Structural localization of pathogenic mutations in the central nucleotide-binding domain (NBD) of nucleotide-binding oligomerization domain-2 (NOD2) protein and their inference in inflammatory disorders.

The human NBD domain which is centrally located in the NOD2 protein displays an essential role in oligomerization and initiates the immune response via CARD-RIPK2 interaction. The mutations associated with the NBD domain have been largely implicated in inflammatory disorders such as Blau syndrome and sarcoidosis. This study aims to determine the structural and phenotypic effect of a lethal mutation that occurs in the NBD domain which has an axiomatic impact on protein dysfunction. Initially, the most deleterious missense mutations were screened through various in silico analysis. Out of 33 variants, I-Mutant 3.0, SIFT, PolyPhen 2, Align GVGD, PHD SNP and SNP&GO have statistically identified 5 variants (R42W, D90E, E91K, G189D & W198L) as less stable, deleterious and damaging. Our predicted models have paved the way to understand the various structural properties such as physiochemical, secondary structural arrangements and stabilizing residues in folding associated with the native and mutant NBD domain especially of the functionally important regions. From the aforementioned results, R42W and G189D were found to be the more predominant among the mutants. Precisely, through molecular simulation, we have strongly justified the significant conformational disruption of R42W and G189D through the stabilization factors, folding and essential dynamics. Conclusively, these regions (α341-44, α13185-191 and ß6133-143ß7) seem to adopt such structures that are not conducive to wild-type-like functionality. Our prediction and validation of lethal mutations based on structural stability may be useful for conducting experimental studies in detail to uncover the protein deregulation leading to inflammatory disorders.

Differentially expressed gene (DEG) based protein-protein interaction (PPI) network identifies a spectrum of gene interactome, transcriptome and correlated miRNA in nondisjunction Down syndrome.

Down syndrome, a genetic disorder of known attribution reveals several types of brain abnormalities resulting in mental retardation, inadequacy in speech and memory. In this study, we have presented a consolidative network approach to comprehend the intricacy of the associated genes of Down syndrome. In this analysis, the differentially expressed genes (DEG's) were identified and the central networks were constructed as upregulated and downregulated. Subsequently, GNB5, CDC42, SPTAN1, GNG2, GNAZ, PRKACB, SST, CD44, FGF2, PHLPP1, APP, and FYN were identified as the candidate hub genes by using topological parameters. Later, Fpclass a PPI tool identified WASP gene, a co-expression interacting partner with highest network topology. Moreover, an enhanced enrichment pathway namely Opioid signaling was obtained using ClueGo, depicting the roles of the hub genes in signaling and neuronal mechanisms. The transcriptional regulatory factors and the common miRNA connected to them were identified by using MatInspector and miRTarbase. Later, a regulatory network constructed showed that PLAG, T2FB, CREB, NEUR, and GATA were the most commonly connected transcriptional factors and hsa-miR-122-5p was the most prominent miRNA. In a nutshell, these hub genes and the enriched pathway could help understand at a molecular level and eventually used as therapeutic targets for Down syndrome.