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Despite their large, solvent-accessible pores, connexin channels exhibit distinct conductance, selectivity, and rectification properties, but the molecular mechanisms underlying these behaviors remain incompletely understood. Here, we performed \u223c67 \u03bcs of all-atom computational electrophysiology simulations of connexin-46 (Cx46), connexin-50 (Cx50), and heterotypic Cx46\/50 gap junction channels based on high-resolution open-state structures, enabling characterization of both ion permeation and long-timescale channel dynamics. Simulations reveal a multi-ion, multi-pathway permeation mechanism governed by isoform-specific energetic barriers and transient ion coordination sites that shape conductance and selectivity. In heterotypic Cx46\/50 channels, asymmetric energetic landscapes establish a mechanistic basis for rectification. Unexpectedly, the microsecond-timescale simulations further revealed dynamic interactions between the intracellular loop (ICL) region and N-terminal domain (NT) that transiently constrict the pore and attenuate ionic currents. These findings suggest that the open-state comprises an ensemble of rapidly interconverting conductance microstates rather than a single static conformation, providing structural information of potential mechanistic importance beyond what has been learned from cryo-EM studies. Together, our results provide a mechanistic basis for ion permeation and current modulation in gap junction channels and highlight the importance of long-timescale protein dynamics in shaping intercellular communication.<\/jats:p>","DOI":"10.64898\/2026.08.12.744469","type":"posted-content","created":{"date-parts":[[2026,8,13]],"date-time":"2026-08-13T13:25:13Z","timestamp":1786627513000},"source":"Crossref","is-referenced-by-count":1,"title":["Multi-ion permeation and dynamic conductance modulation in connexin gap junction channels"],"prefix":"10.64898","author":[{"ORCID":"https:\/\/orcid.org\/0000-0003-1305-0261","authenticated-orcid":false,"given":"Bassam G.","family":"Haddad","sequence":"first","affiliation":[{"name":"Department of Chemistry, Portland State University, Portland, OR 97201"},{"name":"Institute of Neurophysiology, Hannover Medical School, Hannover, Germany, 30625"},{"name":"Institute for Biological Information Processing, Molekular- und Zellphysiologie (IBI-1), Forschungszentrum J\u00fclich, J\u00fclich, Germany 52428"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-7662-2031","authenticated-orcid":false,"given":"Daniel M.","family":"Zuckerman","sequence":"additional","affiliation":[{"name":"Department of Biomedical Engineering, Oregon Health & Science University, Portland, OR 97239"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-5276-7690","authenticated-orcid":false,"given":"Steve L.","family":"Reichow","sequence":"additional","affiliation":[{"name":"Department of Chemical Physiology & Biochemistry, Oregon Health & Science University, Portland, OR 97239"},{"name":"Vollum Institute, Oregon Health & Science University, Portland, OR 97239"},{"name":"Department of Chemistry, Portland State University, Portland, OR 97201"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"54368","reference":[{"key":"2026081711153154000_2026.08.12.744469v1.1","doi-asserted-by":"publisher","DOI":"10.1085\/jgp.201812090"},{"key":"2026081711153154000_2026.08.12.744469v1.2","doi-asserted-by":"publisher","DOI":"10.1002\/cphy.c110047"},{"key":"2026081711153154000_2026.08.12.744469v1.3","doi-asserted-by":"publisher","DOI":"10.1146\/annurev.biophys.34.040204.144655"},{"key":"2026081711153154000_2026.08.12.744469v1.4","doi-asserted-by":"publisher","DOI":"10.1038\/35102067"},{"key":"2026081711153154000_2026.08.12.744469v1.5","doi-asserted-by":"publisher","DOI":"10.1016\/j.cell.2021.08.012"},{"key":"2026081711153154000_2026.08.12.744469v1.6","doi-asserted-by":"publisher","DOI":"10.1038\/s41467-020-18120-5"},{"key":"2026081711153154000_2026.08.12.744469v1.7","doi-asserted-by":"publisher","DOI":"10.1038\/s41586-018-0786-7"},{"key":"2026081711153154000_2026.08.12.744469v1.8","doi-asserted-by":"publisher","DOI":"10.7554\/eLife.87616"},{"key":"2026081711153154000_2026.08.12.744469v1.9","doi-asserted-by":"publisher","DOI":"10.1038\/s41467-023-37040-8"},{"key":"2026081711153154000_2026.08.12.744469v1.10","doi-asserted-by":"publisher","DOI":"10.1093\/jmicro\/dfx035"},{"key":"2026081711153154000_2026.08.12.744469v1.11","doi-asserted-by":"publisher","DOI":"10.1038\/s41467-023-37413-z"},{"key":"2026081711153154000_2026.08.12.744469v1.12","doi-asserted-by":"publisher","DOI":"10.1038\/s41586-019-1781-3"},{"key":"2026081711153154000_2026.08.12.744469v1.13","doi-asserted-by":"publisher","DOI":"10.1038\/s41594-022-00899-0"},{"key":"2026081711153154000_2026.08.12.744469v1.14","doi-asserted-by":"publisher","DOI":"10.1016\/j.jmb.2021.166994"},{"key":"2026081711153154000_2026.08.12.744469v1.15","doi-asserted-by":"publisher","DOI":"10.1101\/cshperspect.a002576"},{"key":"2026081711153154000_2026.08.12.744469v1.16","doi-asserted-by":"publisher","DOI":"10.1016\/j.jbc.2023.105263"},{"key":"2026081711153154000_2026.08.12.744469v1.17","doi-asserted-by":"crossref","unstructured":"Abrams, C. 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