Structural and functional investigation of zebrafish (Danio rerio) NOD1 leucine rich repeat domain and its interaction with iE-DAP

Abstract

Nucleotide binding and oligomerization domain 1 (NOD1), a cytoplasmic pattern recognition receptor (PRR) and is a key component for modulating innate immunity and signaling. It is highly specific to γ-D-Glu-mDAP (iE-DAP), a cell wall component of Gram-negative and few Gram-positive bacteria. In the absence of the experimental structure of NOD1 leucine rich repeat (NOD1-LRR) domain, the NOD signaling cascade mediated through NOD1 and iE-DAP interaction is poorly understood. Herein, we modeled 3D structure of zebrafish NOD1-LRR (zNOD1-LRR) through a protein-threading approach and structural integrity of the model was assessed using molecular dynamics simulations. Molecular interaction analysis of iE-DAP and zNOD1-LRR, their complex stability and binding free energy studies were conducted to anticipate the ligand binding residues in zNOD1. Our study revealed that His775, Lys777, Asp803, Gly805, Trp807, Asn831, Ser833, Ile859 and Trp861 situated in the β-sheet region of zNOD1-LRR could be involved in iE-DAP recognition, which correlates the earlier findings in human. Comparison of binding free energies of native and mutant zNOD1-iE-DAP complexes delineated His775, Lys777, Asp803, Ser833 and Ile859 as the pivotal residues for energetic stability of NOD1 and iE-DAP interaction. This study provides the first comprehensive description of biophysical and biochemical parameters responsible for NOD1 and iE-DAP interaction in zebrafish, which is expected to shed more light on NOD1 signaling and therapeutic applications in other organisms.

Structural Models of Zebrafish (Danio rerio) NOD1 and NOD2 NACHT Domains Suggest Differential ATP Binding Orientations: Insights from Computational Modeling, Docking and Molecular Dynamics Simulations

“…Further, ATP was optimized using AutoDock 4.2 [ 50 ] and used for docking simulations. The docking parameters were acquired from earlier studies [ 26 , 27 ]. The information on ATP binding site was assumed from reported literatures [ 8 , 19 , 51 ].…”

“…In order to study the in vivo relevance of NLR proteins the zebrafish model has been increasingly used [ 24 , 25 ]. Previously, we have predicted the interaction between bacterial PGNs (iE-DAP and MDP) with zebrafish NOD1 (zNOD1) and zNOD2-LRRs [ 26 , 27 ].…”

POP1 might be recruiting its type‐Ia interface for NLRP3‐mediated PYD‐PYD interaction: Insights from MD simulation

“…The functional roles of NLRs depend significantly on their dynamic behavior and conformational states. In this context, MD simulation paves the way in understanding the dynamic aspects of protein structure and the governing biomolecular interactions (either with drug molecules, downstream proteins, or pathogenic ligands) in an important signaling pathway . Although the computational predictions are reliable in envisaging the functional aspects of biological macromolecules (the arbitrated biochemical interactions), the accuracy of prediction depends on selective algorithm, scoring function, and accessible hardware.…”

“…In this context, MD simulation paves the way in understanding the dynamic aspects of protein structure and the governing biomolecular interactions (either with drug molecules, downstream proteins, or pathogenic ligands) in an important signaling pathway. 36,[39][40][41][42] Although the computational predictions are reliable in envisaging the functional aspects of biological macromolecules (the arbitrated biochemical interactions), the accuracy of prediction depends on selective algorithm, scoring function, and accessible hardware. Moreover, the initial conformation of protein structure or, protein-counterpart complex also plays an imperative role in governing the biomolecular interactions.…”

Molecular cloning, GTP recognition mechanism and tissue-specific expression profiling of myxovirus resistance (Mx) protein in Labeo rohita (Hamilton) after Poly I:C induction

“…We have truncated the modeled Mx protein and the N-terminal GTPase (G) domain that binds and hydrolyzes GTP (40–313 aa) was employed to get the starting structure GTPase-GTP staring structure. The parameters and procedure of MD were adopted from our previous studies 79,80 . To investigate the intrinsic dynamics stability, conformational flexibility and of the mode of GTP binding the GTPase domain and GTPase-GTP ligand systems were subjected to 100 ns molecular dynamics simulations in explicit water model using AMBER99Sb force field GROMACSv5.1 81 package.…”