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Dynamics of the HP1 Hinge Region with DNA Measured by Site-Directed Spin Labeling-EPR Spectroscopy

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Abstract

An epigenetic reader, heterochromatin protein 1 (HP1), possesses two conserved domains, the chromoshadow domain (CSD) and chromodomain (CD). The CD and CSD are connected by the hinge region (HR). N, C-tails and HR are estimated to be disordered. In 50% glycerol, EPR spectra from side-chain spin labels of the disordered regions were resolved into two motional fractions or nanoseconds to slower timescales; however, the fraction of slower dynamics was labeled to be site-specific. The slow fraction of the HR (middle region) was abolished by monomer mutation and reduced by N-tail truncation in the dimer state. Within the HR, by truncation of the C-tail, the slow fraction of dynamics of the C-terminal region in the HR were reduced. In addition, the slow fraction of dynamics of the basal region in the C-tail, but not the C-tail end, was significantly reduced by truncating the N-tail-CD-HR. Together, the middle region of the HR was loosely organized by direct or indirect interaction with the N-tail, exerted from one monomer to the other, and the C-terminal region in the HR contacted the C-tail within a monomer in an autoinhibited state, as presumably proposed. Surprisingly, DNA did not affect the spectra, irrespective of glycerol addition, while it clearly restricted the CD and the CSD in HP1α, one of three paralogs. In contrast, DNA did not show a significant effect on the dynamics of all regions examined in another paralog HP1γ. We propose that HP1α undergoes very rapid diffusion due to sliding as a fuzzy complex of the HR and that CD and CSD are tethered with similar dynamics around DNA, which is in agreement with reported molecular dynamics simulations [Watanabe et al., Biophys. J. 114: 2336–2352, 2018].

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Acknowledgements

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Funding

This work was supported by JSPS KAKENHI Grant Numbers JP22K06174(IS), JP18K06095(IS), and the promotion and Mutual Aid Corporation for Private Schools of Japan (PMAC) (IS). IS and TA are grateful to the Collaborative Research Program of the Institute for Protein Research, Osaka University, VFCR-18–03, 19–03, CR-18–02, 19–02, 20–01, 21–01, and 21–02.

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  1. Risa Mutoh

    Present address: Department of Biomolecular Science, Faculty of Science, Toho University, Chiba, 274-8510, Japan

Authors and Affiliations

  1. Institute for Protein Research, Osaka University, Osaka, 565-0871, Japan

    Isao Suetake, Tomoaki Sugishita, Yuichi Mishima, Toshiki Takei, Toshimichi Fujiwara, Akira Shinohara, Hironobu Hojo & Toshiaki Arata

  2. Department of Nutritional Sciences, Graduate School of Nutritional Sciences, Nakamura Gakuen University, Fukuoka, 814-0198, Japan

    Isao Suetake

  3. Department of Chemistry and Molecular Materials Sciences, Graduate School of Science, Osaka Metropolitan University, Osaka, 558-8585, Japan

    Kazunobu Sato & Takeji Takui

  4. Department of Applied Physics, Faculty of Science, Fukuoka University, Fukuoka, 814-0180, Japan

    Risa Mutoh

  5. Department of Biology, Graduate School of Science, Osaka Metropolitan University, Osaka, 558-8585, Japan

    Makoto Miyata & Toshiaki Arata

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Contributions

T.A. and I.S. conceived and supervised the study; T.A. and I.S. designed the experiments; T.A., K.S., and I.S. performed the EPR experiments; T.S. performed phase-contrast microscopy; Y.M., A.S., R.M. and I.S. prepared recombinant proteins; H.H. and To.T. performed structural analysis; Y.M., T.A. and I.S. synthesized the DNA and performed the gel-shift assay; T.A., R.M. and I.S. wrote the manuscript. M.M., Ta.T., T.F., and A.S. contributed to the critical discussion.

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Suetake, I., Sato, K., Sugishita, T. et al. Dynamics of the HP1 Hinge Region with DNA Measured by Site-Directed Spin Labeling-EPR Spectroscopy. Appl Magn Reson 54, 119–141 (2023). https://doi.org/10.1007/s00723-022-01519-2

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