Conformational diversity of human HP1α

Abstract

Heterochromatin protein 1 alpha (HP1α) is an evolutionarily conserved protein that binds chromatin and is important for gene silencing. The protein comprises 191 residues arranged into three disordered regions and two structured domains, the chromo and chromoshadow domain, which associates into a homodimer. While high-resolution structures of the isolated domains of HP1 proteins are known, the structural properties of full-length HP1α remain largely unknown. Using a combination of NMR spectroscopy and structure predictions by AlphaFold2 we provide evidence that the chromo and chromoshadow domain of HP1α engage in direct contacts resulting in a compact chromo/chromoshadow domain arrangement. We further show that HP1β and HP1γ have increased interdomain dynamics when compared to HP1α which may contribute to the distinct roles of different Hp1 isoforms in gene silencing and activation.

Keywords: AlphaFold; HP1α; NMR spectroscopy; chromatin; dynamics; residual dipolar couplings.

FIGURE 1

Structural properties of human full‐length HP1α. (a) Schematic of Hp1 dimer containing the ordered CD and CSD and disordered NTE, HR, and CTE. (b) Amino acid sequence of HP1α. (c) Residue‐specific secondary structure propensity determined by TALOS N+ on the basis of the experimental NMR assignments of full‐length HP1α. (d) Generated model conformations of transient structures in the NTE, HR, and CTE of HP1α. CD, chromodomain; CSD, chromoshadow domain; HR, hinge region.

FIGURE 2

HP1α CD/CSD arrangement differs from HP1β and HP1γ. (a) Aligned errors for five model structures predicted by AlphaFold2 for HP1α (top), HP1β (middle), and HP1γ (bottom). The color at position (x, y) indicates AlphaFold2's expected position error at residue x, when the predicted and true structures are aligned on residue y. (b) HP1α dimer model predicted by the multimer model of AlphaFold2 (Jumper et al., ; Mirdita et al., 2022); residues highlighted in green (CD) and orange (CSD) were used for RDC analysis (see Figure 2c). (c) Correlation between experimental ¹H‐¹⁵N RDCs and RDCs back‐calculated from the AlphaFold2‐predicted 3D structure of the HP1α dimer shown in (b). (d) Ratios of the RDC‐derived alignment tensor magnitudes Da(HN) between the CD and the CSD, that is, Da(HN)^CD/Da(HN)^CSD, in full‐length HP1α (black), AcHP1α (magenta), and HP1β (violet). For comparison, the CSD/CD ratio of alignment magnitudes predicted by PALES for the individual CSD and CD domains of HP1α and HP1β are shown in cyan. Error bars represent std. CD, chromodomain; CSD, chromoshadow domain; RDC, residual dipolar coupling.