Mass Spectrometric Characterization of Protein Structure Details Refines the Proteome Signature for Invasive Ductal Breast Carcinoma

Early diagnosis as well as individualized therapies are necessary to reduce the mortality of breast cancer, and personalized patient care strategies rely on novel prognostic or predictive factors. In this study, with six breast cancer patients, 2D gel analysis was applied for studying protein expression differences in order to distinguish invasive ductal breast carcinoma, the most frequent breast tumor subtype, from control samples. In total, 1203 protein spots were assembled in a 2D reference gel. Differentially abundant spots were subjected to peptide mass fingerprinting for protein identification. Twenty proteins with their corresponding 38 differentially expressed 2D gel spots were contained in our previously reported proteome signature, suggesting that distinct protein forms were contributing. In-depth MS/MS measurements enabled analyses of protein structure details of selected proteins. In protein spots that significantly contributed to our signature, we found that glyceraldehyde-3-phosphate dehydrogenase was N-terminally truncated, pyruvate kinase M2 and nucleoside diphosphate kinase A but not other isoforms of these proteins were of importance, and nucleophosmin phosphorylation at serine residues 106 and 125 were clearly identified. Principle component analysis and hierarchical clustering with normalized quantitative data from the 38 spots resulted in accurate separation of tumor from control samples. Thus, separation of tissue samples as in our initial proteome signature could be confirmed even with a different proteome analysis platform. In addition, detailed protein structure investigations enabled refining our proteome signature for invasive ductal breast carcinoma, opening the way to structure-/function studies with respect to disease processes and/or therapeutic intervention.     

Tandem Mass Spectrometric Characterization of Thiol Peptides Modified by the Chemoselective Cationic Sulfhydryl Reagent (4-Iodobutyl)Triphenylphosphonium—

Fixed charge chemical modifications on peptides and proteins can impact fragmentation behaviors in tandem mass spectrometry (MS/MS). In this study, we employed a thiol-specific cationic alkylation reagent, (4-iodobutyl)triphenylphosphonium (IBTP), to selectively modify cysteine thiol groups in mitochondrial proteome samples. Tandem mass spectrometric characteristics of butyltriphenylphosphonium (BTP)-modified peptides were evaluated by comparison to their carbamidomethylated (CAM) analogues using a quadrupole time-of-flight (Q-TOF) instrument under low energy collision-induced dissociation (CID) conditions. Introduction of the fixed charge modification resulted in the observation of peptide and fragment (b_n and y_n) ions with higher charge states than those observed for CAM-modified analogues. The charged BTP moiety had a significant effect on the neighboring amide bond fragmentation products. A decrease in relative abundances of the product ions at the corresponding cleavage sites was observed compared with those from the CAM-modified derivatives. This effect was particularly noticeable when an Xxx-Pro bond was in the vicinity of a BTP group. We hypothesized that the presence of a phosphonium moiety will reduce the tendency for protonation of the proximal amide bonds in the peptide backbone. Indeed, calculations indicated that proton affinities of backbone amide bonds close to the modified cysteine residues were generally 20–50 kcal/mol lower for BTP-modified peptides than for the unmodified or CAM-modified analogues with the sequence motif -Ala-Cys-Ala_n-Ala₂-, -Ala-Cys-Ala_n-Pro-Ala-, and -Ala-Pro-Ala_n-Cys-Ala-, n = 0–3.     

Insight into the photoinduced ligand exchange reaction pathway of cis-[Rh2(μ-O2CCH3)2(CH3CN)6]2+ with a DNA model chelate

We previously showed that [Rh(2)(O(2)CCH(3))(2)(CH(3)CN)(6)](2+) binds to dsDNA only upon irradiation with visible light and that photolysis results in a 34-fold enhancement of its cytotoxicity toward Hs-27 human skin fibroblasts, making it potentially useful for photodynamic therapy (PDT). With the goal of gaining further insight on the photoinduced binding of DNA to the complex, we investigated by NMR spectroscopy the mechanism by which 2,2'-bipyridine (bpy), a model for biologically relevant bidentate nitrogen donor ligands, binds to [Rh(2)(O(2)CCH(3))(2)(CH(3)CN)(6)](2+) upon irradiation in D(2)O. The photochemical results are compared to the reactivity in the dark in D(2)O and CD(3)CN. The photolysis of [Rh(2)(O(2)CCH(3))(2)(CH(3)CN)(6)](2+) with equimolar bpy solutions in D(2)O with visible light affords [Rh(2)(O(2)CCH(3))(2)(eq/eq-bpy)(CH(3)CN)(2)(D(2)O(ax))(2)](2+) (eq/eq) with the reaction reaching completion in ~8 h. Only vestiges of eq/eq are observed at the same time in the dark, however, and the reaction is ~20 times slower. Conversely, the dark reaction of [Rh(2)(O(2)CCH(3))(2)(CH(3)CN)(6)](2+) with an equimolar amount of bpy in CD(3)CN affords [Rh(2)(O(2)CCH(3))(2)(η(1)-bpy(ax))(CH(3)CN)(5)](2+) (η(1)-bpy(ax)), which remains present even after 5 days of reaction. The photolysis results in D(2)O are consistent with the exchange of one equiv CH(3)CNeq for solvent, and the resulting species quickly reacting with bpy to generate eq/eq; the initial eq ligand dissociation is assisted by absorption of a photon, thus greatly enhancing the reaction rate. The photolytic reaction of [Rh(2)(O(2)CCH(3))(2)(CH(3)CN)(6)](2+):bpy in a 1:2 ratio in D(2)O affords the eq/eq and (eq/eq)(2) adducts. The observed differences in the reactivity in D(2)O vs CD(3)CN are explained by the relative ease of substitution of eq D(2)O vs CD(3)CN by the incoming bpy molecule. These results clearly highlight the importance of dissociation of an eq CH(3)CN molecule from the dirhodium core to attain high reactivity and underscore the importance of light for the reactivity of these compounds, which is essential for PDT agents.     

