{"PubmedArticle":{"MedlineCitation":{"@attributes":{"Status":"MEDLINE","Owner":"NLM","IndexingMethod":"Manual"},"PMID":{"@attributes":{"Version":"1"},"@text":"27396829"},"DateCompleted":{"Year":"2017","Month":"10","Day":"05"},"DateRevised":{"Year":"2020","Month":"12","Day":"09"},"Article":{"@attributes":{"PubModel":"Print-Electronic"},"Journal":{"ISSN":{"@attributes":{"IssnType":"Electronic"},"@text":"1878-4186"},"JournalIssue":{"@attributes":{"CitedMedium":"Internet"},"Volume":"24","Issue":"8","PubDate":{"Year":"2016","Month":"Aug","Day":"02"}},"Title":"Structure (London, England : 1993)","ISOAbbreviation":"Structure"},"ArticleTitle":"Dynamic Local Polymorphisms in the Gbx1 Homeodomain Induced by DNA Binding.","Pagination":{"StartPage":"1372","EndPage":"1379","MedlinePgn":"1372-1379"},"ELocationID":[{"@attributes":{"EIdType":"doi","ValidYN":"Y"},"@text":"10.1016\/j.str.2016.05.013"},{"@attributes":{"EIdType":"pii","ValidYN":"Y"},"@text":"S0969-2126(16)30119-8"}],"Abstract":{"AbstractText":["The Gastrulation Brain Homeobox 1 (Gbx1) gene encodes the Gbx1 homeodomain that targets TAATTA motifs in double-stranded DNA (dsDNA). Residues Glu17 and Arg52 in Gbx1 form a salt bridge, which is preserved in crystal structures and molecular dynamics simulations of homologous homeodomain-DNA complexes. In contrast, our nuclear magnetic resonance (NMR) studies show that DNA binding to Gbx1 induces dynamic local polymorphisms, which include breaking of the Glu17-Arg52 salt bridge. To study this interaction, we produced a variant with Glu17Arg and Arg52Glu mutations, which exhibited the same fold as the wild-type protein, but a 2-fold reduction in affinity for dsDNA. Analysis of the NMR structures of the Gbx1 homeodomain in the free form, the Gbx1[E17R,R52E] variant, and a Gbx1 homeodomain-DNA complex showed that stabilizing interactions of the Arg52 side chain with the DNA backbone are facilitated by transient breakage of the Glu17-Arg52 salt bridge in the DNA-bound Gbx1."],"CopyrightInformation":"Copyright \u00a9 2016 Elsevier Ltd. All rights reserved."},"AuthorList":{"@attributes":{"CompleteYN":"Y"},"Author":[{"@attributes":{"ValidYN":"Y"},"LastName":"Proudfoot","ForeName":"Andrew","Initials":"A","AffiliationInfo":[{"Affiliation":"Department of Integrative Structural and Computational Biology, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, CA 92037, USA; Joint Center for Structural Genomics, La Jolla, CA 92037, USA."}]},{"@attributes":{"ValidYN":"Y"},"LastName":"Geralt","ForeName":"Michael","Initials":"M","AffiliationInfo":[{"Affiliation":"Department of Integrative Structural and Computational Biology, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, CA 92037, USA; Joint Center for Structural Genomics, La Jolla, CA 92037, USA."}]},{"@attributes":{"ValidYN":"Y"},"LastName":"Elsliger","ForeName":"Marc-Andre","Initials":"MA","AffiliationInfo":[{"Affiliation":"Department of Integrative Structural and Computational Biology, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, CA 92037, USA; Joint Center for Structural Genomics, La Jolla, CA 92037, USA."