Deep, S. | bioRxiv Science

bioRxiv2023

Biophysical Characterization and Interaction study of WhiB6 Protein of Mycobacterium tuberculosis with Nucleic Acid

Tuberculosis is an intractable disease because of the peculiar nature of the virulent properties of Mycobacterium tuberculosis. The WhiB6 protein, a transcriptional regulator, plays a crucial role in the virulence systems of Mtb. It regulates the expression of genes essential for the virulence pathways by binding to their promoter region; espA is one such gene. Herein, we have used biophysical methods, including steady-state intrinsic fluorescence spectroscopy, circular dichroism spectroscopy, Isothermal titration calorimetry (ITC), and Surface-Enhanced Raman Spectroscopy (SERS) to understand the interaction of WhiB6 protein with espA promoter DNA. For the first time, we report the conformational details and biophysical parameters related to the WhiB6-espA promoter DNA interaction. WhiB6 binds the DNA with moderate affinity, as revealed by ITC. CD and SERS studies suggest subtle perturbation in the secondary conformation of the protein on binding to the DNA. SERS provided detailed structural insights into the WhiB6 protein and the amino acids involved in the interaction, which could be harnessed to find suitable inhibitors of the protein-DNA interaction. Preventing the binding of WhiB6 with promoter DNA of the virulence genes can hinder the functioning of Mtb and hence can act as an effective therapeutic intervention for tuberculosis.

biochemistry↗

bioRxiv2020

pH Effect on the Dynamics of SARS-CoV-2 Main Protease (Mpro)

The SARS-CoV-2 main protease (Mpro) is a crucial enzyme responsible for the maturation of novel coronavirus, thus it serves as an excellent target for drug discovery. SARS-CoV-2 is found to have similarity with SARS-CoV, which showed conformational changes upon varying pH. There is no study till date on how pH change affect the conformtional flexibilty of SARS-CoV-2 Mpro, therefore, we attempt to find the effect of pH variation through constant pH molecular dynamics simulation studies. Protein is found to be most stable at neutral pH and as pH turns basic protein structure becomes most destabilized. Acidic pH also tends to change the structural properties of Mpro. Our study provides evidence that the flexibility of Mpro is pH dependent like SARS-CoV Mpro.

biophysics↗