Structural Insights into the Role of Pseudouridimycin Binding in Disruption of Bacterial RNA Polymerase Bridge Helix Conformational Arrangement

Abstract

Background: The bridge helix (BH) is a crucial region in bacterial RNA polymerase (RNAP) catalysis. It plays an essential role in the nucleotide addition cycle (NAC) by performing many modulated rearrangements and conformational changes. Any changes in the bridge helix conformational arrangements could perturb the NAC. Objective: Pseudouridimycin (PUM) was recently reported as a new RNAP inhibitor. However, the crucial role of the bridge helix in the inhibitory activity of PUM remains unclear, hence the aim of this study. Method: The PUM interaction and the structural dynamics of bacterial Bridge Helix upon PUM binding were investigated using various dynamic analysis approaches. Results: Besides establishing the importance of the bridge helix residues in the binding of PUM, the findings of this study revealed that the adjacent binding of PUM induces a stabilized and structurally rigid bridge helix characterized by a reduction of individual residue flexibility, which could interfere with its role in the NAC. In addition, a hydrophobic structural rearrangement of the bridge helix is observed, evidenced by the burial and folding of residues into the hydrophobic core and a switch in the secondary structure of some regions of the bridge helix from the turn and bend to the alpha helix. The observed conformational disruption of the bridge helix upon binding of PUM also accounts for the reported inhibitory prowess and broad-spectrum activity as widely reported. Conclusion: We believe findings from this study will further complement current drug discovery knowledge on disrupting bacterial RNAP machinery.