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 = k(obs)[Probe](alpha), for scaling the progress of proteome-wide reactions and use the scaling factor (0 <= alpha <= 1) as an apparent, partial order with respect to the probe to measure the "enzyme-likeness" for a protein in reaction acceleration. Thus, alpha reports the intrinsic reactivity of the protein with the probe. When alpha = 0, the involved protein expedites the reaction to the maximal degree; when alpha = 1, the protein reacts with the probe via an unaccelerated, bimolecular reaction. The selectivity (beta) of the probe reacting with two proteins is calculated as a ratio of conversion factors (k(obs) values) for corresponding power equations. A combination of alpha and beta provides a tiered system for quantitatively assessing the probe efficacy; an ideal probe exhibits high reactivity with its protein targets (low in alpha) and is highly selective (high in beta) 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 beta-lactone.