Structural Elucidation of Inter-CARD Interfaces involved in NOD2 Tandem CARD Association and RIP2 Recognition

Abstract

Nucleotide-binding and oligomerization domaincontaining protein 2 (NOD2) recognizes the muramyl dipeptide and activates the NF-κB signaling cascade following its interaction with receptor-interacting protein 2 (RIP2) via caspase recruitment domains (CARDs). The NOD2−RIP2 interaction is not understood well due to inadequate structural information. Using comparative modeling and multimicrosecond timescale molecular dynamics simulations, we have demonstrated the association of NOD2-CARDs (CARDa−CARDb) and their interaction with RIP2 CARD . Our results suggest that a negatively charged interface of NOD2 CARDa and positively charged type-Ia interface of NOD2 CARDb are crucial for CARDa−CARDb association and the type-Ia interface of NOD2 CARDa and type-Ib interface of RIP2 CARD predicted to be involved in 1:1 CARD−CARD interaction. Moreover, the direct interaction of NOD2 CARDb with RIP2 CARD signifies the importance of both CARDs of NOD2 in RIP2-mediated CARD−CARD interaction. Altogether, the structural results could help in understanding the underlying molecular details of the NOD2−RIP2 association in higher and lower eukaryotes.

Recent advances in the development of RIPK2 modulators for the treatment of inflammatory diseases

“…Although CARD does not participate in the kinase functions of RIPK2, it is essential for RIPK2 activation by interacting with NODs ( vide infra ). The structure of RIPK2 CARD shares similar features with NOD1 CARD, including the arrangement of all but the last of the a -helices ( Fridh and Rittinger, 2012 ; Lin et al, 2015 ; Maharana et al, 2015 ; Goncharuk et al, 2018 ; Maharana et al, 2021 ). The solution structure of human RIPK2 CARD contains six a -helices, that are closely packed ( Figure 2 ) ( Fridh and Rittinger, 2012 ; Lin et al, 2015 ).…”

“…In both reported structures the CARD conformation is stabilized by backbone-backbone and sidechain-backbone H bonds. The core of CARD is highly hydrophobic, while the surface is hydrophilic with many charged residues, which can form salt bridges in CARD-CARD interactions ( Fridh and Rittinger, 2012 ; Maharana et al, 2015 ; Maharana et al, 2021 ). Point mutations in CARD indicate that Arg444, Arg483, and Arg488 are crucial for NOD1 binding as they form ionic interactions with acidic residues of NOD1 CARD ( Goncharuk et al, 2018 ).…”

Exploring the structural assembly of rice ADP-glucose pyrophosphorylase subunits using MD simulation

“…Following the established procedures [11,12,27], we superimposed individual subunits of rice AGPase subunits (OsL1/OsS1) on to refecence structure to generate the heterotetramer complexes. The molecular docking of ATP and the modeling of heterotetrameric complexes were carried out using PyMOL, following the procedures described in our previous studies [27,[36][37][38].…”