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Wnt1 is the first mammalian Wnt gene, which is discovered as proto-oncogene and in human the gene is located on the chromosome 12q13. Mutations in Wnt1 are reported to be associated with various cancers and other human diseases. The structural and functional consequences of most of the non-synonymous SNPs (nsSNPs), present in the human Wnt1 gene, are not known. In the present work, extensive bioinformatics analyses are used to screen 292 nsSNPs of Wnt1 for predicting pathogenic and harmless polymorphisms. We have identified 10 highly deleterious nsSNPs among which 7 are located within the highly conserved areas. These 10 nsSNPs are also predicted to affect the post-translational modifications of Wnt1. Further, structure based stability analyses of these 10 highly deleterious nsSNPs revealed 8 variants as highly destabilizing. These 8 highly destabilizing variants were shown to have high BC score and high RMSIP score from normal mode analyses. Based on the deformation energies, obtained from the normal mode analyses, variants like G169A, G169S, G331R and G331S were found to be unstable. Molecular Dynamics (MD) simulations revealed structural stability and fluctuation of WT Wnt1 and its prioritized variants. RMSD remained fluctuating mostly between 4 and 5 Å and occasionally between 3.5 and 5.5 Å ranges. RMSF in the CTD region (residues 330–360) of the binding pocket were lower compared to that of WT. Studying the impacts of nsSNPs on the binding interface of Wnt1 and seven Frizzled receptors have predicted substitutions which can stabilize or destabilize the binding interface. We have found that Wnt1 and FZD8-CRD is the best docked complex in our study. MD simulation based analyses of wild type Wnt1-FZD8-CRD complex and the 8 prioritized variants revealed that RMSF was higher in the unstructured regions and RMSD remained fluctuating in the region of 5 Å ± 1 Å. We have also observed differential Wnt1 gene expression pattern in normal, tumor and metastatic conditions across different tissues. Wnt1 gene expression was significantly higher in metastatic tissues of lungs, colon and skin; and was significantly lower in metastatic tissues of breast, esophagus and kidney. We have also found that Wnt1 deregulation is associated with survival outcome in patients with gastric and breast cancer. Furthermore, these computationally screened highly deleterious nsSNPs of Wnt1 can be analyzed in population based genetic studies and may help understand the Wnt1 associated diseases. [ABSTRACT FROM AUTHOR]

The importance of metacaspases in programmed cell death and tissue differentiation is known, but their significance in disease stress response, particularly in a crop plant, remained enigmatic. We show the tomato metacaspase expression landscape undergoes differential reprogramming during biotrophic and necrotrophic modes of pathogenesis; also, the metacaspase activity dynamics correlate with the disease progression. These stresses have contrasting effects on the expression pattern of SlMC8, a Type II metacaspase, indicating that SlMC8 is crucial for stress response. In accordance, selected biotic stress-related transcription factors repress SlMC8 promoter activity. Interestingly, SlMC8 exhibits maximum proteolysis at an acidic pH range of 5–6. Molecular dynamics simulation identified the low pH-driven protonation event of Glu246 as critical to stabilize the interaction of SlMC8 with its substrate. Mutagenesis of Glu246 to charge-neutral glutamine suppressed SlMC8's proteolytic activity, corroborating the importance of the amino acid in SlMC8 activation. The glutamic acid residue is found in an equivalent position in metacaspases having acidic pH dependence. SlMC8 overexpression leads to heightened ROS levels, cell death, and tolerance to Pst DC3000, and SlMC8 repression reversed the phenomena. However, the overexpression of SlMC8 increases tomato susceptibility to necrotrophic Alternaria solani. We propose that SlMC8 activation due to concurrent changes in cellular pH during infection contributes to the basal resistance of the plant by promoting cell death at the site of infection, and the low pH dependence acts as a guard against unwarranted cell death. Our study confirms the essentiality of a low pH-driven Type II metacaspase in tomato biotic stress-response regulation. • Pathogens differently modulate tomato metacaspase activity and expression landscape. • The SlMC8 transcript expression depends on the mode of pathogenesis of the microbe. • SlMC8 is acidic pH-activable, and protonation of conserved Glu246 is integral to the activation. • SlMC8 contributes to ROS accumulation and promotes cell death. • Altered SlMC8 expression has a profound effect on disease outcome. [ABSTRACT FROM AUTHOR]

Bcl-2, the prototypic, anti-apoptotic member of Bcl-2 family possesses a long Intrinsically Disordered Region (IDR) of more than sixty amino acid residues. In spite of a number of experimental evidences on the influence of IDR to regulate the function of the protein, the molecular basis is not yet established. The present work with ~8µs conformational sampling of Bcl-2, using molecular dynamics in all atom description, offers a molecular mechanistic insight into the communication between the IDR and the structured region. The results indicate a highly significant role of the IDR in controlling the movements of the atoms which form the primary binding site. Although the influence of the IDR of the wild type Bcl-2 on its structured region, especially on the binding site, seems to be ordinary, but the hidden pathway of communication gets elucidated as the perturbation due to single-site phosphorylation on S70 works as a marker of the path; the contrast brought by the data obtained after truncating the IDR highlights it further. In wild type Bcl-2, apparently there is no direct communication between the IDR and binding site. But in the phosphorylated system, a communication channel between the IDR and the binding site has been established, as evidenced from the network analysis, which results in an increased correlation between the binding pocket residues and that redistributs the sampling of conformations of the system; one of the major consequences of these changes is witnessed in its enhanced affinity for binding with its partner Bax. [Display omitted] • The path and mechanism of communication between the IDR and the structured region of Bcl2 is elucidated. • The impact of modifications on IDR, e.g. deletion, phosphorylation significantly alter the conformational sampling of Bcl2. • The alterations in the intrinsic dynamics upon IDR modifications may favour partner binding, with implications on functions. [ABSTRACT FROM AUTHOR]