A reanalysis of protein tyrosine phosphatases inhibitory studies using the unnatural substrate analogue p-nitrophenyl phosphate

The determination of inhibition mode is extremely important in the understanding of drug interactions and biological mechanisms. The data presented by Hjortness et al. in their recent papers [1,2] on the inhibition of various Protein Tyrosine Phosphatases addresses this issue in an exemplary manner, determining the mode of inhibition based on global fitting of the data to multiple models of inhibition. However, Protein Tyrosine Phosphatases are known to undergo substrate induced conformational changes, so inhibition models which are based on enzyme that adhere to Michaelis-Menten single substrate kinetics may not be appropriate for examining these interactions. To examine the appropriateness of these models, the reported raw data was examined using a recently developed template for global data fitting in Excel. Based on the sum of squared residuals this analysis demonstrates that the excel template was able to match or improve on the reported fittings and demonstrates that a better fit can be achieved with a model that takes into account p-nitrophenyl phosphate-based substrate activation. Whether the substrate activation observed with this model substrate has physiological relevance is debatable, however, it does correspond to the known conformational rearrangement these enzymes undergo when working on their larger peptide substrates.