Ilan Vidavsky

Comparing similar spectra: From similarity index to spectral contrast angle

We investigated a spectral-contrast-angle (θ) method to determine whether mass spectra of structural isomers are the same or significantly different. This method represents collisionally activated dissociation (CAD) spectra as vectors in space. Mass spectra of different isomers are represented as different vectors, having characteristic lengths and direction. The derived spectral contrast angle, which is a measure of the angle between two vectors corresponding to two closely related spectra, is a measure of whether the mass spectra are the same or significantly different. We compare this method with the similarity index (SI) method and show that the spectral contrast angle method is superior and can differentiate between very similar spectra in cases where the SI cannot. Both methods can be implemented simply in situations where the analyst is called on to decide, on the basis of mass or product-ion spectra, whether reference and unknown compounds are the same or to evaluate the reproducibility of spectra comprised of many peaks.

In APCs, the Autologous Peptides Selected by the Diabetogenic I-Ag7 Molecule Are Unique and Determined by the Amino Acid Changes in the P9 Pocket

We demonstrate in this study the great degree of specificity in peptides selected by a class II MHC molecule during processing. In this specific case of the diabetogenic I-Ag7 molecule, the P9 pocket of I-Ag7 plays a critical role in determining the final outcome of epitope selection, a conclusion that is important in interpreting the role of this molecule in autoimmunity. Specifically, we examined the display of naturally processed peptides from APCs expressing either I-Ag7 molecules or a mutant I-Ag7 molecule in which the β57Ser residue was changed to an Asp residue. Using mass spectrometry analysis, we identified over 50 naturally processed peptides selected by I-Ag7-expressing APCs. Many peptides were selected as families with a core sequence and variable flanks. Peptides selected by I-Ag7 were unusually rich in the presence of acidic residues toward their C termini. Many peptides contained short sequences of two to three acidic residues. In binding analysis, we determined the core sequences of many peptides and the interaction of the acidic residues with the P9 pocket. However, different sets of peptides were isolated from APCs bearing a modified I-Ag7 molecule. These peptides did not favor acidic residues toward the carboxyl terminus.

Fast photochemical oxidation of proteins for comparing structures of protein-ligand complexes: the calmodulin-peptide model system.

Fast photochemical oxidation of proteins (FPOP) is a mass spectrometry-based protein footprinting method that modifies proteins on the microsecond time scale. Highly reactive (•)OH, produced by laser photolysis of hydrogen peroxide, oxidatively modifies the side chains of approximately one-half the common amino acids on this time scale. Because of the short labeling exposure, only solvent-accessible residues are sampled. Quantification of the modification extent for the apo and holo states of a protein-ligand complex provides structurally sensitive information at the amino-acid level to compare the structures of unknown protein complexes with known ones. We report here the use of FPOP to monitor the structural changes of calmodulin in its established binding to M13 of the skeletal muscle myosin light chain kinase. We use the outcome to establish the unknown structures resulting from binding with melittin and mastoparan. The structural comparison follows a comprehensive examination of the extent of FPOP modifications as measured by proteolysis and LC-MS/MS for each protein-ligand equilibrium. The results not only show that the three calmodulin-peptide complexes have similar structures but also reveal those regions of the protein that became more or less solvent-accessible upon binding. This approach has the potential for relatively high throughput, information-dense characterization of a series of protein-ligand complexes in biochemistry and drug discovery when the structure of one reference complex is known, as is the case for calmodulin and M13 of the skeletal muscle myosin light chain kinase, and the structures of related complexes are not.

Azithromycin Attenuates Airway Inflammation in a Noninfectious Mouse Model of Allergic Asthma

BACKGROUND Definitive conclusions regarding the antiinflammatory effects of macrolide antibiotics for treatment of asthma are difficult to formulate since their beneficial effects may be related to their antimicrobial action. We hypothesized that azithromycin possesses distinct antiinflammatory properties and tested this assumption in a noninfectious mouse model of allergic asthma. METHODS To induce allergic airway inflammation, 7-week-old BALB/cJ mice underwent intraperitoneal ovalbumin sensitization on days 0 and 7 followed by an intranasal challenge on day 14. Mice were treated with azithromycin or phosphate-buffered saline (PBS) solution on days 13 through 16. On day 17, airway inflammation was assessed by quantifying leukocytes in the airway, expression of multiple inflammatory mediators in the BAL fluid, and mucous cell metaplasia. In a separate set of experiments, azithromycin or PBS solution treatment were initiated after the ovalbumin challenge. Each experiment was repeated 3 times (a total of 9 to 11 mice in each group). RESULTS Compared to treatment with PBS solution, azithromycin attenuated the ovalbumin-dependent airway inflammation. We observed a decrease in total leukocytes in the lung tissue and BAL fluid. In addition, azithromycin attenuated the expression of cytokines (eg, interleukin [IL]-13 and IL-5) and chemokines (eg, CCL2, CCL3, and CCL4) in the BAL fluid and abrogated the extent of mucous cell metaplasia. Similar antiinflammatory effects were observed when azithromycin treatment was initiated after the ovalbumin challenge. CONCLUSION In this noninfectious mouse model of allergic asthma, azithromycin attenuated allergic airway inflammation. These findings demonstrate an antiinflammatory effect of azithromycin and suggest azithromycin may have beneficial effects in treating noninfectious airway inflammatory diseases, including asthma.

