{"doi":"10.1101/2024.03.07.583947","title":"Highly multiplexed design of an allosteric transcription factor to sense novel ligands","abstract":"Allosteric transcription factors (aTF), widely used as biosensors, have proven challenging to design for detecting novel molecules because mutation of ligand-binding residues often disrupts allostery. We developed Sensor-seq, a high-throughput platform to design and identify aTF biosensors that bind to non-native ligands. We screened a library of 17,737 variants of the aTF TtgR, a regulator of a multidrug exporter, against six non-native ligands of diverse chemical structures - four derivatives of the cancer therapeutic tamoxifen, the antimalarial drug quinine, and the opiate analog naltrexone - as well as two native flavonoid ligands, naringenin and phloretin. Sensor-seq identified novel biosensors for each of these ligands with high dynamic range and diverse specificity profiles. The structure of a naltrexone-bound design showed shape-complementary methionine-aromatic interactions driving ligand specificity. To demonstrate practical utility, we developed cell-free detection systems for naltrexone and quinine. Sensor-seq enables rapid, scalable design of new biosensors, overcoming constraints of natural biosensors.","journal":"bioRxiv (Cold Spring Harbor Laboratory)","year":2024,"id":488074,"datarank":0.0,"base_score":0.0,"endowment":0.0,"self_citation_contribution":0.0,"citation_network_contribution":0.0,"self_endowment_contribution":0.0,"citer_contribution":0.0,"corpus_percentile":null,"corpus_rank":null,"citation_count":2,"citer_count":0,"citers_with_citation_signal":0,"citers_with_endowment":0,"datacite_reuse_total":0,"is_dataset":false,"is_dataset_confidence":0.9609,"is_data_producer":false,"deposit_databanks":null,"is_oa":true,"file_count":0,"downloads":0,"has_version_chain":false,"published_date":"2024-01-01","fair_score":null,"fair_percentile":null,"algorithm_id":"datarank_citation_only_1hop_v6","ranking_scope":"data_only","authors":[{"id":934206,"name":"Jackie Chen","orcid":"0000-0001-6833-075X","position":1,"is_corresponding":false},{"id":738603,"name":"Justin Acheson","orcid":"0000-0001-5051-9984","position":2,"is_corresponding":false},{"id":1224029,"name":"Svetlana Harbaugh","orcid":"0000-0001-9051-1397","position":3,"is_corresponding":false},{"id":583220,"name":"Phil Huss","orcid":"0000-0003-4064-9333","position":4,"is_corresponding":false},{"id":1177556,"name":"M Frenkel","orcid":"0000-0002-7208-4587","position":5,"is_corresponding":false},{"id":1185481,"name":"Nathan Novy","orcid":"0000-0003-1587-0482","position":6,"is_corresponding":false},{"id":1224550,"name":"Hailey R. Sieren","orcid":null,"position":7,"is_corresponding":false},{"id":1224551,"name":"Ella C. Lodewyk","orcid":null,"position":8,"is_corresponding":false},{"id":1224030,"name":"Daniel H. Lee","orcid":"0000-0002-5700-2643","position":9,"is_corresponding":false},{"id":1224031,"name":"Jorge L. Chávez","orcid":"0000-0002-0771-6947","position":10,"is_corresponding":false},{"id":492356,"name":"Brian G. Fox","orcid":"0000-0001-9027-5371","position":11,"is_corresponding":false},{"id":991226,"name":"Srivatsan Raman","orcid":"0000-0002-5673-6944","position":12,"is_corresponding":false},{"id":571602,"name":"Kyle Nishikawa","orcid":"0000-0002-9257-0531","position":0,"is_corresponding":true}],"reference_count":79,"raw_metadata":null,"created_at":"2026-07-19T02:08:15.008850Z","pmid":"38496486","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":[]}