{"doi":"10.1093/nar/gkw531","title":"Changes in conformational dynamics of basic side chains upon protein–DNA association","abstract":null,"journal":"Nucleic Acids Research","year":2016,"id":636586,"datarank":0.6141516843333151,"base_score":4.0943445622221,"endowment":4.0943445622221,"self_citation_contribution":0.6141516843333151,"citation_network_contribution":0.0,"self_endowment_contribution":0.6141516843333151,"citer_contribution":0.0,"corpus_percentile":null,"corpus_rank":null,"citation_count":59,"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":405159,"name":"Chuanying Chen","orcid":"0000-0001-8343-8769","position":1,"is_corresponding":false},{"id":234477,"name":"Levani Zandarashvili","orcid":null,"position":2,"is_corresponding":false},{"id":742320,"name":"Sourav Roy","orcid":"0000-0002-0359-994X","position":3,"is_corresponding":false},{"id":1652327,"name":"B. Montgometry Pettitt","orcid":null,"position":4,"is_corresponding":false},{"id":492727,"name":"Junji Iwahara","orcid":"0000-0003-4732-2173","position":5,"is_corresponding":false},{"id":455728,"name":"Alexandre Esadze","orcid":null,"position":0,"is_corresponding":false}],"reference_count":0,"raw_metadata":{"has_enrichment":true,"resolved":true,"title":"Changes in conformational dynamics of basic side chains upon protein–DNA association","abstract":"Basic side chains play major roles in recognition of nucleic acids by proteins. However, dynamic properties of these positively charged side chains are not well understood. In this work, we studied changes in conformational dynamics of basic side chains upon protein-DNA association for the zinc-finger protein Egr-1. By nuclear magnetic resonance (NMR) spectroscopy, we characterized the dynamics of all side-chain cationic groups in the free protein and in the complex with target DNA. Our NMR order parameters indicate that the arginine guanidino groups interacting with DNA bases are strongly immobilized, forming rigid interfaces. Despite the strong short-range electrostatic interactions, the majority of the basic side chains interacting with the DNA phosphates exhibited high mobility, forming dynamic interfaces. In particular, the lysine side-chain amino groups exhibited only small changes in the order parameters upon DNA-binding. We found a similar trend in the molecular dynamics (MD) simulations for the free Egr-1 and the Egr-1-DNA complex. Using the MD trajectories, we also analyzed side-chain conformational entropy. The interfacial arginine side chains exhibited substantial entropic loss upon binding to DNA, whereas the interfacial lysine side chains showed relatively small changes in conformational entropy. These data illustrate different dynamic characteristics of the interfacial arginine and lysine side chains.","is_dataset_classified":null,"base_score":4.0943445622221,"endowment":4.0943445622221,"datacite_reuse_total":0,"file_count":0,"downloads":0,"views":0,"has_version_chain":false,"is_dataset":false,"is_oa":false,"pmid":"27288446","pmcid":"PMC5001603","openalex_id":"https://openalex.org/W2409875835","authors":[],"funders":[{"funder_name":"NIGMS NIH HHS","grant_id":"R01 GM105931","title":null},{"funder_name":"NIGMS NIH HHS","grant_id":"R01 GM107590","title":null},{"funder_name":"NIGMS NIH HHS","grant_id":"R01 GM066813","title":null},{"funder_name":"National Institutes of Health","grant_id":"5R01GM107590-04","title":"Target DNA search by zinc-finger proteins"},{"funder_name":"National Institutes of Health","grant_id":"5R01GM105931-02","title":"Characterizing the ion-pair dynamics and their roles in protein-DNA association"},{"funder_name":"National Science Foundation","grant_id":"1053575","title":"XSEDE: eXtreme Science and Engineering Discovery Environment"},{"funder_name":"National Institutes of Health","grant_id":"3R01GM066813-01A2S1","title":"DNA Near Surfaces in Saline Solution: Theory for Design"}],"total_grants":7,"fwci":5.1313,"citation_percentile":0.95967328,"influential_citations":0,"citation_trend":[{"year":2016,"count":7},{"year":2017,"count":9},{"year":2018,"count":13},{"year":2019,"count":3},{"year":2020,"count":8},{"year":2021,"count":3},{"year":2022,"count":3},{"year":2023,"count":3},{"year":2024,"count":5},{"year":2025,"count":5}],"oa_status":"gold","license":"other-oa","oa_locations":[{"url":"https://academic.oup.com/nar/article-pdf/44/14/6961/17437270/gkw531.pdf","host_type":"journal"},{"url":"https://academic.oup.com/nar/article-pdf/44/14/6961/17437270/gkw531.pdf","host_type":"publisher"},{"url":"http://academic.oup.com/nar/article-pdf/44/14/6961/17437270/gkw531.pdf","host_type":"publisher"},{"url":"https://doi.org/10.1093/nar/gkw531","host_type":"journal"},{"url":"https://pubmed.ncbi.nlm.nih.gov/27288446","host_type":"repository"},{"url":"https://www.ncbi.nlm.nih.gov/pmc/articles/5001603","host_type":"repository"},{"url":"http://nar.oxfordjournals.org/cgi/content/short/44/14/6961","host_type":"repository"},{"url":"https://europepmc.org/articles/PMC5001603","host_type":"Europe_PMC"},{"url":"https://europepmc.org/articles/PMC5001603?pdf=render","host_type":"Europe_PMC"},{"url":"http://dx.doi.org/10.1093/nar/gkw531","host_type":""},{"url":"https://dx.doi.org/10.1093/nar/gkw531","host_type":""}],"fields_of_study":["Protein Structure and Dynamics","DNA and Nucleic Acid Chemistry","Enzyme Structure and Function","0301 basic medicine","0303 health sciences","03 medical and health sciences","Amino Acid Sequence","Amino Acids, Basic","Cations","DNA","Entropy","Humans","Molecular Dynamics Simulation","Nuclear Magnetic Resonance, Biomolecular","Phosphates","Protein Conformation","Proteins","Proton Magnetic Resonance Spectroscopy","Static Electricity","Zinc Fingers"],"mesh_terms":["Amino Acid Sequence","Cations","DNA","Humans","Phosphates","Protein Conformation","Proteins","Zinc Fingers","Entropy","Nuclear Magnetic Resonance, Biomolecular","Amino Acids, Basic","Static Electricity","Molecular Dynamics Simulation","Proton Magnetic Resonance Spectroscopy"],"keywords":["Side chain","Conformational entropy","Molecular dynamics","DNA","Arginine","Lysine","Nucleic acid","Biophysics","Entropy (arrow of time)","Nuclear magnetic resonance spectroscopy","Static electricity","Crystallography","Biology","Biochemistry","Amino acid","Stereochemistry","Chemistry","Molecule","Computational chemistry","Polymer","Protein Conformation","Amino Acids, Basic","Entropy","Proton Magnetic Resonance Spectroscopy","Proteins","Zinc Fingers","Molecular Dynamics Simulation","Phosphates","Structural Biology","Cations","Humans","Amino Acid Sequence","Nuclear Magnetic Resonance, Biomolecular"],"sdg_mappings":[{"sdg_number":3,"sdg_label":"3. 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