MS-based cross-linking analysis reveals the location of the PsbQ protein in cyanobacterial photosystem II

Significance Cyanobacteria, photosynthetic prokaryotes, were primarily responsible to create an oxygen-rich atmosphere on our planet. Photosystem II (PSII), a large membrane-bound pigment protein complex in cyanobacteria, uses light energy to oxidize water to dioxygen. X-ray crystal structures of cyanobacterial PSII have recently been determined. PsbQ, a protein that optimizes PSII-mediated oxygen evolution activity, is ubiquitously present in cyanobacteria. However, PsbQ is absent in the determined structures of PSII. By using protein cross-linking, mutagenesis, and advanced MS techniques, we showed that PsbQ in the model cyanobacterium Synechocystis 6803 binds to CP47 and PsbO, two known protein components of PSII. These results helped determine the location of PsbQ on the lumenal side, near the water oxidation site, of cyanobacterial PSII. PsbQ is a luminal extrinsic protein component that regulates the water splitting activity of photosystem II (PSII) in plants, algae, and cyanobacteria. However, PsbQ is not observed in the currently available crystal structures of PSII from thermophilic cyanobacteria. The structural location of PsbQ within the PSII complex has therefore remained unknown. Here, we report chemical cross-linking followed by immunodetection and liquid chromatography/tandem MS analysis of a dimeric PSII complex isolated from the model cyanobacterium, Synechocystis sp. PCC 6803, to determine the binding site of PsbQ within PSII. Our results demonstrate that PsbQ is closely associated with the PsbO and CP47 proteins, as revealed by cross-links detected between 120K of PsbQ and 180K and 59K of PsbO, and between 102K of PsbQ and 440D of CP47. We further show that genetic deletion of the psbO gene results in the complete absence of PsbQ in PSII complexes as well as the loss of the dimeric form of PSII. Overall, our data provide a molecular-level description of the enigmatic binding site of PsbQ in PSII in a cyanobacterium. These results also help us understand the sequential incorporation of the PsbQ protein during the PSII assembly process, as well as its stabilizing effect on the oxygen evolution activity of PSII.

Online, High-Pressure Digestion System for Protein Characterization by Hydrogen/Deuterium Exchange and Mass Spectrometry

The rapid and complete digestion of proteins is important when protein characterization by hydrogen-deuterium exchange (HDX) is coupled with mass spectrometry. We developed a single-pump, online, high-pressure digestion system that relies on UPLC technology to aid in the digestion of proteins. Two model proteins, amyloid beta-peptide 1-42 (Abeta 1-42) and an HIV-1 capsid mutant protein (NBSA), were used to demonstrate the efficacy of the high-pressure system. Both model proteins readily aggregate and are difficult to digest under normal conditions. Our high-pressure system successfully digests these proteins into small, overlapping peptides. The extra information afforded by overlapping peptides allows us to pinpoint HDX protection to protein segments smaller than the digested peptide. The calculated average segment length (ASL) for both model proteins decreased by 2-fold for high-pressure digestion compared to digestion at ambient pressure.

New acetylenic metabolites from the marine sponge Pellina triangulata

Abstract Six new acetylenic compounds, 1, 7–11, were isolated from the marin sponge Pellina triangulata. Structures were established using NMR spectroscopy and chemical degradation. Collisional activation decomposition (CAD) tandem mass spectrometry of the lithium adducts of the acetylenic compounds was applied to ascertain if charge-remote fragmentation would yield definitive information regarding the site of internal unsaturation in these polyfunctional compounds. Pellynic acid (1) inhibited inosine monophosphate dehydrogenase (LMPDH) in vitro. Six new acetylenic compounds, 1, 7–11, were isolated from the marine sponge Pellina triangulata. Structures were established using NMR spectroscopy, chemical degradation, and collisional activation decomposition (CAD) tandem mass spectrometry. Pellynic acid (1) inhibited IMPDH.

