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Modulation of allostery by protein intrinsic disorder

Nature volume 498, pages 390–394 (2013)Cite this article

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Abstract

Allostery is an intrinsic property of many globular proteins and enzymes that is indispensable for cellular regulatory and feedback mechanisms. Recent theoretical1 and empirical2 observations indicate that allostery is also manifest in intrinsically disordered proteins, which account for a substantial proportion of the proteome3,4. Many intrinsically disordered proteins are promiscuous binders that interact with multiple partners and frequently function as molecular hubs in protein interaction networks. The adenovirus early region 1A (E1A) oncoprotein is a prime example of a molecular hub intrinsically disordered protein5. E1A can induce marked epigenetic reprogramming of the cell within hours after infection, through interactions with a diverse set of partners that include key host regulators such as the general transcriptional coactivator CREB binding protein (CBP), its paralogue p300, and the retinoblastoma protein (pRb; also called RB1)6,7. Little is known about the allosteric effects at play in E1A–CBP–pRb interactions, or more generally in hub intrinsically disordered protein interaction networks. Here we used single-molecule fluorescence resonance energy transfer (smFRET) to study coupled binding and folding processes in the ternary E1A system. The low concentrations used in these high-sensitivity experiments proved to be essential for these studies, which are challenging owing to a combination of E1A aggregation propensity and high-affinity binding interactions. Our data revealed that E1A–CBP–pRb interactions have either positive or negative cooperativity, depending on the available E1A interaction sites. This striking cooperativity switch enables fine-tuning of the thermodynamic accessibility of the ternary versus binary E1A complexes, and may permit a context-specific tuning of associated downstream signalling outputs. Such a modulation of allosteric interactions is probably a common mechanism in molecular hub intrinsically disordered protein function.

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Figure 1: Folding of the intrinsically disordered protein E1A induced by binding to pRb and the TAZ2 domain of CBP/p300.
Figure 2: E1A–TAZ2–pRb ternary complex formation detected by ensemble fluorescence anisotropy.
Figure 3: E1A–TAZ2–pRb allosteric interactions probed using single-molecule fluorescence resonance energy transfer.
Figure 4: E1A functional complexity achieved through binding promiscuity.

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Acknowledgements

We thank E. Manlapaz for technical support, A. Jansma and G. Bhabha for preparation of plasmid constructs, P. Haberz for mass spectrometry, and J. Dyson and M. Martinez-Yamout for discussions. This work was supported by grants GM066833 (A.A.D.) and CA96865 (P.E.W.) from the National Institutes of Health, and the Skaggs Institute for Chemical Biology.

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Author notes

  1. Allan Chris M. Ferreon and Josephine C. Ferreon: These authors contributed equally to this work.

Authors and Affiliations

  1. Department of Integrative Structural and Computational Biology, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, California 92037, USA,

    Allan Chris M. Ferreon, Josephine C. Ferreon, Peter E. Wright & Ashok A. Deniz

  2. Skaggs Institute for Chemical Biology, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, California 92037, USA,

    Peter E. Wright

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  1. Allan Chris M. Ferreon
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Contributions

A.C.M.F. and J.C.F. performed the experiments. A.C.M.F., J.C.F., P.E.W. and A.A.D. designed experiments, analysed data and wrote the manuscript.

Corresponding authors

Correspondence to Peter E. Wright or Ashok A. Deniz.

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The authors declare no competing financial interests.

Supplementary information

Supplementary Information

This file contains Supplementary Tables 1-3 (summary of the experimentally-derived binding constants and the measured FRET efficiencies for different E1A dual-labelled samples in various ligation states) and Supplementary Figures 1-7 (representations of the ensemble and single-molecule ligand binding data, analyses and modelling). (PDF 2986 kb)

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Ferreon, A., Ferreon, J., Wright, P. et al. Modulation of allostery by protein intrinsic disorder. Nature 498, 390–394 (2013). https://doi.org/10.1038/nature12294

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