Abstract

Molecular communication in biology is mediated by protein interactions. According to the current paradigm, the specificity and affinity required for these interactions are encoded in the precise complementarity of binding interfaces. Even proteins that are disordered under physiological conditions or that contain large unstructured regions commonly interact with well-structured binding sites on other biomolecules. Here we demonstrate the existence of an unexpected interaction mechanism: the two intrinsically disordered human proteins histone H1 and its nuclear chaperone prothymosin-α associate in a complex with picomolar affinity, but fully retain their structural disorder, long-range flexibility and highly dynamic character. On the basis of closely integrated experiments and molecular simulations, we show that the interaction can be explained by the large opposite net charge of the two proteins, without requiring defined binding sites or interactions between specific individual residues. Proteome-wide sequence analysis suggests that this interaction mechanism may be abundant in eukaryotes.

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Acknowledgements

We thank S. A. Sjørup and J. H. Martinsen for purification assistance, I. König for a sample of wild-type ProTα, A. Prestel and M. B. Kunze for NMR advice, E. Holmstrom for help with data analysis, D. Mercadante for assistance with electrostatics calculations, R. Sobrino for help with experiments in the early stages of the project, J. Forman-Kay, M. Blackledge, R. Pappu and A. Holehouse for discussions and the Functional Genomics Center Zurich for performing mass spectrometry. This work was supported by the Swiss National Science Foundation (B.S.), the Danish Council for Independent Research (# 4181-00344, B.B.K.), the Novo Nordisk Foundation (B.B.K. and P.O.H.), the Carlsberg Foundation (P.O.H.), and the Intramural Research Program of the National Institute of Diabetes and Digestive and Kidney Diseases of the National Institutes of Health (R.B.B.). This work used the computational resources of the NIH HPC Biowulf cluster (http://hpc.nih.gov).

Author information

Author notes

    • Alessandro Borgia
    • , Madeleine B. Borgia
    •  & Katrine Bugge

    These authors contributed equally to this work.

Affiliations

  1. Department of Biochemistry, University of Zurich, 8057 Zurich, Switzerland

    • Alessandro Borgia
    • , Madeleine B. Borgia
    • , Vera M. Kissling
    • , Pétur O. Heidarsson
    • , Andrea Sottini
    • , Andrea Soranno
    • , Karin J. Buholzer
    • , Daniel Nettels
    •  & Benjamin Schuler
  2. Structural Biology and NMR Laboratory, The Linderstrøm-Lang Centre for Protein Science and Integrative Structural Biology at University of Copenhagen (ISBUC), Department of Biology, University of Copenhagen, 2200 Copenhagen N, Denmark

    • Katrine Bugge
    • , Catarina B. Fernandes
    •  & Birthe B. Kragelund
  3. Department of Biochemistry and Molecular Biophysics, Washington University School of Medicine, St. Louis, Missouri 63110, USA

    • Andrea Soranno
  4. Laboratory of Chemical Physics, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, Maryland 20892-0520, USA

    • Robert B. Best
  5. Department of Physics, University of Zurich, 8057 Zurich, Switzerland

    • Benjamin Schuler

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Contributions

A.B., M.B.B., K.B., B.B.K., R.B.B. and B.S. designed research; M.B.B., A.B., V.M.K. and A.Sot. produced and labelled fluorescent protein variants; A.B. and M.B.B. performed single-molecule experiments; A.B., M.B.B., A.Sor. and D.N. analysed single-molecule data; D.N. developed single-molecule instrumentation and data analysis tools; A.Sot. and A.B. carried out stopped-flow measurements, A.B., M.B.B., K.J.B. and A.Sot. established experimental conditions for single-molecule measurements; C.B.F. and P.O.H. produced protein samples for NMR; K.B. and C.B.F. performed and analysed NMR measurements; A.Sor. carried out the bioinformatics analysis; R.B.B. conducted and analysed simulations; A.B., B.B.K. and C.B.F. carried out circular dichroism experiments; B.B.K., R.B.B. and B.S. supervised research; B.S., A.B., R.B.B., B.B.K. and K.B. wrote the paper with help from all authors.

Competing interests

The authors declare no competing financial interests.

Corresponding authors

Correspondence to Alessandro Borgia or Birthe B. Kragelund or Robert B. Best or Benjamin Schuler.

Reviewer Information Nature thanks E. Zuiderweg and the other anonymous reviewer(s) for their contribution to the peer review of this work.

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    Supplementary Data

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Videos

  1. 1.

    Coarse-grained simulations of the disordered complex of ProT⍺-H1

    A short fragment of the coarse-grained simulation of the ProT⍺-H1 complex. ProT⍺ and H1 are shown in red and blue, respectively. The disordered regions are displayed as stick representation with the folded domain of H1 shown as a smoothed surface. The N-terminal C carbon of each protein is indicated by a sphere. The duration of the trajectory is approximately 5 times the typical autocorrelation time for pair distances within the complex. The total length of the simulation used for FRET calculations was 103 times longer than the fragment shown in the video.

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https://doi.org/10.1038/nature25762

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