Carbamino group formation with peptides and proteins studied by mass spectrometry

Chemoproteomic identification of CO2-dependent lysine carboxylation in proteins

Carbon dioxide is an omnipresent gas that drives adaptive responses within organisms from all domains of life. The molecular mechanisms by which proteins serve as sensors of CO₂ are, accordingly, of great interest. Because CO₂ is electrophilic, one way it can modulate protein biochemistry is by carboxylation of the amine group of lysine residues. However, the resulting CO₂-carboxylated lysines spontaneously decompose, giving off CO₂, which makes studying this modification difficult. Here we describe a method to stably mimic CO₂-carboxylated lysine residues in proteins. We leverage this method to develop a quantitative approach to identify CO₂-carboxylated lysines of proteins and explore the lysine 'carboxylome' of the CO₂-responsive cyanobacterium Synechocystis sp. We uncover one CO₂-carboxylated lysine within the effector binding pocket of the metabolic signaling protein PII. CO₂-carboxylatation of this lysine markedly lowers the affinity of PII for its regulatory effector ligand ATP, illuminating a negative molecular control mechanism mediated by CO₂.

Carbon Dioxide and the Carbamate Post-Translational Modification

Carbon dioxide is essential for life. It is at the beginning of every life process as a substrate of photosynthesis. It is at the end of every life process as the product of post-mortem decay. Therefore, it is not surprising that this gas regulates such diverse processes as cellular chemical reactions, transport, maintenance of the cellular environment, and behaviour. Carbon dioxide is a strategically important research target relevant to crop responses to environmental change, insect vector-borne disease and public health. However, we know little of carbon dioxide’s direct interactions with the cell. The carbamate post-translational modification, mediated by the nucleophilic attack by carbon dioxide on N-terminal α-amino groups or the lysine ɛ-amino groups, is one mechanism by which carbon dioxide might alter protein function to form part of a sensing and signalling mechanism. We detail known protein carbamates, including the history of their discovery. Further, we describe recent studies on new techniques to isolate this problematic post-translational modification.

A methodology for carbamate post-translational modification discovery and its application in Escherichia coli

Carbon dioxide can influence cell phenotypes through the modulation of signalling pathways. CO₂ regulates cellular processes as diverse as metabolism, cellular homeostasis, chemosensing and pathogenesis. This diversity of regulated processes suggests a broadly conserved mechanism for CO₂ interactions with diverse cellular targets. CO₂ is generally unreactive but can interact with neutral amines on protein under normal intracellular conditions to form a carbamate post-translational modification (PTM). We have previously demonstrated the presence of this PTM in a subset of protein produced by the model plant species Arabidopsis thaliana. Here, we describe a detailed methodology for identifying new carbamate PTMs in an extracted soluble proteome under biologically relevant conditions. We apply this methodology to the soluble proteome of the model prokaryote Escherichia coli and identify new carbamate PTMs. The application of this methodology, therefore, supports the hypothesis that the carbamate PTM is both more widespread in biology than previously suspected and may represent a broadly relevant mechanism for CO₂-protein interactions.

The identification of carbon dioxide mediated protein post-translational modifications

Carbon dioxide is vital to the chemistry of life processes including metabolism, cellular homoeostasis, and pathogenesis. CO₂ is generally unreactive but can combine with neutral amines to form carbamates on proteins under physiological conditions. The most widely known examples of this are CO₂ regulation of ribulose 1,5-bisphosphate carboxylase/oxygenase and haemoglobin. However, the systematic identification of CO₂-binding sites on proteins formed through carbamylation has not been possible due to the ready reversibility of carbamate formation. Here we demonstrate a methodology to identify protein carbamates using triethyloxonium tetrafluoroborate to covalently trap CO₂, allowing for downstream proteomic analysis. This report describes the systematic identification of carbamates in a physiologically relevant environment. We demonstrate the identification of carbamylated proteins and the general principle that CO₂ can impact protein biochemistry through carbamate formation. The ability to identify protein carbamates will significantly advance our understanding of cellular CO₂ interactions.

