Improved mass spectrometry-based activity assay reveals oxidative and metabolic stress as sirtuin-1 regulators.

Sirtuin-1 (SirT1) catalyzes NAD+-dependent protein lysine deacetylation and is a critical regulator of energy and lipid metabolism, mitochondrial biogenesis, apoptosis, and senescence. Activation of SirT1 mitigates metabolic perturbations associated with diabetes and obesity. Pharmacologic molecules, cellular redox, and nutritional states can regulate SirT1 activity. Technical barriers against measuring endogenous SirT1 activity have limited characterization of SirT1 in disease and its activation by small molecules. Herein, we developed a relative quantitative mass spectrometry-based technique for measuring endogenous SirT1 activity (RAMSSAY/RelAtive Mass Spectrometry Sirt1 Activity assaY) in cell and tissue homogenates using a biotin-labeled, acetylated p53-derived peptide as a substrate. We demonstrate that oxidative and metabolic stress diminish SirT1 activity in the hepatic cell line HepG2. Moreover, pharmacologic molecules including nicotinamide and EX-527 attenuate SirT1 activity; purported activators of SirT1, the polyphenol S17834, the polyphenol resveratrol, or the non-polyphenolic Sirtris compound SRT1720, failed to activate endogenous SirT1 significantly. Furthermore, we provide evidence that feeding a high fat high sucrose diet (HFHS) to mice inhibits endogenous SirT1 activity in mouse liver. In summary, we introduce a robust, specific and sensitive mass spectrometry-based assay for detecting and quantifying endogenous SirT1 activity using a biotin-labeled peptide in cell and tissue lysates. With this assay, we determine how pharmacologic molecules and metabolic and oxidative stress regulate endogenous SirT1 activity. The assay may also be adapted for other sirtuin isoforms.

Immunogenic HLA-DR-Presented Self-Peptides Identified Directly from Clinical Samples of Synovial Tissue, Synovial Fluid, or Peripheral Blood in Patients with Rheumatoid Arthritis or Lyme Arthritis.

Human leukocyte antigen-antigen D related (HLA-DR) molecules are highly expressed in synovial tissue (ST), the target of the immune response in chronic inflammatory forms of arthritis. Here, we used LC-MS/MS to identify HLA-DR-presented self-peptides in cells taken directly from clinical samples: ST, synovial fluid mononuclear cells (SFMC), or peripheral blood mononuclear cells (PBMC) from five patients with rheumatoid arthritis (RA) and eight with Lyme arthritis (LA). We identified 1593 non-redundant HLA-DR-presented peptides, derived from 870 source proteins. A total of 67% of the peptides identified in SFMC and 55% of those found in PBMC were found in ST, but analysis of SFMC/PBMC also revealed new antigen-presented peptides. Peptides were synthesized and examined for reactivity with the patients' PBMC. To date, three autoantigens in RA and four novel autoantigens in LA, presented in ST and/or PBMC, were shown to be targets of T- and B-cell responses in these diseases; ongoing analyses may add to this list. Thus, immunoprecipitation and LC-MS/MS can now identify hundreds of HLA-DR-presented self-peptides from individual patients' tissues or fluids with mixed cell populations. Importantly, identification of HLA-DR-presented peptides from SFMC or PBMC allows testing of more patients, including those early in the disease. Direct analysis of clinical samples facilitates identification of novel immunogenic T-cell epitopes.

Overexpression of Catalase Diminishes Oxidative Cysteine Modifications of Cardiac Proteins.

Reactive protein cysteine thiolates are instrumental in redox regulation. Oxidants, such as hydrogen peroxide (H2O2), react with thiolates to form oxidative post-translational modifications, enabling physiological redox signaling. Cardiac disease and aging are associated with oxidative stress which can impair redox signaling by altering essential cysteine thiolates. We previously found that cardiac-specific overexpression of catalase (Cat), an enzyme that detoxifies excess H2O2, protected from oxidative stress and delayed cardiac aging in mice. Using redox proteomics and systems biology, we sought to identify the cysteines that could play a key role in cardiac disease and aging. With a 'Tandem Mass Tag' (TMT) labeling strategy and mass spectrometry, we investigated differential reversible cysteine oxidation in the cardiac proteome of wild type and Cat transgenic (Tg) mice. Reversible cysteine oxidation was measured as thiol occupancy, the ratio of total available versus reversibly oxidized cysteine thiols. Catalase overexpression globally decreased thiol occupancy by ≥1.3 fold in 82 proteins, including numerous mitochondrial and contractile proteins. Systems biology analysis assigned the majority of proteins with differentially modified thiols in Cat Tg mice to pathways of aging and cardiac disease, including cellular stress response, proteostasis, and apoptosis. In addition, Cat Tg mice exhibited diminished protein glutathione adducts and decreased H2O2 production from mitochondrial complex I and II, suggesting improved function of cardiac mitochondria. In conclusion, our data suggest that catalase may alleviate cardiac disease and aging by moderating global protein cysteine thiol oxidation.

