Probing allostery through DNA

Sangjin Kim, Erik Broströmer, Dong Xing, Jianshi Jin, Shasha Chong, Hao Ge, Siyuan Wang, Chan Gu, Lijiang Yang, Yi Qin Gao, Xiao Dong Su, Yujie Sun, X. Sunney Xie

Research output: Contribution to journalArticle

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.

Original languageEnglish (US)
Pages (from-to)816-819
Number of pages4
JournalScience
Volume339
Issue number6121
DOIs
StatePublished - Feb 15 2013
Externally publishedYes

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DNA
Proteins
Base Pairing
B-Form DNA
Physiological Phenomena
Nucleosomes
Periodicity
Molecular Dynamics Simulation
Carrier Proteins
Transcription Factors
Bacteria
Gene Expression

ASJC Scopus subject areas

  • General

Cite this

Kim, S., Broströmer, E., Xing, D., Jin, J., Chong, S., Ge, H., ... Xie, X. S. (2013). Probing allostery through DNA. Science, 339(6121), 816-819. https://doi.org/10.1126/science.1229223

Probing allostery through DNA. / Kim, Sangjin; Broströmer, Erik; Xing, Dong; Jin, Jianshi; Chong, Shasha; Ge, Hao; Wang, Siyuan; Gu, Chan; Yang, Lijiang; Gao, Yi Qin; Su, Xiao Dong; Sun, Yujie; Xie, X. Sunney.

In: Science, Vol. 339, No. 6121, 15.02.2013, p. 816-819.

Research output: Contribution to journalArticle

Kim, S, Broströmer, E, Xing, D, Jin, J, Chong, S, Ge, H, Wang, S, Gu, C, Yang, L, Gao, YQ, Su, XD, Sun, Y & Xie, XS 2013, 'Probing allostery through DNA', Science, vol. 339, no. 6121, pp. 816-819. https://doi.org/10.1126/science.1229223
Kim S, Broströmer E, Xing D, Jin J, Chong S, Ge H et al. Probing allostery through DNA. Science. 2013 Feb 15;339(6121):816-819. https://doi.org/10.1126/science.1229223
Kim, Sangjin ; Broströmer, Erik ; Xing, Dong ; Jin, Jianshi ; Chong, Shasha ; Ge, Hao ; Wang, Siyuan ; Gu, Chan ; Yang, Lijiang ; Gao, Yi Qin ; Su, Xiao Dong ; Sun, Yujie ; Xie, X. Sunney. / Probing allostery through DNA. In: Science. 2013 ; Vol. 339, No. 6121. pp. 816-819.
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