Quantitative proteomics with siRNA screening identifies novel mechanisms of trastuzumab resistance in HER2 amplified breast cancers

HER2 is a receptor tyrosine kinase that is overexpressed in 20% to 30% of human breast cancers and which affects patient prognosis and survival. Treatment of HER2-positive breast cancer with the monoclonal antibody trastuzumab (Herceptin) has improved patient survival, but the development of trastuzumab resistance is a major medical problem. Many of the known mechanisms of trastuzumab resistance cause changes in protein phosphorylation patterns, and therefore quantitative proteomics was used to examine phosphotyrosine signaling networks in trastuzumab-resistant cells. The model system used in this study was two pairs of trastuzumab-sensitive and -resistant breast cancer cell lines. Using stable isotope labeling, phosphotyrosine immunoprecipitations, and online TiO2 chromatography utilizing a dual trap configuration, ∼1700 proteins were quantified. Comparing quantified proteins between the two cell line pairs showed only a small number of common protein ratio changes, demonstrating heterogeneity in phosphotyrosine signaling networks across different trastuzumab-resistant cancers. Proteins showing significant increases in resistant versus sensitive cells were subjected to a focused siRNA screen to evaluate their functional relevance to trastuzumab resistance. The screen revealed proteins related to the Src kinase pathway, such as CDCP1/Trask, embryonal Fyn substrate, and Paxillin. We also identify several novel proteins that increased trastuzumab sensitivity in resistant cells when targeted by siRNAs, including FAM83A and MAPK1. These proteins may present targets for the development of clinical diagnostics or therapeutic strategies to guide the treatment of HER2+ breast cancer patients who develop trastuzumab resistance.

Carboxyl-Group Footprinting Maps the Dimerization Interface and Phosphorylation-induced Conformational Changes of a Membrane-associated Tyrosine Kinase

Her4 is a transmembrane receptor tyrosine kinase belonging to the ErbB-EGFR family. It plays a vital role in the cardiovascular and nervous systems, and mutations in Her4 have been found in melanoma and lung cancer. The kinase domain of Her4 forms a dimer complex, called the asymmetric dimer, which results in kinase activation. Although a crystal structure of the Her4 asymmetric dimer is known, the dimer affinity and the effect of the subsequent phosphorylation steps on kinase domain conformation are unknown. We report here the use of carboxyl-group footprinting MS on a recombinant expressed, Her4 kinase-domain construct to address these questions. Carboxyl-group footprinting uses a water-soluble carbodiimide, 1-ethyl-3-(3-dimethylaminopropyl)carbodiimide, in the presence of glycine ethyl ester, to modify accessible carboxyl groups on glutamate and aspartate residues. Comparisons of Her4 kinase-domain monomers versus dimers and of unphosphorylated versus phosphorylated dimers were made to map the dimerization interface and to determine phosphorylation induced-conformational changes. We detected 37 glutamate and aspartate residues that were modified, and we quantified their extents of modification by liquid chromatography MS. Five residues showed changes in carboxyl-group modification. Three of these residues are at the predicted dimer interface, as shown by the crystal structure, and the remaining two residues are on loops that likely have altered conformation in the kinase dimer. Incubating the Her4 kinase dimers with ATP resulted in dramatic increase in Tyr-850 phosphorylation, located on the activation loop, and this resulted in a conformational change in this loop, as evidenced by reduction in carboxyl-group modification. The kinase monomer-dimer equilibrium was measured using a titration format in which the extent of carboxyl-group footprinting was mathematically modeled to give the dimer association constant (1.5–6.8 × 1012 dm2/mol). This suggests that the kinase-domain makes a significant contribution to the overall dimerization affinity of the full-length Her4 protein.

Detection of clobetasol propionate as an undeclared steroid in zinc pyrithione formulations by high-performance liquid chromatography with rapid-scanning ultraviolet spectroscopy and mass spectrometry

Abstract Clobetasol propionate, an anti-inflammatory glucocorticosteroid, was detected in an over-the-counter topical drug product with no indication on the label of this compound as an ingredient. The product was formulated as a topical spray, a cream, or a shampoo and labeled to contain zinc pyrithione as the active ingredient. The finding of clobetasol propionate in the pharmaceutical products was shown by comparison to an authenticated standard of clobetasol propionate by retention time on normal-phase and reversed-phase HPLC, UV spectroscopy, LC–MS and LC–MS–MS. A simple method was developed and validated for the assay of clobetasol propionate by isocratic reversed-phase HPLC. Several lots contained clobetasol propionate at therapeutic levels of 0.02–0.06%. Zinc pyrithione formulations from two other manufacturers were free of clobetasol propionate.