{"doi":"10.1101/2022.06.02.494568","title":"Structure-based prediction and characterization of photo-crosslinking in native protein-RNA complexes","abstract":"Abstract UV-crosslinking of protein and RNA in direct contacts has been widely used to study protein-RNA complexes despite our poor understanding on the mechanisms of photo-crosslinking. This knowledge gap is due to the challenge to precisely map the crosslink sites in protein and RNA simultaneously in their native sequence and structural contexts. Here we developed PxR3D-map, a computational method to analyze protein-RNA interactions and photo-crosslinking by bridging crosslinked nucleotides and amino acids mapped using different assays with protein-RNA complex structures. PxR3D-map reliably predicts crosslink sites using structural information characterizing protein-RNA interaction interfaces. We found that photo-crosslinking is facilitated by base stacking with not only aromatic residues, but also dipeptide bonds that involve glycine, and distinct mechanisms are utilized by different types of RNA-binding domains. Our work suggests protein-RNA photocrosslinking is highly selective in the cellular environment, which can guide interpretation of data generated by UV-crosslinking-based assays and further technology development.","journal":"bioRxiv (Cold Spring Harbor Laboratory)","year":2022,"id":309087,"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":0,"citer_count":0,"citers_with_citation_signal":0,"citers_with_endowment":0,"datacite_reuse_total":0,"is_dataset":false,"is_dataset_confidence":0.9425,"is_data_producer":false,"deposit_databanks":null,"is_oa":true,"file_count":0,"downloads":0,"has_version_chain":false,"published_date":"2022-01-01","fair_score":null,"fair_percentile":null,"algorithm_id":"datarank_citation_only_1hop_v6","ranking_scope":"data_only","authors":[{"id":329195,"name":"Xiang‐Jun Lu","orcid":"0000-0002-8901-7444","position":1,"is_corresponding":false},{"id":669572,"name":"Linxi Liu","orcid":"0000-0003-0507-0510","position":2,"is_corresponding":false},{"id":1004180,"name":"Dmytro Ustianenko","orcid":null,"position":3,"is_corresponding":false},{"id":876251,"name":"Chaolin Zhang","orcid":"0000-0002-0013-5314","position":4,"is_corresponding":false},{"id":406988,"name":"Huijuan Feng","orcid":"0000-0002-4005-560X","position":0,"is_corresponding":true}],"reference_count":59,"raw_metadata":null,"created_at":"2026-07-19T00:33:07.132912Z","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":[]}