Carbon dioxide can interact with proteins to form carbamate post-translational modifications. Here, the authors developed a strategy to identify carbamate post-translational modifications by trapping carbon dioxide and subsequently identifying the carbamylated proteins.

Observation of CO2 and solvent adduct ions during negative mode electrospray ionization Fourier transform ion cyclotron resonance mass spectrometric analysis of monohydric alcohols

RATIONALE

Monohydric alcohols are common in natural products, bio-oils, and medicine. We have found that monohydric alcohols can form O3 (ions containing three oxygen atoms) and O4 adduct ions in negative electrospray ionization (ESI) Fourier transform ion cyclotron resonance mass spectrometry (FT-ICR MS), which would significantly affect the composition analysis of alcohols, especially in a complex mixture. It is necessary to study the reaction pathways and the method to eliminate or reduce the 'artifact' adducts.

METHODS

Octadecanol, cholesterol, squalanol and two complex monohydric alcohol mixtures were selected as model compounds. These samples were subjected to negative ion ESI FT-ICR MS analysis. The composition and formation mechanism of adducts were studied by the ultrahigh-resolution accurate mass measurement for elemental composition, along with the MS(2) isolation and collision-induced dissociation (CID) experiments for structural determination.

RESULTS

The reaction pathway of O3 adduct formation is the coupling of a monohydric alcohol ion with a CO2 to form a stable O3 ionic species by likely a covalent bond (source of CO2 is not clear). The O4 species are formed by O3 ionic species adducted with an alcohol molecule of the solvent, such as methanol or ethanol, by likely a hydrogen bond. These adduct ions could be eliminated or reduced by increasing collision energy. However, excessive collision energy would fragment monohydric alcohol ions.

CONCLUSIONS

The formation mechanisms of O3 and O4 adducts from monohydric alcohols in negative ion ESI FT-ICR MS were proposed. The solvent adduction effects can be eliminated or reduced by optimizing the collision energy of CID in FT-ICR MS.

Tandem mass spectrometry measurement of the collision products of carbamate anions derived from CO2 capture sorbents: paving the way for accurate quantitation

The reaction between CO(2) and aqueous amines to produce a charged carbamate product plays a crucial role in post-combustion capture chemistry when primary and secondary amines are used. In this paper, we report the low energy negative-ion CID results for several anionic carbamates derived from primary and secondary amines commonly used as post-combustion capture solvents. The study was performed using the modern equivalent of a triple quadrupole instrument equipped with a T-wave collision cell. Deuterium labeling of 2-aminoethanol (1,1,2,2,-d(4)-2-aminoethanol) and computations at the M06-2X/6-311++G(d,p) level were used to confirm the identity of the fragmentation products for 2-hydroxyethylcarbamate (derived from 2-aminoethanol), in particular the ions CN(-), NCO(-) and facile neutral losses of CO(2) and water; there is precedent for the latter in condensed phase isocyanate chemistry. The fragmentations of 2-hydroxyethylcarbamate were generalized for carbamate anions derived from other capture amines, including ethylenediamine, diethanolamine, and piperazine. We also report unequivocal evidence for the existence of carbamate anions derived from sterically hindered amines (Tris(2-hydroxymethyl)aminomethane and 2-methyl-2-aminopropanol). For the suite of carbamates investigated, diagnostic losses include the decarboxylation product (-CO(2), 44 mass units), loss of 46 mass units and the fragments NCO(-) (m/z 42) and CN(-) (m/z 26). We also report low energy CID results for the dicarbamate dianion ((-)O(2)CNHC(2)H(4)NHCO(2)(-)) commonly encountered in CO(2) capture solution utilizing ethylenediamine. Finally, we demonstrate a promising ion chromatography-MS based procedure for the separation and quantitation of aqueous anionic carbamates, which is based on the reported CID findings. The availability of accurate quantitation methods for ionic CO(2) capture products could lead to dynamic operational tuning of CO(2) capture-plants and, thus, cost-savings via real-time manipulation of solvent regeneration energies.