A conformational analysis of mouse Nalp3 domain structures by molecular dynamics simulations, and binding site analysis.

Abstract

Scrutinizing various nucleotide-binding oligomerization domain (NOD)-like receptors (NLR) genes in higher eukaryotes is very important for understanding the intriguing mechanism of host defense against pathogens. The nucleotide-binding domain (NACHT), leucine-rich repeat (LRR) and pyrin domain (PYD) containing protein 3 (Nalp3) is an intracellular innate immune receptor, and is associated with several immune system related disorders. Despite of Nalp3’s protective role during pathogenic invasion, the molecular feature, and structural organization of this crucial protein is poorly understood. Using comparative modeling and molecular dynamics simulations, we have studied the structural architecture of Nalp3 domains, and characterized the dynamic and energetic parameters of adenosine triphosphate (ATP) binding in NACHT and pathogen derived ligands muramyl dipeptide (MDP) and imidazoquinoline with LRR domains. The results anticipated walker A, B and extended walker B motifs as the key ATP binding regions in NACHT that mediates self-oligomerization. Analysis of binding sites of MDP and imidazoquinoline revealed LRR7-9 being the most energetically favored site of imidazoquinoline interaction. However, binding free energy calculations using Molecular Mechanics/Possion-Boltzman Surface Area (MM/PBSA) method advocated that MDP is incompatible for activating Nalp3 molecule in monomeric form and suggest its complex nature with NOD2 or other NLRs for MDP recognition. The high binding affinity of ATP with NACHT is correlated to the experimental data for human NLRs. Our binding site prediction for imidazoquinoline in LRR warrants further investigation via in vivo models. This is the first study that provides ligand(s) recognition in mouse Nalp3 and its spatial structural arrangements.