title: Computational studies on receptor-ligand interactions between novel buffalo (Bubalus bubalis) nucleotide-binding oligomerization domain-containing protein 2 (NOD2) variants and muramyl dipeptide (MDP).
abstract: Nucleotide binding and oligomerization domain 2 (NOD2), a member of intracellular NOD-like receptors (NLRs) family, recognizes the bacterial peptidoglycan, muramyl dipeptide (MDP) and initiates host immune response. The precise ligand recognition mechanism of NOD2 has remained elusive, although studies have suggested leucine rich repeat (LRR) region of NOD2 as the possible binding site of MDP. In this study, we identified multiple transcripts of NOD2 gene in buffalo (buNOD2) and at least five LRR variants (buNOD2-LRRW (wild type), buNOD2-LRRV1-V4) were found to be expressed in buffalo peripheral blood mononuclear cells. The newly identified buNOD2 transcripts were shorter in lengths as a result of exon-skipping and frame-shift mutations. Among the variants, buNOD2-LRRW, V1, and V3 were expressed more frequently in the animals studied. A comparative receptor-ligand interaction study through modeling of variants, docking, and molecular dynamics simulation revealed that the binding affinity of buNOD2-LRRW towards MDP was greater than that of the shorter variants. The absence of a LRR segment in the buNOD2 variants had probably affected their affinity toward MDP. Notwithstanding a high homology among the variants, the amino acid residues that interact with MDP were located on different LRR motifs. The binding free energy calculation revealed that the amino acids Arg850(LRR4) and Glu932(LRR7) of buNOD2-LRRW, Lys810(LRR3) of buNOD2-LRRV1, and Lys830(LRR3) of buNOD2-LRRV3 largely contributed towards MDP recognition. The knowledge of MDP recognition and binding modes on buNOD2 variants could be useful to understand the regulation of NOD-mediated immune response as well as to develop next generation anti-inflammatory compounds.
authors.affiliation: Animal Genomics Lab., Animal Biotechnology Centre, National Dairy Research Institute, Karnal 132001, Haryana, India.
authors.forename: Biswajit
authors.initials: B
authors.lastname: Brahma
authors.affiliation: Animal Genomics Lab., Animal Biotechnology Centre, National Dairy Research Institute, Karnal 132001, Haryana, India.
authors.forename: Mahesh Chandra
authors.initials: MC
authors.lastname: Patra
authors.affiliation: Animal Genomics Lab., Animal Biotechnology Centre, National Dairy Research Institute, Karnal 132001, Haryana, India.
authors.forename: Purusottam
authors.initials: P
authors.lastname: Mishra
authors.affiliation: Animal Genomics Lab., Animal Biotechnology Centre, National Dairy Research Institute, Karnal 132001, Haryana, India.
authors.forename: Bidhan Chandra
authors.initials: BC
authors.lastname: De
authors.affiliation: Animal Genomics Lab., Animal Biotechnology Centre, National Dairy Research Institute, Karnal 132001, Haryana, India.
authors.forename: Sushil
authors.initials: S
authors.lastname: Kumar
authors.affiliation: Department of Bioinformatics, Orissa University of Agriculture and Technology, Bhubaneswar 751003, Odisha, India.
authors.forename: Jitendra
authors.initials: J
authors.lastname: Maharana
authors.affiliation: Animal Genomics Lab., Animal Biotechnology Centre, National Dairy Research Institute, Karnal 132001, Haryana, India.
authors.forename: Ashutosh
authors.initials: A
authors.lastname: Vats
authors.affiliation: Animal Genomics Lab., Animal Biotechnology Centre, National Dairy Research Institute, Karnal 132001, Haryana, India.
authors.forename: Sonika
authors.initials: S
authors.lastname: Ahlawat
authors.affiliation: Animal Genomics Lab., Animal Biotechnology Centre, National Dairy Research Institute, Karnal 132001, Haryana, India.
authors.forename: Tirtha Kumar
authors.initials: TK
authors.lastname: Datta
authors.affiliation: Animal Genomics Lab., Animal Biotechnology Centre, National Dairy Research Institute, Karnal 132001, Haryana, India. Electronic address: sachinandan@ndri.res.in.
authors.forename: Sachinandan
authors.initials: S
authors.lastname: De
mesh_terms: D000119:Acetylmuramyl-Alanyl-Isoglutamine / Q000737:chemistry* / Q000276:immunology; D017398:Alternative Splicing; D000595:Amino Acid Sequence; D000818:Animals; D001665:Binding Sites; D002020:Buffaloes; D005091:Exons; D005786:Gene Expression Regulation; D007438:Introns; D007963:Leukocytes, Mononuclear / Q000166:cytology / Q000276:immunology*; D008024:Ligands; D062105:Molecular Docking Simulation; D056004:Molecular Dynamics Simulation; D009154:Mutation; D053473:Nod2 Signaling Adaptor Protein / Q000737:chemistry* / Q000235:genetics / Q000276:immunology; D009711:Nucleotides / Q000737:chemistry* / Q000276:immunology; D011485:Protein Binding; D054730:Protein Interaction Domains and Motifs; D017433:Protein Structure, Secondary; D012333:RNA, Messenger / Q000235:genetics* / Q000276:immunology; D016415:Sequence Alignment; D013816:Thermodynamics
chemical_list: D008024:Ligands; D053473:Nod2 Signaling Adaptor Protein; D009711:Nucleotides; D012333:RNA, Messenger; D000119:Acetylmuramyl-Alanyl-Isoglutamine
keywords: Buffalo; MDP binding; NOD2; Splicing; Transcript variants