title: Probing allostery through DNA.
abstract: Allostery is well documented for proteins but less recognized for DNA-protein interactions. Here, we report that specific binding of a protein on DNA is substantially stabilized or destabilized by another protein bound nearby. The ternary complex's free energy oscillates as a function of the separation between the two proteins with a periodicity of ~10 base pairs, the helical pitch of B-form DNA, and a decay length of ~15 base pairs. The binding affinity of a protein near a DNA hairpin is similarly dependent on their separation, which-together with molecular dynamics simulations-suggests that deformation of the double-helical structure is the origin of DNA allostery. The physiological relevance of this phenomenon is illustrated by its effect on gene expression in live bacteria and on a transcription factor's affinity near nucleosomes.
authors: Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA 02138, USA.
authors: Sangjin
authors: S
authors: Kim
authors: Erik
authors: E
authors: Broströmer
authors: Dong
authors: D
authors: Xing
authors: Jianshi
authors: J
authors: Jin
authors: Shasha
authors: S
authors: Chong
authors: Hao
authors: H
authors: Ge
authors: Siyuan
authors: S
authors: Wang
authors: Chan
authors: C
authors: Gu
authors: Lijiang
authors: L
authors: Yang
authors: Yi Qin
authors: YQ
authors: Gao
authors: Xiao-dong
authors: XD
authors: Su
authors: Yujie
authors: Y
authors: Sun
authors: X Sunney
authors: XS
authors: Xie
mesh_terms: D000494:Allosteric Regulation; D001483:Base Sequence; D001665:Binding Sites; D059371:DNA, B-Form / Q000737:chemistry*; D004268:DNA-Binding Proteins / Q000737:chemistry*; D012321:DNA-Directed RNA Polymerases / Q000737:chemistry; D004926:Escherichia coli / Q000235:genetics / Q000378:metabolism; D015870:Gene Expression; D015964:Gene Expression Regulation, Bacterial; D056968:Lac Repressors / Q000737:chemistry; D056004:Molecular Dynamics Simulation; D009707:Nucleosomes / Q000737:chemistry; D011485:Protein Binding; D017434:Protein Structure, Tertiary; D011965:Receptors, Glucocorticoid / Q000737:chemistry; D014157:Transcription Factors / Q000737:chemistry*; D014764:Viral Proteins / Q000737:chemistry
chemical_list: D059371:DNA, B-Form; D004268:DNA-Binding Proteins; D056968:Lac Repressors; D009707:Nucleosomes; D011965:Receptors, Glucocorticoid; D014157:Transcription Factors; D014764:Viral Proteins; C062210:bacteriophage T7 RNA polymerase; D012321:DNA-Directed RNA Polymerases