ace4efae952125.json"}}, {"family": "Heusser", "given": "Stephanie A", "initials": "SA", "orcid": "0000-0003-3224-4547", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/d850b540ae3b408cbefb79c20b010a9a.json"}}, {"family": "Howard", "given": "Rebecca", "initials": "R"}, {"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": "2021-10-15", "journal": {"title": "Elife", "issn": "2050-084X", "volume": "10", "issn-l": "2050-084X"}, "abstract": "Ligand-gated ion channels conduct currents in response to chemical stimuli, mediating electrochemical signaling in neurons and other excitable cells. For many channels, the details of gating remain unclear, partly due to limited structural data and simulation timescales. Here, we used enhanced sampling to simulate the pH-gated channel GLIC, and construct Markov state models (MSMs) of gating. Consistent with new functional recordings, we report in oocytes, our analysis revealed differential effects of protonation and mutation on free-energy wells. Clustering of closed- versus open-like states enabled estimation of open probabilities and transition rates, while higher-order clustering affirmed conformational trends in gating. Furthermore, our models uncovered state- and protonation-dependent symmetrization. This demonstrates the applicability of MSMs to map energetic and conformational transitions between ion-channel functional states, and how they reproduce shifts upon activation or mutation, with implications for modeling neuronal function and developing state-selective drugs.", "doi": "10.7554/eLife.68369", "pmid": "34652272", "labels": [], "xrefs": [{"db": "pmc", "key": "PMC8635979"}, {"db": "pii", "key": "68369"}], "notes": [], "created": "2026-08-20T13:53:46.502Z", "modified": "2026-08-20T13:53:46.591Z"}, {"entity": "publication", "iuid": "b78f0d3a0ba7431ba0d9e6aca153f29a", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/b78f0d3a0ba7431ba0d9e6aca153f29a.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/b78f0d3a0ba7431ba0d9e6aca153f29a"}}, "title": "Author response: Markov state models of proton- and pore-dependent activation in a pentameric ligand-gated ion channel", "authors": [{"family": "Bergh", "given": "Cathrine", "initials": "C", "orcid": "0000-0001-7540-5887", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/5c8a3efa976b41edb6ace4efae952125.json"}}, {"family": "Heusser", "given": "Stephanie A", "initials": "SA", "orcid": "0000-0003-3224-4547", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/d850b540ae3b408cbefb79c20b010a9a.json"}}, {"family": "Howard", "given": "Rebecca", "initials": "R"}, {"family": "Lindahl", "given": "Erik", "initials": "E", "orcid": "0000-0002-2734-2794", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/9eb30fa60f9b4b95842ac9d9f3a0eaa9.json"}}], "type": "peer-review", "published": "2021-10-01", "journal": {"issn-l": null}, "abstract": null, "doi": "10.7554/elife.68369.sa2", "pmid": null, "labels": [], "xrefs": [], "notes": [], "created": "2026-08-20T13:53:48.370Z", "modified": "2026-08-20T13:53:48.431Z"}, {"entity": "publication", "iuid": "5c28dc8f28bb4a51bd6d7c86acf4bbda", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/5c28dc8f28bb4a51bd6d7c86acf4bbda.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/5c28dc8f28bb4a51bd6d7c86acf4bbda"}}, "title": "Probing solution structure of the pentameric ligand-gated ion channel GLIC by small-angle neutron scattering.", "authors": [{"family": "Lycksell", "given": "Marie", "initials": "M", "orcid": "0000-0003-3271-7973", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/0833a696c9ec497bae99bbe631af624f.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": "Bergh", "given": "Cathrine", "initials": "C", "orcid": "0000-0001-7540-5887", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/5c8a3efa976b41edb6ace4efae952125.json"}}, {"family": "Johansen", "given": "Nicolai T", "initials": "NT"}, {"family": "Martel", "given": "Anne", "initials": "A"}, {"family": "Porcar", "given": "Lionel", "initials": "L"}, {"family": "Arleth", "given": "Lise", "initials": "L", "orcid": "0000-0002-4694-4299", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/6c2d657efee34051a6d80a6ca776b076.