Molecular dynamics simulation analysis
To understand the effect of mutations in277NPDKV281and200DGGGR204 motifs on the
structure and function of RpoE10, the RpoE10 model was subjected toin silico substitution of200DGG202 to AAA and278PDK280 to AAA to generate
RpoE10(Mut1) RpoE10(Mut2) models, respectively. Furthermore, we carried
out an 800 ns MD simulation study to evaluate the effect of these
mutations and partial deletion of SnoaL_2 domain on the overall
conformational dynamics, structural stability, compactness of domains,
and structural features conferring the enhancement/elimination of
promoter activation. According to our simulation studies, the two most
common measures of structural fluctuations, root-mean-square deviation
(RMSD) and root-mean-square fluctuation (RMSF), and a measure of
compactness (radius of gyration, i.e., Rg) explain the structural
effects caused due to mutations in the NPDKV and DGGGR motifs, and its
impact on promoter activation.