Structural insights into the MDP binding and CARD-CARD interaction in zebrafish (Danio rerio) NOD2: a molecular dynamics approach.
Nucleotide binding and oligomerization domain (NOD2) is a key component of innate immunity that is highly specific for muramyl dipeptide (MDP)-a peptidoglycan component of bacterial cell wall. MDP recognition by NOD2-leucine rich repeat (LRR) domain activates NF-κB signaling through a protein-protein interaction between caspase activating and recruitment domains (CARDs) of NOD2 and downstream receptor interacting and activating protein kinase 2 (RIP2). Due to the lack of crystal/NMR structures, MDP recognition and CARD-CARD interaction are poorly understood. Herein, we have predicted the probable MDP and CARD-CARD binding surfaces in zebrafish NOD2 (zNOD2) using various in silico methodologies. The results show that the conserved residues Phe819, Phe871, Trp875, Trp929, Trp899, and Arg845 located at the concave face of zNOD2-LRR confer MDP recognition by hydrophobic and hydrogen bond (H-bond) interactions. Molecular dynamics simulations reveal a stable association between the electropositive surface on zNOD2-CARDa and the electronegative surface on zRIP2-CARD reinforced mostly by H-bonds and electrostatic interactions. Importantly, a 3.5 Å salt bridge is observed between Arg60 of zNOD2-CARDa and Asp494 of zRIP2-CARD. Arg11 and Lys53 of zNOD2-CARDa and Ser498 and Glu508 of zRIP2-CARD are critical residues for CARD-CARD interaction and NOD2 signaling. The 2.7 Å H-bond between Lys104 of the linker and Glu508 of zRIP2-CARD suggests a possible role of the linker for shaping CARD-CARD interaction. These findings are consistent with existing mutagenesis data. We provide first insight into MDP recognition and CARD-CARD interaction in the zebrafish that will be useful to understand the molecular basis of NOD signaling in a broader perspective.
Biotechnology Laboratory, Central Inland Fisheries Research Institute, Kolkata, 700120, West Bengal, India.
Jitendra
J
Maharana
Mahesh Chandra
MC
Patra
Bidhan Chandra
BC
De
Bikash Ranjan
BR
Sahoo
Bijay Kumar
BK
Behera
Sachinandan
S
De
Sukanta Kumar
SK
Pradhan
D000119:Acetylmuramyl-Alanyl-Isoglutamine / Q000378:metabolism*; D000818:Animals; D006801:Humans; D007113:Immunity, Innate / Q000502:physiology; D056004:Molecular Dynamics Simulation; D053473:Nod2 Signaling Adaptor Protein / Q000378:metabolism*; D011485:Protein Binding; D015027:Zebrafish; D029961:Zebrafish Proteins / Q000378:metabolism*
D053473:Nod2 Signaling Adaptor Protein; D029961:Zebrafish Proteins; D000119:Acetylmuramyl-Alanyl-Isoglutamine
CARD-CARD interaction; NOD2; RIP2; molecular dynamics; muramyl dipeptide; protein threading; zebrafish