}]},{"@attributes":{"ValidYN":"Y"},"LastName":"Wilson","ForeName":"Ian A","Initials":"IA","AffiliationInfo":[{"Affiliation":"Department of Integrative Structural and Computational Biology, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, CA 92037, USA; Joint Center for Structural Genomics, La Jolla, CA 92037, USA."}]},{"@attributes":{"ValidYN":"Y"},"LastName":"W\u00fcthrich","ForeName":"Kurt","Initials":"K","AffiliationInfo":[{"Affiliation":"Department of Integrative Structural and Computational Biology, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, CA 92037, USA; Joint Center for Structural Genomics, La Jolla, CA 92037, USA; Skaggs Institute for Chemical Biology, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, CA 92037, USA. Electronic address: wuthrich@scripps.edu."}]},{"@attributes":{"ValidYN":"Y"},"LastName":"Serrano","ForeName":"Pedro","Initials":"P","AffiliationInfo":[{"Affiliation":"Department of Integrative Structural and Computational Biology, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, CA 92037, USA. Electronic address: serrano@scripps.edu."}]}]},"Language":["eng"],"GrantList":{"@attributes":{"CompleteYN":"Y"},"Grant":[{"GrantID":"U54 GM094586","Acronym":"GM","Agency":"NIGMS NIH HHS","Country":"United States"}]},"PublicationTypeList":{"PublicationType":[{"@attributes":{"UI":"D016428"},"@text":"Journal Article"}]},"ArticleDate":[{"@attributes":{"DateType":"Electronic"},"Year":"2016","Month":"07","Day":"07"}]},"MedlineJournalInfo":{"Country":"United States","MedlineTA":"Structure","NlmUniqueID":"101087697","ISSNLinking":"0969-2126"},"ChemicalList":{"Chemical":[{"RegistryNumber":"0","NameOfSubstance":{"@attributes":{"UI":"C422443"},"@text":"GBX1 protein, human"}},{"RegistryNumber":"0","NameOfSubstance":{"@attributes":{"UI":"D018398"},"@text":"Homeodomain Proteins"}},{"RegistryNumber":"0","NameOfSubstance":{"@attributes":{"UI":"D011994"},"@text":"Recombinant Proteins"}},{"RegistryNumber":"9007-49-2","NameOfSubstance":{"@attributes":{"UI":"D004247"},"@text":"DNA"}}]},"CitationSubset":["IM"],"MeshHeadingList":{"MeshHeading":[{"DescriptorName":{"@attributes":{"UI":"D000595","MajorTopicYN":"N"},"@text":"Amino Acid Sequence"}},{"DescriptorName":{"@attributes":{"UI":"D019943","MajorTopicYN":"Y"},"@text":"Amino Acid Substitution"}},{"DescriptorName":{"@attributes":{"UI":"D001665","MajorTopicYN":"N"},"@text":"Binding Sites"}},{"DescriptorName":{"@attributes":{"UI":"D003001","MajorTopicYN":"N"},"@text":"Cloning, Molecular"}},{"DescriptorName":{"@attributes":{"UI":"D004247","MajorTopicYN":"N"},"@text":"DNA"},"QualifierName":[{"@attributes":{"UI":"Q000737","MajorTopicYN":"Y"},"@text":"chemistry"},{"@attributes":{"UI":"Q000235","MajorTopicYN":"N"},"@text":"genetics"},{"@attributes":{"UI":"Q000378","MajorTopicYN":"N"},"@text":"metabolism"}]},{"DescriptorName":{"@attributes":{"UI":"D004926","MajorTopicYN":"N"},"@text":"Escherichia coli"},"QualifierName":[{"@attributes":{"UI":"Q000235","MajorTopicYN":"N"},"@text":"genetics"},{"@attributes":{"UI":"Q000378","MajorTopicYN":"N"},"@text":"metabolism"}]},{"DescriptorName":{"@attributes":{"UI":"D015870","MajorTopicYN":"N"},"@text":"Gene Expression"}},{"DescriptorName":{"@attributes":{"UI":"D018398","MajorTopicYN":"N"},"@text":"Homeodomain