{"doi":"10.1101/2020.04.28.058271","title":"A Ribosome Interaction Surface Sensitive to mRNA GCN Periodicity","abstract":"ABSTRACT GCN codons are over-represented in initial codons of ORFs of prokaryote and eukaryote mRNAs. We describe a ribosome rRNA-protein surface that interacts with an mRNA GCN codon when next-in-line for the ribosome A site. The interaction surface is comprised of the edges of two stacked rRNA bases: the Watson-Crick edge of 16S/18S rRNA C1054 and adjacent Hoogsteen edge of A1196 ( Escherichia coli 16S rRNA numbering). Also part of the interaction surface, the planar guanidinium group of a conserved Arginine (R146 of yeast ribosomal protein Rps3) is stacked adjacent to A1196. On its other side, the interaction surface is anchored to the ribosome A site through base stacking of C1054 with the wobble anticodon base of the A-site tRNA. Using Molecular Dynamics simulations of a 495-residue subsystem of translocating ribosomes, we observe base pairing of C1054 to nucleotide G at position 1 of the next-in-line codon, consistent with previous cryo-EM observations, and hydrogen bonding of A1196 and R146 to C at position 2. Hydrogen bonding to both of these codon positions is significantly weakened when C at position 2 is changed to G, A or U. These sequence-sensitive mRNA-ribosome interactions at the C 1054- A 1196- R 146 (CAR) surface potentially contribute to GCN-mediated regulation of protein translation.","journal":"bioRxiv (Cold Spring Harbor Laboratory)","year":2020,"id":122069,"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":5,"citer_count":0,"citers_with_citation_signal":0,"citers_with_endowment":0,"datacite_reuse_total":0,"is_dataset":false,"is_dataset_confidence":0.9608,"is_data_producer":false,"deposit_databanks":null,"is_oa":true,"file_count":0,"downloads":0,"has_version_chain":false,"published_date":"2020-01-01","fair_score":null,"fair_percentile":null,"algorithm_id":"datarank_citation_only_1hop_v6","ranking_scope":"data_only","authors":[{"id":356267,"name":"Elliot Williams","orcid":"0000-0001-7839-3658","position":1,"is_corresponding":false},{"id":445074,"name":"Abdelrahman Elsayed","orcid":"0000-0003-3381-066X","position":2,"is_corresponding":false},{"id":523677,"name":"William Barr","orcid":"0000-0001-6723-7684","position":3,"is_corresponding":false},{"id":446230,"name":"Daniel Krizanc","orcid":null,"position":4,"is_corresponding":false},{"id":149354,"name":"Kelly M. Thayer","orcid":"0000-0001-7437-9517","position":5,"is_corresponding":false},{"id":445076,"name":"Michael P. Weir","orcid":"0000-0002-5999-4199","position":6,"is_corresponding":false},{"id":445073,"name":"Kristen Scopino","orcid":"0000-0002-4934-3659","position":0,"is_corresponding":true}],"reference_count":47,"raw_metadata":null,"created_at":"2026-07-18T23:14:51.076430Z","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":[]}