Dynamic Solution Structures of Whole Human NAP1 Dimer Bound to One and Two Histone H2A-H2B Heterodimers Obtained by Integrative Methods

• Published in: Journal of molecular biology 2023-08, Vol.435 (15), p.168189-168189, Article 168189
• Main Authors: Ohtomo, Hideaki, Yamane, Tsutomu, Oda, Takashi, Kodera, Noriyuki, Kurita, Jun-ichi, Tsunaka, Yasuo, Amyot, Romain, Ikeguchi, Mitsunori, Nishimura, Yoshifumi
• Format: Article
• Language: English
• Subjects: AFM; histone chaperone; Histones - metabolism; Humans; molecular dynamics simulation; NMR; Nucleosome Assembly Protein 1 - chemistry; Nucleosome Assembly Protein 1 - genetics; Nucleosome Assembly Protein 1 - metabolism; Nucleosomes; Protein Binding; SAXS; Scattering, Small Angle; X-Ray Diffraction
• ISSN: 0022-2836; 1089-8638
• DOI: 10.1016/j.jmb.2023.168189

[Display omitted] •NMR models reveal the interaction modes of hNAP1 CTAD with H2AH2B.•AFM reveals the stable homo-dimer formation of an hNAP1 mutant.•SEC-SAXS reveals profiles of hNAP1 in complex with one or two molecules of H2AH2B.•MD simulations refine the structures of hNAP1 bound to one or two molecules of H2AH2B. Nucleosome assembly protein 1 (NAP1) binds to histone H2A-H2B heterodimers, mediating their deposition on and eviction from the nucleosome. Human NAP1 (hNAP1) consists of a dimerization core domain and intrinsically disordered C-terminal acidic domain (CTAD), both of which are essential for H2A-H2B binding. Several structures of NAP1 proteins bound to H2A-H2B exhibit binding polymorphisms of the core domain, but the distinct structural roles of the core and CTAD domains remain elusive. Here, we have examined dynamic structures of the full-length hNAP1 dimer bound to one and two H2A-H2B heterodimers by integrative methods. Nuclear magnetic resonance (NMR) spectroscopy of full-length hNAP1 showed CTAD binding to H2A-H2B. Atomic force microscopy revealed that hNAP1 forms oligomers of tandem repeated dimers; therefore, we generated a stable dimeric hNAP1 mutant exhibiting the same H2A-H2B binding affinity as wild-type hNAP1. Size exclusion chromatography (SEC), multi-angle light scattering (MALS) and small angle X-ray scattering (SAXS), followed by modelling and molecular dynamics simulations, have been used to reveal the stepwise dynamic complex structures of hNAP1 binding to one and two H2A-H2B heterodimers. The first H2A-H2B dimer binds mainly to the core domain of hNAP1, while the second H2A-H2B binds dynamically to both CTADs. Based on our findings, we present a model of the eviction of H2A-H2B from nucleosomes by NAP1.