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"}], "type": "journal article", "published": "2021-09-14", "journal": {"title": "Proc. Natl. Acad. Sci. U.S.A.", "issn": "1091-6490", "volume": "118", "issue": "37", "issn-l": "0027-8424"}, "abstract": "Pentameric ligand-gated ion channels undergo subtle conformational cycling to control electrochemical signal transduction in many kingdoms of life. Several crystal structures have now been reported in this family, but the functional relevance of such models remains unclear. Here, we used small-angle neutron scattering (SANS) to probe ambient solution-phase properties of the pH-gated bacterial ion channel GLIC under resting and activating conditions. Data collection was optimized by inline paused-flow size-exclusion chromatography, and exchanging into deuterated detergent to hide the micelle contribution. Resting-state GLIC was the best-fit crystal structure to SANS curves, with no evidence for divergent mechanisms. Moreover, enhanced-sampling molecular-dynamics simulations enabled differential modeling in resting versus activating conditions, with the latter corresponding to an intermediate ensemble of both the extracellular and transmembrane domains. This work demonstrates state-dependent changes in a pentameric ion channel by SANS, an increasingly accessible method for macromolecular characterization with the coming generation of neutron sources.", "doi": "10.1073/pnas.2108006118", "pmid": "34504004", "labels": [], "xrefs": [{"db": "pmc", "key": "PMC8449418"}, {"db": "pii", "key": "2108006118"}], "notes": [], "created": "2026-08-20T09:30:59.463Z", "modified": "2026-08-20T09:30:59.654Z"}, {"entity": "publication", "iuid": "9052237cb1ce4ec4ae7cda7d2d116f90", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/9052237cb1ce4ec4ae7cda7d2d116f90.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/9052237cb1ce4ec4ae7cda7d2d116f90"}}, "title": "Probing solution structure of the pentameric ligand-gated ion channel GLIC by small-angle neutron scattering", "authors": [{"family": "Lycksell", "given": "Marie", "initials": "M"}, {"family": "Rov\u0161nik", "given": "Ur\u0161ka", "initials": "U", "orcid": "0000-0001-5889-6899", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/f0ab87a8712f4ad886da61c1edcf679f.json"}}, {"family": "Bergh", "given": "Cathrine", "initials": "C", "orcid": "0000-0001-7540-5887", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/5c8a3efa976b41edb6ace4efae952125.json"}}, {"family": "Johansen", "given": "Nicolai T", "initials": "NT", "orcid": "0000-0002-8596-548X", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/613a030fb0aa4a25abd49457d02deb64.json"}}, {"family": "Martel", "given": "Anne", "initials": "A"}, {"family": "Porcar", "given": "Lionel", "initials": "L"}, {"family": "Arleth", "given": "Lise", "initials": "L", "orcid": "0000-0002-4694-4299", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/6c2d657efee34051a6d80a6ca776b076.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": "2021-04-11", "journal": {"issn-l": null}, "abstract": null, "doi": "10.1101/2021.04.10.439285", "pmid": null, "labels": [], "xrefs": [], "notes": [], "created": "2026-08-20T10:03:50.498Z", "modified": "2026-08-20T10:03:50.593Z"}, {"entity": "publication", "iuid": "39115549ae2445cfbc8ce863fe090a2f", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/39115549ae2445cfbc8ce863fe090a2f.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/39115549ae2445cfbc8ce863fe090a2f"}}, "title": "Markov State Models of Proton- and Gate-Dependent Activation in a Pentameric Ligand-Gated Ion Channel", "authors": [{"family": "Bergh", "given": "Cathrine", "initials": "C", "orcid": "0000-0001-7540-5887", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/5c8a3efa976b41edb6ace4efae952125.json"}}, {"family": "Heusser", "given": "Stephanie A", "initials": "SA", "orcid": "0000-0003-3224-4547", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/d850b540ae3b408cbefb79c20b010a9a.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": "2021-03-12", "journal": {"issn-l": null}, "abstract": null, "doi": "10.1101/2021.03.12.435097", "pmid": null, "labels": [], "xrefs": [], "notes": [], "created": "2026-08-20T10:03:09.282Z", "modified": "2026-08-20T10:03:09.324Z"}]}