Protein Expression by Human Pulmonary Artery Smooth Muscle Cells Containing a BMPR2 Mutation and the Action of ET-1 as Determined by Proteomic Mass Spectrometry.

Pulmonary arterial hypertension (PAH) is a disease characterized by increased pulmonary vascular resistance and remodeling. Increase in the population of vascular smooth muscle cells is among the key events contributing to the remodeling. Endothelin-1 (ET-1), a potent vasoconstrictor, is linked to the etiology and progression of PAH. Here we analyze changes in protein expressions in response to ET-1 in pulmonary arterial smooth muscle cells (PASMC) from a healthy Control (non-PAH) and a PAH subject presenting a bone morphogenetic protein type II receptor (BMPR2) mutation with exon 1-8 deletion. Protein expressions were analyzed by proteomic mass spectrometry using label-free quantitation and the correlations were subjected to Ingenuity™ Pathway Analysis. The results point to eIF2/mTOR/p70S6K, RhoA/actin cytoskeleton/integrin and protein unbiquitination as canonical pathways whose protein expressions increase with the development of PAH. These pathways have an intimal function in the PAH-related physiology of smooth muscle proliferation, apoptosis, contraction and cellular stress. Exposure of the cells to ET-1 further increases protein expression within these pathways. Thus our results show changes in signaling pathways as a consequence of PAH and the effect of ET-1 interference on Control and PAH-affected cells.

A novel human autoantigen, endothelial cell growth factor, is a target of T and B cell responses in patients with Lyme disease.

OBJECTIVE: Autoantigen presentation by HLA-DR molecules is thought to be a central component of many autoimmune diseases, but identifying disease-relevant autoantigens has been a difficult challenge. In this study we aimed to identify autoantigens in patients with antibiotic-refractory Lyme arthritis, in which infection-induced autoimmunity is thought to play an important role. METHODS: Using tandem mass spectrometry, naturally presented HLA-DR self peptides from a patient's synovium were identified, synthesized, and reacted with his peripheral blood mononuclear cells (PBMCs). Immunoreactive peptides and their source proteins were then tested for T and B cell responses using large numbers of patient cells or sera. RESULTS: Of 120 HLA-DR-presented self peptides identified from one patient, one peptide derived from endothelial cell growth factor (ECGF) caused his PBMCs to proliferate. T and B cell responses to ECGF occurred systemically in ∼10-30% of patients with early or late manifestations of Lyme disease, primarily in those with refractory arthritis-associated HLA-DR alleles, such as DRB1*0101 and 0401. Compared with patients with antibiotic-responsive arthritis, those with antibiotic-refractory arthritis had significantly higher concentrations of ECGF in synovial fluid (P<0.0001) and more often had ECGF antibody reactivity. Among non-antibiotic-treated historical patients who developed arthritis, 26% had ECGF reactivity, which often developed before the onset of arthritis and was associated with significantly longer courses of arthritis. CONCLUSION: T and B cell responses to ECGF occur in a subset of patients with Lyme disease, particularly in those with antibiotic-refractory arthritis, providing the first direct evidence of autoimmune T and B cell responses in this illness.

Histidine-containing radicals in the gas phase.

