Mechanisms

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,
but they will be maintained consistent throughout. The table below  lists the symbols, their meaning and the default units.

SymbolsDescriptionUnits
app as superscript to a parameter = apparent value in the presence of modifier-
[E], [S], [X]Free concentrations of enzyme, substrate and modifier, respectivelyμM
KmMichaelis constantμM
KXInhibition or activation dissociation constant of the modifierμM
kcatCatalytic constants−1
kcat/KmSpecificity constantµM−1s−1
Km/kcatReciprocal specificity constantµM s
v0Initial velocity in the absence of modifierµM s−1
vXInitial velocity in the presence of modifierµM s−1
vGeneric initial velocityµM s−1
v/[E]tInitial velocity divided by the total, titrated enzyme active site concentrations−1
σ = [S]/KmNormalized substrate concentrationpure number
σ/(1+σ)Specific velocitypure number
αReciprocal allosteric coupling constantpure number
βFactor by which the modifier affects the catalytic constantpure number