Computational Saturation Mutagenesis to predict structural consequences of systematic mutations on protein stability and rifampin interactions in the β subunit of RNA polymerase inMycobacterium leprae

Abstract

The functional consequences of missense mutations within the  subunit of RNA polymerase in Mycobacterium leprae (M. leprae) contribute to phenotypic rifampin resistance in leprosy. Here we report in-silico saturation mutagenesis of the  subunit of RNA polymerase to all other 19 amino acid types and predicted their impacts on thermodynamic stability, interactions at subunit interfaces,  subunit-RNA and rifampin affinities using state-of-the-art structure, sequence and normal mode analysis methods. A total of 21,394 mutations were analysed, and it was noted that mutations in the conserved residues that line the active-site cleft show largely destabilizing effects, resulting in increased relative solvent accessibility and concomitant decrease in depth of the mutant residues. The mutations at residues S437, G459, H451, P489, K884 and H1035 are identified as extremely detrimental as they induce highly destabilizing effects on stability, nucleic acid and rifampin affinities. Destabilizing effects were predicted for all the experimentally identified rifampin-resistant mutations in M. leprae indicating that this model can be used as a surveillance tool to monitor emerging detrimental mutations conferring rifampin resistance in leprosy.