Nucleotide-binding oligomerization domain-containing protein 1 (NOD1) is an intracellular pattern recognition receptor that recognizes bacterial peptidoglycan (PG) containing meso -diaminopimelic acid ( meso DAP) and activates the innate immune system. Interestingly, few pathogenic and commensal bacteria modify their PG stem peptide by amidation of meso DAP ( meso DAPNH2). In this study, NOD1 stimulation assays were performed using bacterial PG containing meso DAP (PGDAP) and meso DAPNH2 (PGDAPNH2) to understand the differences in their biomolecular recognition mechanism. PGDAP was effectively recognized, while PGDAPNH2 showed reduced recognition by NOD1 receptor. Re-stimulation of the NOD1 receptor which was initially stimulated with PGDAP, using PGDAPNH2, did not show any further NOD1 activation levels than PGDAP alone. But NOD1 receptor, initially stimulated with PGDAPNH2 responded effectively to re-stimulation with PGDAP. The biomolecular structure-recognition relationship of the ligand sensing LRR domain of human NOD1 (NOD1-LRR) with PGDAP and PGDAPNH2 was studied by different computational techniques to further understand the molecular basis of our experimental observations. The D-Glu- meso DAP motif of GMTPDAP, which is the minimum essential motif for NOD1 activation, was found involved in specific interactions at the recognition site, but the interactions of the corresponding D-Glu- meso DAP motif of PGDAPNH2 occurs away from the recognition site of NOD1 receptor. Hot-spot residues identified for effective PG recognition by NOD1-LRR include W820, G821, D826 and N850, which are evolutionarily conserved across different host species. These integrated results thus successfully provided the atomic level and biochemical insight on how PGs containing meso DAPNH2 evade NOD1-LRR receptor recognition.
S. Vijayrajratnam, Pushkaran, A. Choorakott, Balakrishnan, A., Vasudevan, A., Biswas, R., and Dr. Gopi Mohan C., “Bacterial Peptidoglycan with Amidated meso -diaminopimelic acid Evades NOD1 Recognition: An insight on NOD1 Structure-Recognition Study”, Biochemical Journal, 2016.