Proteins"},"QualifierName":[{"@attributes":{"UI":"Q000737","MajorTopicYN":"Y"},"@text":"chemistry"},{"@attributes":{"UI":"Q000235","MajorTopicYN":"N"},"@text":"genetics"},{"@attributes":{"UI":"Q000378","MajorTopicYN":"N"},"@text":"metabolism"}]},{"DescriptorName":{"@attributes":{"UI":"D006801","MajorTopicYN":"N"},"@text":"Humans"}},{"DescriptorName":{"@attributes":{"UI":"D062105","MajorTopicYN":"N"},"@text":"Molecular Docking Simulation"}},{"DescriptorName":{"@attributes":{"UI":"D056004","MajorTopicYN":"N"},"@text":"Molecular Dynamics Simulation"}},{"DescriptorName":{"@attributes":{"UI":"D009154","MajorTopicYN":"N"},"@text":"Mutation"}},{"DescriptorName":{"@attributes":{"UI":"D019906","MajorTopicYN":"N"},"@text":"Nuclear Magnetic Resonance, Biomolecular"}},{"DescriptorName":{"@attributes":{"UI":"D011485","MajorTopicYN":"N"},"@text":"Protein Binding"}},{"DescriptorName":{"@attributes":{"UI":"D000072756","MajorTopicYN":"N"},"@text":"Protein Conformation, alpha-Helical"}},{"DescriptorName":{"@attributes":{"UI":"D000072757","MajorTopicYN":"N"},"@text":"Protein Conformation, beta-Strand"}},{"DescriptorName":{"@attributes":{"UI":"D054730","MajorTopicYN":"N"},"@text":"Protein Interaction Domains and Motifs"}},{"DescriptorName":{"@attributes":{"UI":"D011994","MajorTopicYN":"N"},"@text":"Recombinant Proteins"},"QualifierName":[{"@attributes":{"UI":"Q000737","MajorTopicYN":"N"},"@text":"chemistry"},{"@attributes":{"UI":"Q000235","MajorTopicYN":"N"},"@text":"genetics"},{"@attributes":{"UI":"Q000378","MajorTopicYN":"N"},"@text":"metabolism"}]},{"DescriptorName":{"@attributes":{"UI":"D016415","MajorTopicYN":"N"},"@text":"Sequence Alignment"}},{"DescriptorName":{"@attributes":{"UI":"D013816","MajorTopicYN":"N"},"@text":"Thermodynamics"}}]},"KeywordList":[{"@attributes":{"Owner":"NOTNLM"},"Keyword":[{"@attributes":{"MajorTopicYN":"N"},"@text":"Binding affinity"},{"@attributes":{"MajorTopicYN":"N"},"@text":"J-UNIO"},{"@attributes":{"MajorTopicYN":"N"},"@text":"NMR structure determination"},{"@attributes":{"MajorTopicYN":"N"},"@text":"protein:DNA complex"}]}]},"PubmedData":{"History":{"PubMedPubDate":[{"@attributes":{"PubStatus":"received"},"Year":"2016","Month":"1","Day":"19"},{"@attributes":{"PubStatus":"revised"},"Year":"2016","Month":"3","Day":"30"},{"@attributes":{"PubStatus":"accepted"},"Year":"2016","Month":"5","Day":"6"},{"@attributes":{"PubStatus":"entrez"},"Year":"2016","Month":"7","Day":"12","Hour":"6","Minute":"0"},{"@attributes":{"PubStatus":"pubmed"},"Year":"2016","Month":"7","Day":"12","Hour":"6","Minute":"0"},{"@attributes":{"PubStatus":"medline"},"Year":"2017","Month":"10","Day":"6","Hour":"6","Minute":"0"},{"@attributes":{"PubStatus":"pmc-release"},"Year":"2016","Month":"11","Day":"15"}]},"PublicationStatus":"ppublish","ArticleIdList":{"ArticleId":[{"@attributes":{"IdType":"pubmed"},"@text":"27396829"},{"@attributes":{"IdType":"mid"},"@text":"NIHMS827800"},{"@attributes":{"IdType":"pmc"},"@text":"PMC5109927"},{"@attributes":{"IdType":"doi"},"@text":"10.1016\/j.str.2016.05.013"},{"@attributes":{"IdType":"pii"},"@text":"S0969-2126(16)30119-8"}]},"ReferenceList":[{"Reference":[{"Citation":"Babin 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