{"doi":"10.1101/2023.06.29.547112","title":"Chemically induced partial unfolding of the multifunctional Apurinic/apyrimidinic endonuclease 1","abstract":"Abstract Apurinic/apyrimidinic endonuclease I (APE1) acts as both an endonuclease and a redox factor to ensure cell survival. The two activities require different conformations of APE1. As an endonuclease, APE1 is fully folded. As a redox factor, APE1 must be partially unfolded to expose the buried residue Cys65, which reduces transcription factors including AP-1, NF-κB, and HIF-1α and thereby enables them to bind DNA. To determine a molecular basis for partial unfolding associated with APE1’s redox activity, we characterized specific interactions of a known redox inhibitor APX3330 with APE1 through waterLOGSY and 1 H- 15 N HSQC NMR approaches using ethanol and acetonitrile as co-solvents. We find that APX3330 binds to the endonuclease active site in both co-solvents and to a distant small pocket in acetonitrile. Prolonged exposure of APE1 with APX3330 in acetonitrile resulted in a time-dependent loss of 1 H- 15 N HSQC chemical shifts (∼35%), consistent with partial unfolding. Regions that are partially unfolded include adjacent N- and C-terminal beta strands within one of the two sheets comprising the core, which converge within the small binding pocket defined by the CSPs. Removal of APX3330 via dialysis resulted in a slow reappearance of the 1 H- 15 N HSQC chemical shifts suggesting that the effect of APX3330 is reversible. APX3330 significantly decreases the melting temperature of APE1 but has no effect on endonuclease activity using a standard assay in either co-solvent. Our results provide insights on reversible partial unfolding of APE1 relevant for its redox function as well as the mechanism of redox inhibition by APX3330. TOC graphic","journal":"bioRxiv (Cold Spring Harbor Laboratory)","year":2023,"id":393428,"datarank":0.24141568686511508,"base_score":1.6094379124341003,"endowment":1.6094379124341003,"self_citation_contribution":0.24141568686511508,"citation_network_contribution":0.0,"self_endowment_contribution":0.24141568686511508,"citer_contribution":0.0,"corpus_percentile":null,"corpus_rank":null,"citation_count":4,"citer_count":0,"citers_with_citation_signal":0,"citers_with_endowment":0,"datacite_reuse_total":0,"is_dataset":false,"is_dataset_confidence":0.9567,"is_data_producer":false,"deposit_databanks":null,"is_oa":true,"file_count":0,"downloads":0,"has_version_chain":false,"published_date":"2023-01-01","fair_score":null,"fair_percentile":null,"algorithm_id":"datarank_citation_only_1hop_v6","ranking_scope":"data_only","authors":[{"id":1167994,"name":"Olabode Dawodu","orcid":null,"position":1,"is_corresponding":false},{"id":542531,"name":"Jingwei Meng","orcid":"0000-0003-1550-2719","position":2,"is_corresponding":false},{"id":406885,"name":"Steven M. Johnson","orcid":"0000-0001-7254-4128","position":3,"is_corresponding":false},{"id":479022,"name":"Jonah Z. Vilseck","orcid":"0000-0001-7076-8996","position":4,"is_corresponding":false},{"id":269873,"name":"Mark R. Kelley","orcid":"0000-0001-9472-1826","position":5,"is_corresponding":false},{"id":730386,"name":"Joshua J. Ziarek","orcid":"0000-0002-3740-9999","position":6,"is_corresponding":false},{"id":468331,"name":"Millie M. Georgiadis","orcid":"0000-0003-2976-4576","position":7,"is_corresponding":false},{"id":973110,"name":"Ratan Kumar","orcid":"0000-0001-6015-5539","position":0,"is_corresponding":true}],"reference_count":67,"raw_metadata":{"citation_network_status":"fetched"},"created_at":"2026-07-19T01:19:05.913428Z","pmid":"37425839","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":[]}