Radicals containing the histidine residue have been generated in the gas phase by femtosecond electron transfer to protonated histidine-N-methylamide (1H+), Nalpha-acetylhistidine-N-methylamide (2H+), Nalpha-glycylhistidine (3H+), and Nalpha-histidylglycine (4H+). Radicals generated by collisional electron transfer from dimethyldisulfide to ions 1H+ and 2H+ at 7 keV collision energies were found to dissociate completely on the microsecond time scale, as probed by reionization to cations. The main dissociations produced fragments from the imidazole side chain and the cleavage of the C(alpha)CO bond, whereas products of NCalpha bond cleavage were not observed. Electron transfer from gaseous potassium atoms to ions 3H+ and 4H+ at 2.97 keV collision energies not only caused backbone NCalpha bond dissociations but also furnished fractions of stable radicals that were detected after conversion to anions. Ion structures, ion-electron recombination energies, radical structures, electron affinities, and dissociation and transition-state energies were obtained by combined density functional theory and Møller-Plesset perturbational calculations (B3-PMP2) and basis sets ranging from 6-311+G(2d,p) to aug-cc-pVTZ. The Rice-Ramsperger-Kassel-Marcus theory was used to calculate rate constants on the B3-PMP2 potential energy surfaces to aid interpretation of the mass spectrometric data. The stability of Nalpha-histidylglycine-derived radicals is attributed to an exothermic isomerization in the imidazole ring, which is internally catalyzed by reversible proton transfer from the carboxyl group. The isomerization depends on the steric accessibility of the histidine side chain and the carboxyl group and involves a novel cation radical-COO salt-bridge intermediate.

Electron transfer to protonated beta-alanine N-methylamide in the gas phase: an experimental and computational study of dissociation energetics and mechanisms.

Ammonium radicals derived from protonated beta-alanine N-methyl amide (BANMA) were generated by femtosecond collisional electron transfer to gas-phase cations prepared by chemical ionization and electrospray. Regardless of the mode of precursor ion preparation, the radicals underwent complete dissociation on the time scale of 5.15 micros. Deuterium isotope labeling and product analysis pointed out several competitive and convergent dissociation pathways that were not completely resolved by experiment. Ab initio calculations, which were extrapolated up to the CCSD(T)/6-311++G(3df,2p) level of theory, provided the proton affinity and gas-phase basicity of BANMA as PA = 971 kJ mol-1 and GB = 932 kJ mol-1 to form the most stable ion structure 1c+ in which the protonated ammonium group was internally solvated by hydrogen bonding to the amide carbonyl. Ion 1c+ was calculated to have an adiabatic recombination energy of 3.33 eV to form ammonium radical 1c*. The potential energy surface for competitive and consecutive isomerizations and dissociations of 1c* was investigated at correlated levels of theory and used for Rice-Ramsperger-Kassel-Marcus (RRKM) calculations. RRKM unimolecular rate constants suggested that dissociations starting from the ground electronic state of radical 1c* were dominated by loss of an ammonium hydrogen atom. In contrast, dissociations starting from the B excited state were predicted to proceed by reversible isomerization to an aminoketyl radical (1f*). The latter can in part dissociate by N-Calpha bond cleavage leading to the loss of the amide methyl group. This indicates that apparently competitive dissociations observed for larger amide and peptide radicals, such as backbone cleavages and losses of side-chain groups, may originate from different electronic states and proceed on different potential energy surfaces.

Gas-phase tautomers of protonated 1-methylcytosine. Preparation, energetics, and dissociation mechanisms.

Tautomers of 1-methylcytosine that are protonated at N-3 (1+) and C-5 (2+) have been specifically synthesized in the gas phase and characterized by tandem mass spectrometry and quantum chemical calculations. Ion 1+ is the most stable tautomer in aqueous and methanol solution and is likely to be formed by electrospray ionization of 1-methylcytosine and transferred in the gas phase. Gas-phase protonation of 1-methylcytosine produces a mixture of 1+ and the O-2-protonated tautomer (3+), which are nearly isoenergetic. Dissociative ionization of 6-ethyl-5,6-dihydro-1-methylcytosine selectively forms isomer 2+. Upon collisional activation, ions 1+ and 3+ dissociate by loss of ammonia and [C,H,N,O], whose mechanisms have been established by deuterium labeling and ab initio calculations. The main dissociations of 2+ following collisional activation are losses of CH2=C=NH and HN=C=O. The mechanisms of these dissociations have been elucidated by deuterium labeling and theoretical calculations.

Photophysics of pyrene-labelled compounds of biophysical interest.

