Probing the electron capture dissociation mass spectrometry of phosphopeptides with traveling wave ion mobility spectrometry and molecular dynamics simulations

Electron capture dissociation mass spectrometry offers several advantages for the analysis of peptides, most notably that backbone c and z fragments typically retain labile modifications such as phosphorylation. We have shown previously that, in some cases, the presence of phosphorylation has a deleterious effect on peptide sequence coverage, and hypothesized that intramolecular interactions involving the phosphate group were preventing separation of backbone fragments. In the present work, we seek to rationalize the observed ECD behavior through a combination of ECD of model peptides, traveling wave ion mobility mass spectrometry and molecular dynamics simulations. The results suggest that for doubly protonated ions of phosphopeptide APLpSFRGSLPKSYVK a salt-bridge structure is favored, whereas for the doubly-protonated ions of APLSFRGSLPKpSYVK ionic hydrogen bonds predominate.

Mechanistic consequences of chiral radical clock probes: analysis of the mononuclear non-heme iron enzyme HppE with 2-hydroxy-3-methylenecyclopropyl radical clock substrates

(S)-2-Hydroxypropylphosphonic acid [(S)-HPP] epoxidase (HppE) is a mononuclear iron enzyme that catalyzes the last step in the biosynthesis of the antibiotic fosfomycin. HppE also processes the (R)-enantiomer of HPP but converts it to 2-oxo-propylphosphonic acid. In this study, all four stereoisomers of 3-methylenecyclopropyl-containing substrate analogues, (2R, 3R)-8, (2R, 3S)-8, (2S, 3R)-8, and (2S, 3S)-8, were synthesized and used as radical probes to investigate the mechanism of the HppE-catalyzed reaction. Upon treatment with HppE, (2S, 3R)-8 and (2S, 3S)-8 were converted via a C1 radical intermediate to the corresponding epoxide products, as anticipated. In contrast, incubation of HppE with (2R, 3R)-8 led to enzyme inactivation, and incubation of HppE with (2R, 3S)-8 yielded the 2-keto product. The former finding is consistent with the formation of a C2 radical intermediate, where the inactivation is likely triggered by radical-induced ring cleavage of the methylenecyclopropyl group. Reaction with (2R, 3S)-8 is predicted to also proceed via a C2 radical intermediate, but no enzyme inactivation and no ring-opened product were detected. These results strongly suggest that an internal electron transfer to the iron center subsequent to C-H homolysis competes with ring-opening in the processing of the C2 radical intermediate. The different outcomes of the reactions with (2R, 3R)-8 and (2R, 3S)-8 demonstrate the need to carefully consider the chirality of substituted cyclopropyl groups as radical reporting groups in studies of enzymatic mechanisms.

Label-free quantitative proteomics analysis of antibiotic response in Staphylococcus aureus to oxacillin

Methicillin-resistant Staphylococcus aureus (MRSA) is the leading cause of fatal bacterial infections in hospitals and has become a global health threat. Although the resistance mechanisms of β-lactam antibiotics have been studied for decades, there are few attempts at systems-wide investigations into how the bacteria respond to antibiotic stress. Spectral counting-based label-free quantitative proteomics has been applied to study global responses in MRSA and methicillin-susceptible S. aureus (MSSA) treated with subinhibitory doses of oxacillin, a model β-lactam antibiotic. We developed a simple and easily repeated sample preparation procedure that is effective for extracting surface-associated proteins. On average, 1025 and 1013 proteins were identified at a false discovery rate threshold of 0.01, for the untreated group of MRSA and MSSA. Upon treatment with oxacillin, 81 proteins (65 up-regulated, 16 down-regulated) were shown differentially expressed in MRSA (p < 0.05). In comparison, 225 proteins (162 up-regulated, 63 down-regulated) were shown differentially expressed in oxacillin-treated MSSA. β-Lactamase and penicillin-binding protein 2a were observed up-regulated uniquely in oxacillin-treated MRSA, which is consistent with the known β-lactam resistance mechanisms of S. aureus. More interestingly, the peptidoglycan biosynthesis pathway and the pantothenate and CoA biosynthesis pathway were found to be up-regulated in both oxacillin-treated MRSA and MSSA, and a series of energy metabolism pathways were up-regulated uniquely in oxacillin-treated MSSA. These new data offer a more complete view of the proteome changes in bacteria in response to the antibiotic. This report is the first in using label-free quantitative proteomics to study β-lactam antibiotic responses in S. aureus.

