title: 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.
authors.affiliation: Biotechnology Laboratory, Central Inland Fisheries Research Institute, Barrackpore, Kolkata-700120, West Bengal, India. jitued@gmail.com.
authors.forename: Jitendra
authors.initials: J
authors.lastname: Maharana
authors.forename: Bikash Ranjan
authors.initials: BR
authors.lastname: Sahoo
authors.forename: Aritra
authors.initials: A
authors.lastname: Bej
authors.forename: Mahesh Chandra
authors.initials: MC
authors.lastname: Patra
authors.forename: Budheswar
authors.initials: B
authors.lastname: Dehury
authors.forename: Gopal Krushna
authors.initials: GK
authors.lastname: Bhoi
authors.forename: Santosh Kumar
authors.initials: SK
authors.lastname: Lenka
authors.forename: Jyoti Ranjan
authors.initials: JR
authors.lastname: Sahoo
authors.forename: Ajaya Kumar
authors.initials: AK
authors.lastname: Rout
authors.forename: Bijay Kumar
authors.initials: BK
authors.lastname: Behera
mesh_terms: D000595:Amino Acid Sequence; D000818:Animals; D001665:Binding Sites; D017124:Conserved Sequence; D003960:Diaminopimelic Acid / Q000031:analogs & derivatives* / Q000737:chemistry / Q000378:metabolism; D006801:Humans; D056004:Molecular Dynamics Simulation; D053474:Nod1 Signaling Adaptor Protein / Q000737:chemistry* / Q000378:metabolism*; D011485:Protein Binding; D017433:Protein Structure, Secondary; D015398:Signal Transduction; D015027:Zebrafish / Q000378:metabolism*; D029961:Zebrafish Proteins / Q000737:chemistry* / Q000378:metabolism*
chemical_list: C000598686:NOD1 protein, zebrafish; D053474:Nod1 Signaling Adaptor Protein; D029961:Zebrafish Proteins; D003960:Diaminopimelic Acid; C034331:N(2)-(gamma-D-glutamyl)-meso-2,2'-diaminopimelic acid