The effects of the chemical constitution and structure of the substituent on the excited state dynamics of several model fluorescent pyrene-labelled molecules of biophysical interest have been examined. Nine new 1-substituted pyrenyl compounds, Py-NH-CO-C2H5, Py-NH-CO-Leu-Boc, Py-CH2-NH-CO-C2H5, Py-CH2-NH-CO-Leu-Boc, Py-CO-NH-C3H7, Py-CO-NH-Leu-OMe, Py-CH2-CO-NH-C3H7, Py-CH2-CO-NH-Leu-OMe and Py-C3H6-CO-NH-Leu-OMe, have been synthesized and their electronic spectra, fluorescence quantum yields and excited state lifetimes measured. These data have been used to calculate the radiative, kr, and non-radiative decay constants of their S1 states and the values of these constants correlated with the structures of the tethers. Non-radiative S1 decay rates (mainly intersystem crossing to T1) vary in parallel with the radiative rates so that the excited state lifetimes and radiative rate constants change considerably with the structure of the substituent whereas the quantum yields of fluorescence do not. An excellent correlation between [epsilon]max of the S1-S0 transition and either kr or the excited state lifetime is observed as long as no additional intermolecular or intramolecular excited state decay process of significant rate competes with the 'normal' radiative and non-radiative (ISC) decay processes of the pyrenyl chromophore. This correlation may have predictive value. Rates of bimolecular quenching of the S1 states of these molecules by molecular oxygen have been measured. The quenching process is diffusion-controlled with a spin statistical factor of 1, indicating that the S1-T1 electronic energy spacings of all the derivatives exceed the O2(1Deltag-3Sigmag-) electronic excitation energy of ca. 1 eV.

Hypervalent ammonium radicals. Competitive N-C and N-H bond dissociations in methyl ammonium and ethyl ammonium.

The title hypervalent ammonium radicals were investigated by neutralization-reionization mass spectrometry and quantum chemical calculations. Methyl ammonium (1) forms a small fraction of metastable radicals from isotopomers CH3ND3 (la) and CD3NH3 (1b) when these are produced by femtosecond electron transfer to vibrationally excited precursor cations. The branching ratios for dissociations of the N-C and N-(H,D) bonds in 1 favor the latter, k(N-C)/k(N-H) = 0.39. The experimental results are in accord with ab initio/RRKM calculations that quantitatively reproduce the branching ratios for dissociations of 1. A small fraction of high-energy 1 dissociates to form ammonium methylide, -CH2NH3+. Ethyl ammonium (2) and its CH3CH2ND3 isotopomer (2a) dissociate completely on the microsecond time scale. The branching ratios for dissociations of the N-C and N-(H,D) bonds favor the former, k(N-C)/k(N-H) = 2.04. This result is incompatible with the calculated potential energy surface of the ground doublet electronic state in 2 and is attributed to the formation and dissociations of excited electronic states.

Peptide cation-radicals. A computational study of the competition between peptide N-Calpha bond cleavage and loss of the side chain in the [GlyPhe-NH2 + 2H]+. cation-radical.

Cation-radicals and dications corresponding to hydrogen atom adducts to N-terminus-protonated N(alpha)-glycylphenylalanine amide (Gly-Phe-NH(2)) are studied by combined density functional theory and Møller-Plesset perturbational computations (B3-MP2) as models for electron-capture dissociation of peptide bonds and elimination of side-chain groups in gas-phase peptide ions. Several structures are identified as local energy minima including isomeric aminoketyl cation-radicals, and hydrogen-bonded ion-radicals, and ylid-cation-radical complexes. The hydrogen-bonded complexes are substantially more stable than the classical aminoketyl structures. Dissociations of the peptide N-C(alpha) bonds in aminoketyl cation-radicals are 18-47 kJ mol(-1) exothermic and require low activation energies to produce ion-radical complexes as stable intermediates. Loss of the side-chain benzyl group is calculated to be 44 kJ mol(-1) endothermic and requires 68 kJ mol(-1) activation energy. Rice-Ramsperger-Kassel-Marcus (RRKM) and transition-state theory (TST) calculations of unimolecular rate constants predict fast preferential N-C(alpha) bond cleavage resulting in isomerization to ion-molecule complexes, while dissociation of the C(alpha)bond;CH(2)C(6)H(5) bond is much slower. Because of the very low activation energies, the peptide bond dissociations are predicted to be fast in peptide cation-radicals that have thermal (298 K) energies and thus behave ergodically.