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CBFβ allosterically regulates the Runx1 Runt domain via a dynamic conformational equilibrium

Nature Structural & Molecular Biology volume 11, pages 901–906 (2004)Cite this article

Abstract

Core binding factors (CBFs) are heterodimeric transcription factors consisting of a DNA-binding CBFα subunit and non-DNA-binding CBFβ subunit. The CBFβ subunit increases the affinity of the DNA-binding Runt domain of CBFα for DNA while making no direct contacts to the DNA. We present evidence for conformational exchange in the S-switch region in a Runt domain–DNA complex that is quenched upon CBFβ binding. Analysis of 15N backbone relaxation parameters shows that binding of CBFβ reduces the backbone dynamics in the microsecond-to-millisecond time frame for several regions of the Runt domain that make energetically important contacts with the DNA. The DNA also undergoes conformational exchange in the Runt domain–DNA complex that is quenched in the presence of CBFβ. Our results indicate that allosteric regulation by the CBFβ subunit is mediated by a shift in an existing dynamic conformational equilibrium of both the Runt domain and DNA.

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Figure 1: 13C-1H HSQC spectra of labeled DNA.
Figure 2: Results of ModelFree analysis (Ss2, τe, Rex) of the relaxation data and R1R2 values plotted versus the primary sequence for residues in the Runt domain–DNA and CBFβ–Runt domain–DNA complexes.
Figure 3: Differences in the ModelFree parameters for residues for which values are available in both complexes (values were calculated as CBFβ–Runt domain–DNA minus Runt domain–DNA).
Figure 4: Ribbon representations of the structure of the Runt domain (PDB entry 1H9D) colored according to dynamic behavior.
Figure 5: ITC measurements of the binding of the Runt domain (RD) and the RD–CBFβ complex to DNA.
Figure 6: Alignment of the Runt domain and DNA from the CBFβ–Runt domain–DNA complex (PDB entry 1H9D) and the free Runt domain (PDB entry 1EAN).

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Acknowledgements

This work was supported by grants R01 AI39536 and R01 AI42097 from the US Public Health Service (US National Institutes of Health) to J.H.B. We thank R. Biltonen for a number of useful discussions in the preparation of the manuscript.

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Author notes

  1. Jiangli Yan

    Present address: Pfizer, 10770 Science Center Drive, San Diego, California, 92121, USA

  2. Jiangli Yan and Yizhou Liu: These authors contributed equally to this work.

Authors and Affiliations

  1. Departments of Molecular Physiology and Biological Physics, University of Virginia, Charlottesville, 22906, Virginia, USA

    Jiangli Yan, Yizhou Liu & John H Bushweller

  2. Department of Chemistry, University of Virginia, Charlottesville, 22906, Virginia, USA

    Stephen M Lukasik & John H Bushweller

  3. Department of Biochemistry, Dartmouth Medical School, Hanover, 03755, New Hampshire, USA

    Nancy A Speck

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  1. Jiangli Yan
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Correspondence to John H Bushweller.

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Supplementary information

Supplementary Fig. 1

Selected regions of 15N-1H HSQC spectra of 15N specifically labeled Runt domain (RD) in the RD–DNA and CBFβ–RD–DNA complexes. (PDF 185 kb)

Supplementary Fig. 2

15N T1 and T2 relaxation curves. (PDF 165 kb)

Supplementary Fig. 3

Plots of relaxation values versus sequence. (PDF 96 kb)

Supplementary Table 1

Relaxation and ModelFree data for Runt domain–DNA and CBFβ–Runt domain–DNA complexes. (PDF 28 kb)

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Yan, J., Liu, Y., Lukasik, S. et al. CBFβ allosterically regulates the Runx1 Runt domain via a dynamic conformational equilibrium. Nat Struct Mol Biol 11, 901–906 (2004). https://doi.org/10.1038/nsmb819

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