PhoQ serves as the sensor protein in the PhoQ/PhoP two-component system found in bacteria, which plays a vital role in detecting environmental signals such as magnesium levels, antimicrobial peptides, pH levels, and fatty acids, impacting bacterial virulence. By combining AlphaFold2 predictions with molecular modeling and Molecular Dynamics (MD) simulations, we identified three PhoQ conformations (phoq_af, phoq_c, phoq_hybrid). One conformation suggests a repressed state with Mg2+ linking the sensor domain to the membrane (phoq_c), while another indicates significant hydration (phoq_hybrid), implying water-mediated conformational changes during signaling. These insights not only illuminate PhoQ activation but also provide valuable information on histidine kinase signaling mechanisms, offering potential for developing new therapeutics targeting bacterial modulation.
Each Folder contains:
- Tcl Scripts used to extract information from simulations
- Outputs folder with the raw data extracted from the simulations
- Python and Jupyter-notebooks to plot and analyze the data
Data: 10.5281/zenodo.10988292