SARS-CoV-2 envelope protein attain Kac mediated dynamical interaction network to adopt 'histone mimic' at BRD4 interface

Abstract

Interface mimicry, achieved by recognition of host-pathogen interactions, is the basis by which pathogen proteins can hijack the host machinery. The envelope (E) protein of SARS-CoV-2 is reported to mimic the histones at the BRD4 surface via establishing the structural mimicry; however, the underlying mechanism of E protein mimicking the histones is still elusive. To explore the mimics at dynamic and structural residual network level an extensive docking, and MD simulations were carried out in a comparative manner between complexes of H3-, H4-, E-, and apo-BRD4. We identified that E peptide is able to attain an 'interaction network mimicry', as its acetylated lysine (Kac) achieves orientation and residual fingerprint similar to histones, including water-mediated interactions for both the Kac positions. We identified Y59 of E, playing an anchor role to escort lysine positioning inside the binding site. Furthermore, the binding site analysis confirms that E peptide needs a higher volume, similar to the H4-BRD4 where both the lysine's (Kac5 and Kac8) can accommodate nicely, however, the position of Kac8 is mimicked by two additional water molecules other than four water-mediated bridging's, strengthening the possibility that E peptide could hijack host BRD4 surface. These molecular insights seem pivotal for mechanistic understanding and BRD4-specific therapeutic intervention. KEY POINTSMolecular mimicry is reported in hijacking and then outcompeting the host counterparts so that pathogens can rewire their cellular function by overcoming the host defense mechanism.The molecular recognition process is the basis of molecular mimicry. The E peptide of SARS-CoV-2 is reported to mimic host histone at the BRD4 surface by utilizing its C-terminally placed acetylated lysine (K_ac63) to mimic the N-terminally placed acetylated lysine K_ac5GGK_ac8 histone (H4) by interaction network mimicry identified through microsecond molecular dynamics (MD) simulations and post-processing extensive analysis.There are two steps to mimic: firstly, tyrosine residues help E to anchor at the BRD4 surface to position K_ac and increase the volume of the pocket. Secondary, after positioning of K_ac, a common durable interaction network N140:K_ac5; K_ac5:W1; W1:Y97; W1:W2; W2:W3; W3:W4; W4:P82 is established between K_ac5, with key residues P82, Y97, N140, and four water molecules through water mediate bridge. Furthermore, the second acetylated lysine K_ac8 position and its interaction as polar contact with K_ac5 were also mimicked by E peptide through interaction network P82:W5; W5:K_ac63; W5:W6; W6:K_ac63.The binding event at BRD4/BD1 seems an induced-fit mechanism as a bigger binding site volume was identified at H4-BRD4 on which E peptide attains its better stability than H3-BRD4.We identified the tyrosine residue Y59 of E that acts like an anchor on the BRD4 surface to position K_ac inside the pocket and attain the interaction network by using aromatic residues of the BRD4 surface.Communicated by Ramaswamy H. Sarma.

Keywords: BRD4/BD1; Kac; SARS-CoV-2; envelope protein; interaction mimicry; molecular dynamics simulation; molecular mimicry; protein–protein interaction.