Evidence for radical-mediated catalysis by HppE: a study using cyclopropyl and methylenecyclopropyl substrate analogues

(S)-2-Hydroxypropylphosphonic acid epoxidase (HppE) is an unusual mononuclear iron enzyme that catalyzes the oxidative epoxidation of (S)-2-hydroxypropylphosphonic acid ((S)-HPP) in the biosynthesis of the antibiotic fosfomycin. HppE also recognizes (R)-2-hydroxypropylphosphonic acid ((R)-HPP) as a substrate and converts it to 2-oxo-propylphosphonic acid. To probe the mechanisms of these HppE-catalyzed oxidations, cyclopropyl- and methylenecyclopropyl-containing compounds were synthesized and studied as radical clock substrate analogues. Enzymatic assays indicated that the (S)- and (R)-isomers of the cyclopropyl-containing analogues were efficiently converted to epoxide and ketone products by HppE, respectively. In contrast, the ultrafast methylenecyclopropyl-containing probe inactivated HppE, consistent with a rapid radical-triggered ring-opening process that leads to enzyme inactivation. Taken together, these findings provide, for the first time, experimental evidence for the involvement of a C2-centered radical intermediate with a lifetime on the order of nanoseconds in the HppE-catalyzed oxidation of (R)-HPP.

A facile method to synthesize histones with posttranslational modification mimics

Using an evolved pyrrolysyl-tRNA synthetase-tRNA(Pyl) pair, a Se-alkylselenocysteine was genetically incorporated into histone H3 with a high protein expression yield. Quantitative oxidative elimination of Se-alkylselenocysteine followed by Michael addition reactions with various thiol nucleophiles generated biologically active mimics of H3 with posttranslational modifications including lysine methylation, lysine acetylation, and serine phosphorylation.

Ion mobility-mass spectrometry (IM-MS) for top-down proteomics: increased dynamic range affords increased sequence coverage

A general approach that combines mass spectrometry (MS), collision-induced dissociation (CID), ion mobility (IM), and MS for top-down proteomics is described, denoted as MS-CID-IM-MS. Using this approach, CID product ions are dispersed in two dimensions, specifically size-to-charge (IM) and mass-to-charge (MS), and the resulting 2D data display greatly facilitates peptide/protein mass mapping, amino acid sequence analysis, and determination of site-specific protein modifications. Also, this approach alleviates some of the inherent limitations of top-down proteomics, viz. the limitations in dynamic range for fragment ion abundances owing to the number of fragmentation channels available to large ionic systems as well as the resulting spectral congestion. For large peptides such as melittin (2845 Da), CID of the [M + 3H](3+), [M + 4H](4+), and [M + 5H](5+) ions yields amino acid sequence coverage of 42.3%, 38.5%, and 7.7%, respectively, whereas the hybrid MS-CID-IM-MS approach yields amino acid sequence coverages of 84.6%, 65.4%, and 69.2%, respectively. For large biomolecules such as ubiquitin (8565 Da), the amino acid sequence coverage increases from 39% to 76%. The MS-CID-IM-MS top-down approach allows for greater depth of information by allowing the assignment and study of internal fragment ions. Lastly, analysis of the methyl esterification of ubiquitin and single point mutation of human iron sulfur cluster U (HISCU, 14.3 kDa) demonstrates the ability of MS-CID-IM-MS to rapidly identify the presence and sites of modifications.

