β-hexosaminidase A (HexA) protein is responsible for the degradation of GM2 gangliosides in the central and peripheral nervous systems. Tay-Sachs disease occurs when HexA within Hexosaminidase does not properly function and harmful GM2 gangliosides begin to build up within the neurons. In this study, in silico methods such as SIFT, PolyPhen-2, PhD-SNP, and MutPred were utilized to analyze the effects of nonsynonymous single nucleotide polymorphisms (nsSNPs) on HexA in order to identify possible pathogenetic and deleterious variants. Molecular dynamics (MD) simulations showed that two mutants, P25S and W485R, experienced an increase in structural flexibility compared to the native protein. Particularly, there was a decrease in the overall number and frequencies of hydrogen bonds for the mutants compared to the wildtype. MM/GBSA calculations were performed to help assess the change in binding affinity between the wildtype and mutant structures and a mechanism-based inhibitor, NGT, which is known to help increase the residual activity of HexA. Both of the mutants experienced a decrease in the binding affinity from -23.8 kcal/mol in wildtype to -20.9 and -18.7 kcal/mol for the P25S and W485R variants of HexA, respectively.
Keywords: MM/GBSA; MutPred; NAG-thiazoline (NGT); PhD-SNP; PolyPhen-2; SIFT; Tay-Sachs disease (TSD); binding affinity; hydrogen bonding; molecular dynamic simulation; nonsynonymous single nucleotide polymorphism (nsSNP); β-hexosaminidase A (HexA).
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