Computational analysis of missense variants in MMP2 gene linked with Winchester syndrome and Nodulosis-Arthropathy-Osteolysis reveals structural shift in protein-protein and protein-ligand complexes

Biological significance and pathophysiological role of Matrix Metalloproteinases in the Central Nervous System

Matrix Metalloproteinases (MMPs), which are endopeptidase reliant on zinc, are low in embryonic tissues but increases in response to a variety of physiological stimulus and pathological stresses. Neuro-glial cells, endothelial cells, fibroblasts, and leucocytes secrete MMPs, which cleave extracellular matrix proteins in a time-dependent manner. MMPs affect synaptic plasticity and the development of short-term memory by controlling the size, shape, and excitatory synapses' function through the lateral diffusion of receptors. In addition, MMPs influence the Extracellular Matrix proteins in the Peri-Neuronal Net at the Neuro-glial interface, which aids in the establishment of long-term memory. Through modulating neuronal, and glial cells migration, differentiation, Neurogenesis, and survival, MMPs impact brain development in mammals. In adult brains, MMPs play a beneficial role in physiological plasticity, which includes learning, memory consolidation, social interaction, and complex behaviors, by proteolytically altering a wide variety of factors, including growth factors, cytokines, receptors, DNA repair enzymes, and matrix proteins. Additionally, stress, depression, addiction, hepatic encephalopathy, and stroke may all have negative effects on MMPs. In addition to their role in glioblastoma development, MMPs influence neurological diseases such as epilepsy, schizophrenia, autism spectrum disorder, brain damage, pain, neurodegeneration, and Alzheimer's and Parkinson's. To help shed light on the potential of MMPs as a therapeutic target for neurodegenerative diseases, this review summarizes their regulation, mode of action, and participation in brain physiological plasticity and pathological damage. Finally, by employing different MMP-based nanotools and inhibitors, MMPs may also be utilized to map the anatomical and functional connectome of the brain, analyze its secretome, and treat neurodegenerative illnesses.

Computational analysis of sodium-dependent phosphate transporter SLC20A1/PiT1 gene identifies missense variations C573F, and T58A as high-risk deleterious SNPs

SLC20A1/PiT1 is a sodium-dependent inorganic phosphate transporter, initially recognized as the retroviral receptor for Gibbon Ape Leukemia Virus in humans. SNPs in SLC20A1 is associated with Combined Pituitary Hormone Deficiency and Sodium Lithium Counter transport. Using in silico techniques, we have screened the nsSNPs for their deleterious effect on the structure and function of SLC20A1. Screening with sequence and structure-based tools on 430 nsSNPs, filtered 17 nsSNPs which are deleterious. To evaluate the role of these SNPs, protein modeling and MD simulations were performed. A comparative analysis of model generated with SWISS-MODEL and AlphaFold shows that many residues are in the disallowed region of Ramachandran plot. Since SWISS-MODEL structure has a 25-residue deletion, the AlphaFold structure was used to perform MD simulation for equilibration and structure refinement. Further, to understand perturbation of energetics, we performed in silico mutagenesis and ΔΔG calculation using FoldX on MD refined structures, which yielded SNPs that are neutral (3), destabilizing (12) and stabilizing (2) on protein structure. Furthermore, to elucidate the impact of SNPs on structure, we performed MD simulations to discern the changes in RMSD, Rg, RMSF and LigPlot of interacting residues. RMSF profiles of representative SNPs revealed that A114V (neutral) and T58A (positive) were more flexible & C573F (negative) was more rigid compared to wild type, which is also reflected in the changes in number of local interacting residues in LigPlot and ΔΔG. Taken together, our results show that SNPs can lead to structural perturbations and impact the function of SLC20A1 with potential implications for disease.Communicated by Ramaswamy H. Sarma.

In-silico analysis unravels the structural and functional consequences of non-synonymous SNPs in the human IL-10 gene

Background

Interleukin-10 (IL-10) is an anti-inflammatory cytokine that affects different immune cells. It is also associated with the stimulation of the T and B cells for the production of antibodies. Several genetic polymorphisms in the IL-10 gene have been reported to cause or aggravate certain diseases like inflammatory bowel disease, rheumatoid arthritis, systemic sclerosis, asthma, etc. However, the disease susceptibility and abnormal function of the mutated IL-10 variants remain obscure.

Results

In this study, we used seven bioinformatics tools (SIFT, PROVEAN, PMut, PANTHER, PolyPhen-2, PHD-SNP, and SNPs&GO) to predict the disease susceptible non-synonymous SNPs (nsSNPs) of IL-10. Nine nsSNPs of IL-10 were predicted to be potentially deleterious: R42G, R45Q, F48L, E72G, M95T, A98D, R125S, Y155C, and I168T. Except two, all of the putative deleterious mutations are found in the highly conserved region of IL-10 protein structure, thus affecting the protein's stability. The 3-D structure of mutant proteins was modeled by project HOPE, and the protein–protein interactions were assessed with STRING. The predicted nsSNPs: R42Q, R45Q, F48L, E72G, and I168T are situated in the binding site region of the IL-10R1 receptor. Disruption of binding affinity with its receptor leads to deregulation of the JAK-STAT pathway and results in enhanced inflammation that imbalance in cellular signaling. Finally, Kaplan–Meier Plotter analysis displayed that deregulation of IL-10 expression affects gastric and ovarian cancer patients' survival rate. Thus, IL-10 could be useful as a potential prognostic marker gene for some cancers.

Conclusion

This study has determined the deleterious nsSNPs of IL-10 that might contribute to the malfunction of IL-10 protein and ultimately lead to the IL-10 associated diseases.