Damping factor links periodic focusing and uniform field ion mobility for accurate determination of collision cross sections

The methodology for obtaining accurate ion-neutral collision cross section (Ω) values for peptides and proteins using periodic focusing ion mobility spectrometry (PF IMS) is presented. A mobility dampening factor (represented by the term α) is introduced to account for the relative increase in ion-neutral collisions in PF IMS compared to uniform field ion mobility spectrometry (UF IMS) for equivalent operating conditions. The results show that α may be easily quantified both theoretically and empirically for a specific PF IMS design operating at a given pressure based upon the charge state of the analyte. By simply incorporating an α term into traditional UF IMS expressions, accurate Ω values were obtained with excellent agreement (≤4% difference) compared to UF IMS measurements found in the current literature.

Saccharomyces cerevisiae THI4p is a suicide thiamine thiazole synthase

Thiamin pyrophosphate 1 (Figure 1A) is an essential cofactor in all living systems¹. Its biosynthesis involves the separate syntheses of the pyrimidine 2 and thiazole 3 precursors, which are then coupled². Two biosynthetic routes to the thiamin thiazole have been identified. In prokaryotes, five enzymes act on three substrates to produce the thiazole via a complex oxidative condensation reaction, the mechanistic details of which are now well established^2–6. In contrast, only one gene-product is involved in thiazole biosynthesis in eukaryotes (THI4p in Saccharomyces cerevisiae)⁷. Identification of three adenylated metabolites (structures 5, 12 and 17 in Figure 1B), co-purifying with THI4p, provided three molecular snapshots of the reaction pathway catalyzed by this protein. In addition, two partially active mutants were identified (C204A and H200N), which catalyzed the conversion of NAD (nicotinamide adenine dinucleotide) 6 and glycine 9 to an advanced intermediate 12⁸. A mechanism for thiazole formation, consistent with these observations, is outlined in Figure 1B.^8–11 However, the source of the thiazole sulfur remained elusive, precluding us from deciphering the subsequent steps leading to the adenylated thiazole 5. Here we report the preparation of fully active recombinant wild type THI4p, the identification of an iron-dependent sulfide transfer reaction from the protein to a reaction intermediate and the demonstration that THI4p is a suicidal enzyme undergoing only a single turnover.

Efficient electrophoretic method to remove neutral additives from protein solutions followed by mass spectrometry analysis

A mass spectrometry (MS)-compatible, isoelectric point-based separation method for removal of neutral additives from protein solutions is described. The separation is performed by electrophoretic migration and trapping using a device referred to as membrane separated wells for isoelectric focusing and trapping (MSWIFT). Electrophoretic separation in the MSWIFT device is fast; the entire process can be carried out in a matter of minutes, and it does not require further sample cleanup prior to MS analysis. Proof-of-concept experiments in which neutral additives (e.g., Triton X-100, Tween 20, poly(ethylene glycol)) are removed from protein solutions using the MSWIFT device followed by MS analysis are described. Coupling the MSWIFT separation with ion mobility MS provides additional separation via the gas phase and assists in achieving higher quality ESI mass spectra when small amounts of additives remain in solution.

The de novo engineering of pyrrolysyl-tRNA synthetase for genetic incorporation of L-phenylalanine and its derivatives

Using evolved pyrrolysyl-tRNA synthetase-tRNA(CUA)(Pyl) pairs, L-phenylalanine, p-iodo-L-phenylalanine and p-bromo-L-phenylalanine have been genetically incorporated into proteins at amber mutation sites in E. coli.

A genetically encoded photocaged Nepsilon-methyl-L-lysine

A photocaged N(epsilon)-methyl-L-lysine has been genetically incorporated into proteins at amber codon positions in Escherichia coli using an evolved pyrrolysyl-tRNA synthetase-pylT pair. Its genetic incorporation and following photolysis to recover N(epsilon)-methyl-L-lysine at physiological pH provide a convenient method for the biosynthesis of proteins with monomethylated lysines at specific sites.

