{"doi":"10.1016/j.jbc.2022.102366","title":"Reisomerization of retinal represents a molecular switch mediating Na+ uptake and release by a bacterial sodium-pumping rhodopsin","abstract":null,"journal":"Journal of Biological Chemistry","year":2022,"id":653816,"datarank":0.6520277479878531,"base_score":2.9444389791664403,"endowment":2.9444389791664403,"self_citation_contribution":0.44166584687496613,"citation_network_contribution":0.21036190111288694,"self_endowment_contribution":0.44166584687496613,"citer_contribution":0.21036190111288694,"corpus_percentile":null,"corpus_rank":null,"citation_count":18,"citer_count":14,"citers_with_citation_signal":10,"citers_with_endowment":10,"datacite_reuse_total":0,"is_dataset":false,"is_dataset_confidence":null,"is_data_producer":false,"deposit_databanks":null,"is_oa":false,"file_count":0,"downloads":0,"has_version_chain":false,"published_date":null,"fair_score":null,"fair_percentile":null,"algorithm_id":"datarank_citation_only_1hop_v6","ranking_scope":"data_only","authors":[{"id":1706017,"name":"Kouta Kinoue","orcid":null,"position":1,"is_corresponding":false},{"id":1706018,"name":"Ryouhei Seike","orcid":null,"position":2,"is_corresponding":false},{"id":1706019,"name":"Takashi Kikukawa","orcid":"0000-0002-6185-7281","position":3,"is_corresponding":false},{"id":1706020,"name":"Masashi Unno","orcid":null,"position":4,"is_corresponding":false},{"id":1706016,"name":"Tomotsumi Fujisawa","orcid":null,"position":0,"is_corresponding":false}],"reference_count":0,"raw_metadata":{"has_enrichment":true,"resolved":true,"title":"Reisomerization of retinal represents a molecular switch mediating Na+ uptake and release by a bacterial sodium-pumping rhodopsin","abstract":"Sodium-pumping rhodopsins (NaRs) are membrane transporters that utilize light energy to pump Na + across the cellular membrane. Within the NaRs, the retinal Schiff base chromophore absorbs light, and a photochemically induced transient state, referred to as the \"O intermediate\", performs both the uptake and release of Na + . However, the structure of the O intermediate remains unclear. Here, we used time-resolved cryo-Raman spectroscopy under preresonance conditions to study the structure of the retinal chromophore in the O intermediate of an NaR from the bacterium Indibacter alkaliphilus . We observed two O intermediates, termed O1 and O2, having distinct chromophore structures. We show O1 displays a distorted 13- cis chromophore, while O2 contains a distorted all- trans structure. This finding indicated that the uptake and release of Na + are achieved not by a single O intermediate but by two sequential O intermediates that are toggled via isomerization of the retinal chromophore. These results provide crucial structural insight into the unidirectional Na + transport mediated by the chromophore-binding pocket of NaRs.","is_dataset_classified":null,"base_score":2.9444389791664403,"endowment":2.9444389791664403,"datacite_reuse_total":0,"file_count":0,"downloads":0,"views":0,"has_version_chain":false,"is_dataset":false,"is_oa":false,"pmid":"35963435","pmcid":"PMC9483557","openalex_id":"https://openalex.org/W4290988149","authors":[],"funders":[{"funder_name":"Japan Society for the Promotion of Science","grant_id":"21K04997","title":null},{"funder_name":"Japan Society for the Promotion of Science","grant_id":"22K05037","title":null},{"funder_name":"Sumitomo Foundation","grant_id":"","title":null}],"total_grants":3,"fwci":1.3796,"citation_percentile":0.7911956,"influential_citations":0,"citation_trend":[{"year":2022,"count":1},{"year":2023,"count":7},{"year":2024,"count":6},{"year":2025,"count":1},{"year":2026,"count":3}],"oa_status":"gold","license":"cc-by","oa_locations":[{"url":"http://www.jbc.org/article/S0021925822008092/pdf","host_type":"journal"},{"url":"http://www.jbc.org/article/S0021925822008092/pdf","host_type":"publisher"},{"url":"https://api.elsevier.com/content/article/PII:S0021925822008092?httpAccept=text/xml","host_type":"publisher"},{"url":"https://api.elsevier.com/content/article/PII:S0021925822008092?httpAccept=text/plain","host_type":"publisher"},{"url":"https://doi.org/10.1016/j.jbc.2022.102366","host_type":"journal"},{"url":"https://pubmed.ncbi.nlm.nih.gov/35963435","host_type":"repository"},{"url":"https://www.ncbi.nlm.nih.gov/pmc/articles/9483557","host_type":"repository"},{"url":"https://europepmc.org/articles/PMC9483557","host_type":"Europe_PMC"},{"url":"https://europepmc.org/articles/PMC9483557?pdf=render","host_type":"Europe_PMC"}],"fields_of_study":["Photoreceptor and optogenetics research","Neuroscience and Neuropharmacology Research","Receptor Mechanisms and Signaling","Bacteriorhodopsins","Bacteroidetes","Ion Transport","Light","Schiff Bases","Sodium","Spectrum Analysis, Raman","Indibacter alkaliphilus"],"mesh_terms":["Bacteriorhodopsins","Light","Schiff Bases","Sodium","Spectrum Analysis, Raman","Ion Transport","Bacteroidetes"],"keywords":["Chromophore","Rhodopsin","Retinal","Photochemistry","Isomerization","Chemistry","Biophysics","Retinaldehyde","Schiff base","Stereochemistry","Biochemistry","Biology","Catalysis","Vibrational spectroscopy","photoreceptor","Microbial Rhodopsin","Low-temperature Spectroscopy","Membrane Transporter Protein"],"sdg_mappings":[{"sdg_number":0,"sdg_label":"Affordable and clean energy"},{"sdg_number":0,"sdg_label":"Clean water and sanitation"}],"linked_datasets":[],"clinical_trials":[],"software_tools":[],"database_accessions":[{"name":"gen"},{"name":"pdb"}],"source":"live","citation_network_status":"fetched"},"created_at":"2026-08-11T01:07:51.594761Z","pmid":null,"pmcid":null,"fwci":null,"citation_percentile":null,"influential_citations":0,"oa_status":null,"license":null,"views":0,"total_file_size_bytes":0,"version_count":0,"fair_f":null,"fair_a":null,"fair_i":null,"fair_r":null,"fair_zscore":null,"fair_rationale":null,"fair_model":null,"fair_agent_version":null,"fair_fulltext_source":null,"fair_has_llm":null,"fair_computed_at":null,"clinical_trials":[],"software_tools":[],"db_accessions":[],"linked_datasets":[],"topics":[]}