Scaling Proteome-Wide Reactions of Activity-Based Probes

Unified analysis
of complex reactions of an activity-based probe
with proteins in a proteome remains an unsolved challenge. We propose
a power expression, rate = kobs[Probe]α, for scaling the progress of proteome-wide reactions
and use the scaling factor (0 ≤ α ≤ 1) as an apparent,
partial order with respect to the probe to measure the “enzyme-likeness”
for a protein in reaction acceleration. Thus, α reports the
intrinsic reactivity of the protein with the probe. When α =
0, the involved protein expedites the reaction to the maximal degree;
when α = 1, the protein reacts with the probe via an unaccelerated,
bimolecular reaction. The selectivity (β) of the probe reacting
with two proteins is calculated as a ratio of conversion factors (kobs values) for corresponding power equations.
A combination of α and β provides a tiered system for
quantitatively assessing the probe efficacy; an ideal probe exhibits
high reactivity with its protein targets (low in α) and is highly
selective (high in β) in forming the probe–protein adducts.
The scaling analysis was demonstrated using proteome-wide reactions
of HT-29 cell lysates with a model probe of threonine β-lactone.