Hepatic phenotype of liver fatty acid binding protein gene-ablated mice

Although the function of liver fatty acid binding protein in hepatic fatty acid metabolism has been extensively studied, its potential role in hepatic cholesterol homeostasis is less clear. Although hepatic cholesterol accumulation was initially reported in L-FABP-null female mice, that study was performed with early N2 backcross generation mice. To resolve whether the hepatic cholesterol phenotype in these L-FABP(-/-) mice was attributable to genetic inhomogeneity, these L-FABP(-/-) mice were further backcrossed to C57Bl/6 mice up to the N10 (99.9% homogeneity) generation. Hepatic total cholesterol accumulation was observed in female, but not male, L-FABP(-/-) mice at all (N2, N4, N6, N10) backcross generations examined. The greater total cholesterol was due to increased hepatic levels of both unesterified (free) cholesterol and esterified cholesterol. Altered hepatic cholesterol accumulation correlated directly with L-FABP's ability to bind cholesterol with high affinity as shown by direct L-FABP binding of fluorescent cholesterol analogs (NBD-cholesterol, dansyl-cholesterol), a photoactivatable cholesterol analog [free cholesterol benzophenone (FCBP)], and free cholesterol (circular dichroism, isothermal titration microcalorimetry). One mole of fluorescent sterol was bound per mole of L-FABP. This was confirmed by photo-cross-linking studies with the photoactivatable cholesterol analog FCBP and by isothermal titration calorimetry with free cholesterol, which showed that L-FABP bound only one sterol molecule per L-FABP molecule. In contrast, the hepatic phenotype of male, but not female, L-FABP(-/-) mice was characterized by decreased hepatic triacylglycerol levels at all backcross generations examined. Taken together, these data support the hypothesis that L-FABP plays a role in physiological regulation of not only hepatic fatty acid metabolism, but also that of hepatic cholesterol.

Linkage and branch determination of N-linked oligosaccharides using sequential degradation/closed-ring chromophore labeling/negative ion trap mass spectrometry

A method based on sequential degradation, p-aminobenzoic ethyl ester (ABEE) closed-ring labeling, and negative ion electrospray ionization tandem mass spectrometry is presented for the study of linkage and branch determination for N-linked oligosaccharides. Closed-ring labeling provides greater linkage information than the more popular open-ring reductive amination approach. In addition, after high-performance liquid chromatography (HPLC) separation, closed-ring labeling allows for regeneration of the underivatized oligosaccharide, a requirement for alkaline sequential degradation. The analytical scheme presented here uses HPLC separation of closed-ring labeled oligosaccharides to resolve the mixture into individual forms that undergo subsequent structural analysis by negative ion tandem mass spectrometry. To facilitate complete structural analysis, particularly for larger sugars, the closed-ring labels are removed and the sugars are sequentially degraded by controlled alkaline hydrolysis. It is noteworthy that for sugars containing sialic acid moieties, a protecting group must be used to stabilize sialic acid groups during sequential alkaline degradation. This described approach was applied to two high mannose oligosaccharides M5G2, M6G2 cleaved from the ribonuclease B and a complex oligosaccharide A2 cleaved from transferrin.

Rapid protein identification using a disposable on-line clean-up/concentrating device and electrospray ionization mass spectrometry

A simple, low-cost, expedient method has been developed for identification of proteins isolated from two-dimensional (2D) gels. The method described uses a disposable on-line clean-up device, a syringe infusion pump and electrospray ionization mass spectrometry (ESI-MS). The on-line clean-up and concentrating device is a tapered capillary column filled with 1.5 cm of 5 microm C18 particles. The short column was easily prepared and was connected directly to the ESI source through a low-flow ESI sprayer. Peptides resulting from enzymatic digestion of proteins were eluted from the short column isocratically using a syringe infusion pump and analyzed by ESI-MS. This simple set-up was found useful in the analysis of proteins isolated from 2D gels. Compared to the more conventional micro-liquid chromatography/tandem mass spectrometry (microLC/MS/MS), this method can identify proteins rapidly without the need for an HPLC pump and removes the problem of cross-contamination caused by system carryover. These advantages make the method described competitive with conventional LC/MS even though the latter method gives slightly expanded sequence coverage.