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

Publication date: Available online 17 January 2020Source: Computational and Structural Biotechnology JournalAuthor(s): Sundeep Chaitanya Vedithi, Carlos H.M. Rodrigues, Stephanie Portelli, Marcin J. Skwark, Madhusmita Das, David B. Ascher, Tom L Blundell, Sony MalhotraAbstractRifampin resistance in leprosy may remain undetected due to the lack of rapid and effective diagnostic methods. A quick and reliable method is essential to determine the impacts of emerging detrimental mutations. The functional consequences of missense mutations within the β-subunit of RNA polymerase (RNAP) in Mycobacterium leprae (M. leprae) contribute to phenotypic rifampin resistance outcomes in leprosy. Here we report in-silico saturation mutagenesis of all residues in the β-subunit of RNAP to all other 19 amino acid types and predict their impacts on overall thermodynamic stability, on interactions at subunit interfaces, and on β-subunit-RNA and rifampin affinities (only for the rifampin binding site) using state-of-the-art structure, sequence and normal mode analysis-based 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 residue-depth (the extent to which a residue is buried in the protein structure space) of the mutant residues. The mutations at residues S437, G459, H451, P489, K884 and ...
Source: Computational and Structural Biotechnology Journal - Category: Biotechnology Source Type: research