Molecular and functional characterization of spotted snakehead NOD1 with an emphasis on structural insights into iE-DAP binding motifs employing advanced bioinformatic tools

Nucleotide-binding and oligomerization domain (NOD)-like receptors (NLRs) are cytosolic receptors implicated in recognition of intracellular pathogen associated molecular patterns (PAMPs) and danger associated molecular patterns (DAMPs). Depending upon their effector binding domain (EBD) at the C-terminal, the NLRs are categorized into NLRA, NLRB, NLRC, NLRP and NLRX. NOD1 is a pivotal player in immune responses against bacterial and viral invasions and interacts with pathogens via C-terminal leucine rich repeat (LRR) domain. This study aims at characterizing NOD1 in an economically important teleost of the Indian subcontinent, spotted snakehead Channa punctata . The understanding of pathogen-receptor interaction in teleosts is still obscure. In light of this, combinatorial approach involving protein modeling, docking, MD simulation and binding free energy calculation were employed to identify key motifs involved in binding iE-DAP. In silico analysis revealed that NOD1 consists of 943 amino acids comprising of one caspase recruitment domain (CARD) at N-terminal, one central NACHT domain and nine leucine rich repeat (LRR) regions at C-terminal. Structural dynamics study showed that the C-terminal β-sheet LRR4-7 region is involved in iE-DAP binding. NOD1 was ubiquitously and constitutively expressed in all tissues studied. Differential expression profile of NOD1 induced by Aeromonas hydrophila infection was also investigated. Lymphoid organs and phagocytes of infected spotted snakehead showed significant downregulation of NOD1 expression. The current study thus gives an insight into structural and functional dynamics of NOD1 which might have future prospect for structure-based drug designing in teleosts. Communicated by Ramaswamy H. Sarma