Influence of sequence length and charged residues on Swc5 binding with histone H2A‐H2B

• Published in: Proteins, structure, function, and bioinformatics Vol. 89; no. 5; pp. 512 - 520
• Main Authors: Chu, Wen‐Ting, Wang, Jin
• Format: Journal Article
• Language: English
• Published: Hoboken, USA John Wiley & Sons, Inc 01-05-2021; Wiley Subscription Services, Inc
• Subjects: Binding sites; Chromatin; Dimers; Dynamic structural analysis; Electrostatic properties; histone; Histone H2A; Histones; Molecular dynamics; Molecular structure; protein binding; sequence; Swc; sequence; histone; molecular dynamics; protein binding; Swc
• ISSN: 0887-3585; 1097-0134
• DOI: 10.1002/prot.26035

SWR is a member of chromatin remodeler family and participates the replacement of histone H2A with H2A.Z. One of the SWR subunits, Swc5, has an intrinsically disordered region and binds to H2A‐H2B dimer. Though the binding structure of Swc5 and H2A‐H2B has been resolved recently, it is still challenging to investigate the binding mechanism as well as the role of the charge interactions between Swc5 and H2A‐H2B. Here we developed a coarse‐grained structure‐based model and performed molecular dynamics simulations to investigate the binding processes of two Swc5 regions with different lengths (swc5‐a and swc5‐b) to H2A‐H2B. The simulation results suggest a different role of electrostatic interactions between swc5‐a/swc5‐b and H2A‐H2B on binding. The electrostatic interactions between swc5‐a/swc5‐b and H2A‐H2B can not only accelerate the initial capture step of binding, but can also trap the swc5‐a/swc5‐b at the wrong binding site on H2A. Besides, the conserved DEF/Y‐2 motif of Swc5 is important for the binding affinity and the recognition with H2A‐H2B at the initial step. Both swc5‐a and swc5‐b undergo a structural shift before reaching the final bound state. This theoretical study provides important details and the underlying physical mechanisms of the binding processes of swc5‐a/swc5‐b and H2A‐H2B.