In this project, we performed a chemical shift perturbation analysis on the Nucleotide-Binding Domain (NBD) of Hsp70. The analysis aimed to investigate the interactions between the Nucleotide-Binding Domain and compound A, a putative inhibitor of chaperone ATPase activity.
Using 1H and 15N chemical shift data recorded in the presence and absence of compound A, we calculated the total chemical shift perturbations (CSPs) for each NBD residue. The CSPs were calculated using the provided equation and considering the differences in proton and nitrogen chemical shifts.
The CSPs were then plotted as a function of residue numbers, and residues with significant CSPs (>0.2 ppm) were identified. The resulting plot can be seen below:
In the plot, the black line represents the CSPs, and the red dashed line indicates the threshold of 0.2 ppm. Residues above this threshold are considered to have significant CSPs.
The observed CSPs provide insights into the binding site(s) and possible mechanism(s) of action for compound A. Further experiments can be conducted to validate these suggestions.