Chemoproteomics has enabled the rapid and proteome-wide discovery of functional, redox-sensitive, and ligandable cysteine residues. Despite widespread adoption and considerable advances in both sample-preparation workflows and MS instrumentation, chemoproteomics experiments still typically only identify a small fraction of all cysteines encoded by the human genome. Here, we develop an optimized sample-preparation workflow that combines enhanced peptide labeling with singlepot, solid-phase-enhanced sample-preparation (SP3) to improve the recovery of biotinylated peptides, even from small sample sizes. By combining this improved workflow with on-line highfield asymmetric waveform ion mobility spectrometry (FAIMS) separation of labeled peptides, we achieve unprecedented coverage of > 14000 unique cysteines in a single-shot 70 min experiment. Showcasing the wide utility of the SP3-FAIMS chemoproteomic method, we find that it is also compatible with competitive small-molecule screening by isotopic tandem orthogonal proteolysis-activity-based protein profiling (isoTOP-ABPP). In aggregate, our analysis of 18 samples from seven cell lines identified 34225 unique cysteines using only~28 h of instrument time. The comprehensive spectral library and improved coverage provided by the SP3-FAIMS chemoproteomics method will provide the technical foundation for future studies aimed at deciphering the functions and druggability of the human cysteineome.

Responsive 1,2-dioxetane chemiluminescent probes have been developed that display instantaneous, sensitive, and selective responses to H2S and are capable of imaging H2S in living mice.

Within the accompanying paper (Reger, A. S, Wu, R., Dunaway-Mariano, D. and Gulick, A. M. (2008) Crystallographic trapping of a 140° domain movement in the two-step reaction catalyzed by 4 chlorobenzoate:CoA ligase. Biochemistry) we reported the X-ray structure of 4-chlorobenzoate: CoA ligase (CBL) bound with 4-chlorobenzoyl-adenylate (4-CB-AMP) and the X-ray structure of CBL bound with 4-chlorophenacyl-CoA (4-CP-CoA) (an inert analog of the product 4-chlorobenzoyl-coenzyme A (4-CB-CoA)) and AMP. These structures defined two CBL conformational states. In conformation 1, CBL is poised to catalyze the adenylation of 4-chlorobenzoate (4-CB) with ATP (partial reaction 1) and in conformation 2, CBL is poised to catalyze the formation of 4-CB-CoA from 4-CB-AMP and CoA (partial reaction 2). These two structures showed that, by switching from conformation 1 to conformation 2, the cap domain rotates about the domain linker and thereby changes its interface with the N-terminal domain. The present work was carried out to determine the contributions made by each of the active site residues in substrate/cofactor binding and catalysis, and also to test the role of domain alternation in catalysis. In this paper, we report the results of steady-state kinetic and transient state kinetic analysis of wild-type CBL and of a series of site-directed CBL active site mutants. The major findings are as follows. First, wild-type CBL is activated by Mg+2 (a 12 to 75-fold increase in activity is observed depending on assay conditions) and its kinetic mechanism (ping-pong) supports the structure-derived prediction that PPi dissociation must precede the switch from conformation 1 to conformation 2 and therefore, CoA binding. Also, transient kinetic analysis of wild-type CBL identified the rate-limiting step of the catalyzed reaction as one that follows the formation of 4-CB-CoA (viz. CBL conformational change and/or product dissociation). The single turnover rate of 4-CB and ATP to form 4-CB-AMP and PPi (k= 300 s−1) is not effected by the presence of CoA, and it is ~3-fold faster than the turnover rate of 4-CB-AMP and CoA to form 4-CB-CoA and AMP (k= 120 s−1). Second, the active site mutants screened via steady-state kinetic analysis, were ranked based on the degree of reduction observed in any one of the substrate kcat/Km values, and those scoring higher than a 50-fold reduction in kcat/Km value were selected for further evaluation via transient state kinetic analysis. The single-turnover time courses, measured for the first partial reaction, and then for the full reaction, were analyzed to define the microscopic rate constants for the adenylation reaction and the thioesterification reaction. Based on our findings we propose a catalytic mechanism that centers on a small group of key residues (some of which serve in more than one role) and that includes several residues that function in domain alternation.