In silico screening identifies SHPRH as a novel nucleosome acidic patch interactor

Area of Science:

• Molecular Biology
• Structural Biology
• Biochemistry

Background:

• Nucleosomes are the core structural units of eukaryotic chromatin.
• The H2A-H2B acidic patch is a key platform for protein interactions with nucleosomes.
• These interactions are crucial for regulating chromatin structure and function, including DNA repair and transcription.

Purpose of the Study:

• To identify novel human proteins that bind to the nucleosomal acidic patch.
• To structurally characterize the interaction between a candidate protein and the nucleosome.
• To elucidate the mechanism of nucleosome recognition by identified proteins.

Main Methods:

• Utilized AlphaFold-Multimer for in silico screening of over 7000 human proteins against the nucleosomal acidic patch.
• Determined the cryo-electron microscopy (cryo-EM) structure of the SHPRH protein bound to a nucleosome at 2.8 Å resolution.
• Bioinformatic analysis and structural interpretation to define protein-nucleosome interaction interfaces and domain functions.

Main Results:

• Identified 41 potential human protein binders of the nucleosomal acidic patch.
• Confirmed the acidic patch interaction for the protein SHPRH through structural analysis.
• The cryo-EM structure revealed that the SHPRH ATPase binds to a distinct nucleosomal DNA region compared to other SF2-type ATPases.
• Clarified the specific roles of SHPRH's domains in mediating nucleosome recognition.

Conclusions:

• In silico screening with AlphaFold-Multimer is an effective high-throughput method for identifying specific nucleosome-interacting proteins.
• Expanded the repertoire of known acidic patch binding factors.
• Provided structural insights into the unique nucleosome binding and ATPase engagement of SHPRH, contributing to understanding chromatin regulation.