Computational saturation mutagenesis to predict structural consequences of systematic mutations in the beta subunit of RNA polymerase in Mycobacterium leprae

• DOI: 10.1016/j.csbj.2020.01.002
• Publication Date: 2020-01-17T16:43:49Z
• Authors: Sundeep Chaitanya...; Carlos H.M. Rodri...; Stephanie Portelli; Marcin J. Skwark; Madhusmita Das; David B. Ascher; Tom L. Blundell; Sony Malhotra
• Keywords: Saturated mutagenesis; Mycobacterium leprae

Rifampin resistance in leprosy may remain undetected due to the lack of rapid and effective diagnostic tools. A quick reliable method is essential determine impacts emerging detrimental mutations drug targets. The functional consequences missense β-subunit RNA polymerase (RNAP) Mycobacterium leprae (M. leprae) contribute phenotypic rifampin leprosy. Here, we report in-silico saturation mutagenesis all residues RNAP other 19 amino acid types (generating 21,394 for 1126 residues) predict their on overall thermodynamic stability, interactions at subunit interfaces, β-subunit-RNA affinities (only binding site) using state-of-the-art structure, sequence normal mode analysis-based methods. Mutations conserved that line active-site cleft show largely destabilizing effects, resulting increased relative solvent accessibility a concomitant decrease residue-depth (the extent which residue buried protein structure space) mutant residues. positions S437, G459, H451, P489, K884 H1035 are identified as extremely they induce highly effects nucleic affinities. Destabilizing were predicted clinically/experimentally rifampin-resistant M. indicating this model can be used surveillance tool monitor destabilise RNAP-rifampin confer leprosy.The emergence primary secondary growing concern poses threat control elimination measures globally. In absence an in-vitro system detect leprosy, diagnosis mainly relies presence determining regions rpoB gene encodes leprae. Few labs world perform mouse food pad propagation drugs (rifampin) growth patterns confirm resistance, however duration these methods lasts from 8 12 months making them impractical diagnosis. Understanding molecular mechanisms vital associating clinically detected Here propose approach comprehensively elucidate structural implications any exist or arise Most not occur fitness costs but information thus generated by help decipher across conversely enable identification stable least impacted (mutation coolspots) potential choice small molecule guided discovery.