{"doi":"10.1074/jbc.m115.637678","title":"The Wrapping Loop and Rap1 C-terminal (RCT) Domain of Yeast Rap1 Modulate Access to Different DNA Binding Modes","abstract":null,"journal":"Journal of Biological Chemistry","year":2015,"id":656517,"datarank":0.3958585994422889,"base_score":2.639057329615259,"endowment":2.639057329615259,"self_citation_contribution":0.3958585994422889,"citation_network_contribution":0.0,"self_endowment_contribution":0.3958585994422889,"citer_contribution":0.0,"corpus_percentile":null,"corpus_rank":null,"citation_count":13,"citer_count":0,"citers_with_citation_signal":0,"citers_with_endowment":0,"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":814746,"name":"Paolo De Bona","orcid":null,"position":1,"is_corresponding":false},{"id":814233,"name":"Roberto Galletto","orcid":"0000-0001-6435-122X","position":2,"is_corresponding":false},{"id":1713794,"name":"Erik A. Feldmann","orcid":null,"position":0,"is_corresponding":false}],"reference_count":0,"raw_metadata":{"has_enrichment":true,"resolved":true,"title":"The Wrapping Loop and Rap1 C-terminal (RCT) Domain of Yeast Rap1 Modulate Access to Different DNA Binding Modes","abstract":"Budding yeast Rap1 is a specific double-stranded DNA-binding protein involved in repression and activation of gene transcription and in the establishment of the nucleoprotein complex formed at telomeres. The DNA-binding domain (DBD) of Rap1 forms a high affinity complex with DNA where both Myb-like domains bind to the recognition site. However, we recently showed that the DBD can also access an alternative, lower affinity DNA-binding mode where a single Myb-like domain binds. This results in Rap1-DNA complexes with stoichiometry higher than previously anticipated. In this work, we show that the ability of the DBD to form higher stoichiometry complexes on DNA is maintained also in larger Rap1 constructs. This indicates that transition between at least two DNA-binding modes is a general property of the protein and not a specific feature of the DBD in isolation. The transition between binding modes is modulated by the C-terminal wrapping loop within the DBD, consistent with the proposed model in which the transient opening of this region allows a switch between binding modes. Finally, we provide evidence that the Rap1 C terminus interacts with the DNA-binding domain, suggesting a complex network of interactions that couples changes in conformation of the protein to the binding of its DNA recognition sequence. Background: Rap1 is a general regulator of transcription and a component of the telomere. Results: Rap1 binds DNA in at least two binding modes. Conclusion: Access to binding modes in vitro is affected by different regions of the protein. Significance: The ability of Rap1 to access different binding modes may impact its functions.","is_dataset_classified":null,"base_score":2.639057329615259,"endowment":2.639057329615259,"datacite_reuse_total":0,"file_count":0,"downloads":0,"views":0,"has_version_chain":false,"is_dataset":false,"is_oa":false,"pmid":"25805496","pmcid":"PMC4416850","openalex_id":"https://openalex.org/W1977080611","authors":[],"funders":[{"funder_name":"National Institutes of Health","grant_id":"GM098509","title":null},{"funder_name":"NIGMS NIH HHS","grant_id":"R01 GM098509","title":null}],"total_grants":2,"fwci":0.828,"citation_percentile":0.71735986,"influential_citations":0,"citation_trend":[{"year":2016,"count":2},{"year":2017,"count":2},{"year":2018,"count":2},{"year":2019,"count":2},{"year":2021,"count":2},{"year":2022,"count":1},{"year":2023,"count":1},{"year":2025,"count":1}],"oa_status":"hybrid","license":"cc-by","oa_locations":[{"url":"http://www.jbc.org/article/S0021925820569858/pdf","host_type":"journal"},{"url":"http://www.jbc.org/article/S0021925820569858/pdf","host_type":"publisher"},{"url":"https://api.elsevier.com/content/article/PII:S0021925820569858?httpAccept=text/xml","host_type":"publisher"},{"url":"https://api.elsevier.com/content/article/PII:S0021925820569858?httpAccept=text/plain","host_type":"publisher"},{"url":"https://syndication.highwire.org/content/doi/10.1074/jbc.M115.637678","host_type":"publisher"},{"url":"https://doi.org/10.1074/jbc.m115.637678","host_type":"journal"},{"url":"https://pubmed.ncbi.nlm.nih.gov/25805496","host_type":"repository"},{"url":"https://www.ncbi.nlm.nih.gov/pmc/articles/4416850","host_type":"repository"}],"fields_of_study":["DNA Repair Mechanisms","Telomeres, Telomerase, and Senescence","Genomics and Chromatin Dynamics","DNA, Fungal","Models, Molecular","Nucleic Acid Conformation","Protein Binding","Protein Structure, Tertiary","Saccharomyces cerevisiae","Saccharomyces cerevisiae Proteins","Shelterin Complex","Telomere-Binding Proteins","Transcription Factors"],"mesh_terms":["Shelterin Complex","DNA, Fungal","Models, Molecular","Nucleic Acid Conformation","Protein Binding","Saccharomyces cerevisiae","Transcription Factors","Protein Structure, Tertiary","Saccharomyces cerevisiae Proteins","Telomere-Binding Proteins"],"keywords":["DNA-binding domain","Telomere-binding protein","DNA","Binding domain","HMG-box","Rap1","DNA binding site","Biology","Binding site","Biophysics","Cell biology","Transcription factor","Molecular biology","DNA-binding protein","Chemistry","Biochemistry","Gene","Promoter","Gene expression","Transcription","Fluorescence anisotropy","Telomere","Analytical Ultracentrifugation","Isothermal Titration Calorimetry (Itc)","Binding Modes"],"sdg_mappings":[],"linked_datasets":[],"clinical_trials":[],"software_tools":[],"database_accessions":[],"source":"live","citation_network_status":"fetched"},"created_at":"2026-08-11T21:08:11.332594Z","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":[]}