An in silico approach for screening non-synonymous SNPs in Mycobacterium tuberculosis PPE68 protein and impact on structure

PPE68 has been implicated through computational methods in ethambutol (EMB) resistance, plausibly through gene-gene interactions with embA. The interest of the current study was to use in silico approaches to gain insights into the effects of mutations on the structure and function of PPE68. Drug-resistant clinical isolate sequences from the NCBI Database were studied. PPE68 missense nsSNPs were analysed using bioinformatics tools. Isolated sequences which harboured mutations that could be key in driving a drug-resistant phenotype were selected for structural modelling and molecular dynamics simulations- mutations likely occurring in conserved regions of the N-terminal domain, including A26T/Q92K, L163F/L167R, L167P, L167R and E44G. The 83 sequences that were aligned exhibited some clustering with an interest on the variants A26T/Q92K, L167P, L167R and L163F/L167R appearing to cluster together, with the exception of E44G. There was a significant shift in the conformation of the mutants with A26T/Q92K (9.99 ± 2.05 Å) and L167P (10.03 ± 2.14 Å), undergoing the greatest change. L163F/L167R and A26T/Q92K displayed the most stability, whilst being the most loosely packed. This is in contrast to the unstable E44G, L167P and L167R which were more compact than the wildtype. Considering that the PPE family of proteins are highly disordered in their native form and presumably in their most stable conformation, these outcomes are conceivable.