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

Nucleotide-binding and oligomerization domain-containing 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.