Know the kinetic mechanism of your modifier
In the study of enzyme-modifiers, the identification of a particular mechanism of action implies that the experimenter is conversant with the palette of all interactions that can occur between enzymes, substrates, inhibitors and activators.
Before starting with properly designed measurements aimed at gathering new data, one should be prepared to master not only expected but also apparently odd results. As an example, inhibition at low substrate concentration can first disappear and then turn into net activation just by increasing the substrate concentration while the modifier concentration remains constant.
This page describes the classification of kinetic mechanisms on the basis of intrinsic properties of the interactions between enzymes, modifiers and substrates, which logically lead to the systematics of inhibition and activation as
Systematics = Taxonomy + Nomenclature
The two subsections herein will describe the properties of the basic modifier mechanisms
In the pages of this website, with the exception of ‘Published examples’, the variables will be shown without units for practical reasons, but they will be maintained consistent throughout. The table below lists the symbols, their meaning and the default units.
| Symbols | Description | Units |
|---|---|---|
| app | as superscript to a parameter = apparent value in the presence of modifier | - |
| [E], [S], [X] | Free concentrations of enzyme, substrate and modifier, respectively | μM |
| Km | Michaelis constant | μM |
| KX | Inhibition or activation dissociation constant of the modifier | μM |
| kcat | Catalytic constant | s−1 |
| kcat/Km | Specificity constant | µM−1s−1 |
| Km/kcat | Reciprocal specificity constant | µM s |
| v0 | Initial velocity in the absence of modifier | µM s−1 |
| vX | Initial velocity in the presence of modifier | µM s−1 |
| v | Generic initial velocity | µM s−1 |
| v/[E]t | Initial velocity divided by the total, titrated enzyme active site concentration | s−1 |
| σ = [S]/Km | Normalized substrate concentration | pure number |
| σ/(1+σ) | Specific velocity | pure number |
| α | Reciprocal allosteric coupling constant | pure number |
| β | Factor by which the modifier affects the catalytic constant | pure number |