Effect of electronic structure on the photoinduced ligand exchange of Ru(II) polypyridine complexes

The series of complexes [Ru(bpy)(2)(L)](2+), where bpy = 2,2'-bipyridine and L = 3,6-dithiaoctane (bete, 1), 1,2-bis(phenylthio)ethane (bpte, 2), ethylenediamine (en, 3), and 1,2-dianilinoethane (dae, 4), were synthesized, and their photochemistry was investigated. Photolysis experiments show that the bisthioether ligands in 1 and 2 are more easily photosubstituted by chloride ions, bpy, and H(2)O than the corresponding diammine complexes in 3 and 4 to generate the bis-substituted products. Electronic structure calculations show that bond elongation in the lowest energy triplet metal-to-ligand charge transfer ((3)MLCT) state compared to the ground state is greater for complexes containing bisthioether ligands than those with coordinated bidentate nitrogen atoms. This elongation in the excited state is attributed to Ru-S π-bonding character of the highest occupied molecular orbitals, which is not present in the diamine complexes. In the Ru→bpy (3)MLCT state, the lower electron density on the metal-centered highest occupied molecular orbital (HOMO) weakens the Ru-S bond and results in the greater photoreactivity of 1 and 2 relative to that of 3 and 4. The more efficient photoinduced ligand exchange of the complexes possessing thioether ligands results in binding of 1 and 2 to DNA upon irradiation.     

Effect of shear on vesicle and lamellar phases of DDAB/lecithin ternary systems

The influence of shear flow on bilayer structures (vesicle and planar lamellar phases, L(α)), formed in DDAB/lecithin ternary systems, is studied by means of conventional rheology, Rheo NMR, and optical microscopy. The vesicles in the diluted (Lam(1)) phase are polydisperse multilamellae which turn into smaller monodisperse vesicles under shear. The concentrated (Lam(2)) phase is formed by non-oriented lamellae that do not surprisingly exhibit any pronounced shear-induced alignment prior to the transition into giant multilamellar vesicles. The biphasic region (Lam(1)+Lam(2)) shows a mosaic texture with a powder pattern indicating the prevalence of lamellae that transform into onions under shear.     

Fully reversible hydrogen absorption and desorption reactions with Sc(Al1−xMgx), x=0.0, 0.15, 0.20

The hydrogen storage properties of Sc(Al_1−xMg_x), x=0.0, 0.15, 0.20, have been studied by X-ray powder diffraction, thermal desorption spectroscopy, pressure-composition-isotherms and scanning electron microscopy techniques. Hydrogen is absorbed from the gas phase at 70 kPa and 400 °C under the formation of ScH₂ and aluminium with magnesium in solid solution. The reaction is fully reversible in vacuum at 500 °C and shows the hydrogenation-disproportionation-desorption-recombination (HDDR) behaviour. The activation energy of desorption was determined by the Kissinger method to 185 kJ/mol. The material is stable up to at least six absorption-desorption cycles and there is no change in particle size during cycling.     

Alternative approach to post column online isotope dilution ICP-MS

An alternative post column online double isotope dilution inductively coupled plasma mass spectrometry (ID-ICP-MS) method was developed. The resulting equation allows a straightforward calculation of the mass concentration of the analyte in the sample from the measured isotope ratio chromatogram. The use of a balance to determine and monitor the mass flow of the spike and a solution of the species under investigation as the reference are the two core components of this new method. Changes in the viscosity of the system eluent-analyte-spike will not affect the results due to the direct determination of the mass flow rate. The use of the species under investigation as the reference makes the method independent of the injected volume. To simplify matters, the integration of the isotope ratio chromatogram was done with Excel using Simpson's rule instead of sophisticated programs for transformation and integration. The advantages of the new approach were demonstrated with the help of the determination of selenomethionine in the selenized yeast reference material SELM-1 with liquid chromatography coupled to ICP-MS (HPLC ID-ICP-MS) applying the new online double IDMS method.     

Diels-Alder reactions of nitrobenzofurans: a simple dibenzofuran Synthesis. Theoretical studies using DFT methods

2- and 3-nitrobenzofurans are studied in polar thermal Diels-Alder reactions with normal electron demand using several structurally different dienes. A very strong electron-acceptor group, such as the nitro group, pushes the dienophilic character of these heterocyclic compounds. Since this substituent is easily extruded under thermal conditions, this reaction sequence becomes a simple method for the preparation of families of organic compounds with heteroatom rings. Part of this work is specifically concerned with theoretical studies using DFT methods. The global and local electrophilicity and nucleophilicity indices were calculated for the dienophiles and dienes used in this study. When 2-nitrobenzofuran and 3-nitrobenzofuran were reacted with isoprene, 1-trimethylsilyloxy-1,3-butadiene and Danishesfky’s diene, under different thermal reaction conditions they showed their dienophilic character taking part in normal-demand polar DA cycloaddition reactions.