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1878-41862482016Aug02Structure (London, England : 1993)StructureDynamic Local Polymorphisms in the Gbx1 Homeodomain Induced by DNA Binding.137213791372-137910.1016/j.str.2016.05.013S0969-2126(16)30119-8The 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.Copyright © 2016 Elsevier Ltd. All rights reserved.ProudfootAndrewADepartment 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.GeraltMichaelMDepartment 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.ElsligerMarc-AndreMADepartment 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.WilsonIan AIADepartment 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.WüthrichKurtKDepartment 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.SerranoPedroPDepartment 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.engU54 GM094586GMNIGMS NIH HHSUnited StatesJournal Article20160707
United StatesStructure1010876970969-21260GBX1 protein, human0Homeodomain Proteins0Recombinant Proteins9007-49-2DNAIMAmino Acid SequenceAmino Acid SubstitutionBinding SitesCloning, MolecularDNAchemistrygeneticsmetabolismEscherichia coligeneticsmetabolismGene ExpressionHomeodomain ProteinschemistrygeneticsmetabolismHumansMolecular Docking SimulationMolecular Dynamics SimulationMutationNuclear Magnetic Resonance, BiomolecularProtein BindingProtein Conformation, alpha-HelicalProtein Conformation, beta-StrandProtein Interaction Domains and MotifsRecombinant ProteinschemistrygeneticsmetabolismSequence AlignmentThermodynamicsBinding affinityJ-UNIONMR structure determinationprotein:DNA complex2016119201633020165620167126020167126020171066020161115ppublish27396829NIHMS827800PMC510992710.1016/j.str.2016.05.013S0969-2126(16)30119-8Babin V, Wang D, Rose RB, Sagui C. Binding polymorphism in the DNA bound state of the Pdx1 homeodomain. 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