Resolving the composition of protein complexes using a MALDI LTQ orbitrap

Current biological studies have been advanced by the continuous development of robust, accurate, and sensitive mass spectrometric technologies. The MALDI LTQ Orbitrap is a new addition to the Orbitrap configurations, known for their high resolving power and accuracy. This configuration provides features inherent to the MALDI source, such as reduced spectra complexity, forgiveness to contaminants, and sample retention for follow-up analyses with targeted or hypothesis-driven questions. Here we investigate its performance for characterizing the composition of isolated protein complexes. To facilitate the assessment, we selected two well characterized complexes from Saccharomyces cerevisiae, Apl1 and Nup84. Manual and automatic MS and MS/MS analyses readily resolved their compositions, with increased confidence of protein identification compared with our previous reports using MALDI QqTOF and MALDI IT. CID fragmentation of singly-charged peptides provided sufficient information for conclusive identification of the isolated proteins. We then assessed the resolution, accuracy, and sensitivity provided by this instrument in the context of analyzing the isolated protein assemblies. Our analysis of complex mixtures of singly-charged ions up to m/z 4000 showed that (1) the resolving power, inversely proportional to the square root of m/z, had over four orders of magnitude dynamic range; (2) internal calibration led to improved accuracy, with an average absolute mass error of 0. 5 ppm and a distribution centered at 0 ppm; and (3) subfemtomole sensitivity was achieved using both CHCA and DHB matrices. Additionally, our analyses of a synthetic phosphorylated peptide in mixtures showed subfemtomole level of detection using neutral loss scanning.     

Luminescence of Eu(DBM)3Phen-doped in azobenzene-containing copolymers—Effects of absorption overlapping of two components

Poly(N-isopropylacrylamide)-b-poly{6-[4-(4-methylphenyl-azo)phenoxy]hexylmethacrylate} (PNIPAM₃₂-b-PAzoMM₈) and poly(N-isopropylacrylamide)-b-poly{6-[methyl(4-nitrophenyldiazenyl)phenyl]aminohexylmethacrylate} (PNIPAM₃₂-b-PAzoNO₁₀) were prepared by reversible addition–fragmentation chain transfer (RAFT) radical polymerization. The optical properties of Eu(DBM)₃Phen (Eu, Europium; DBM, dibenzoylmethide; Phen, 1,10-phenanthroline)-doped azobenzene-containing copolymer vesicle solutions were studied by UV–vis and fluorescence spectroscopy. When the electronic transition bands of azobenzene and Eu(DBM)₃Phen overlapped at about 350 nm in PNIPAM₃₂-b-PAzoMM₈, the fluorescent emission intensity at 612 nm of Eu(DBM)₃Phen could be modulated by irradiation with UV and visible light. However, when the absorption of the azobenzene-moiety red-shifted to 477 nm in PNIPAM₃₂-b-PAzoNO₁₀, the luminescence intensity of Eu(DBM)₃Phen was not affected any longer. The difference between these two systems was possibly caused by the energy allocation in the luminescence process, which was discussed in detail.     

Toxicokinetics and the related metabolites in rainbow trout (Oncorhynchus mykiss) after exposure to decabromodiphenyl ether

Decabromodiphenyl ether (BDE209) is poorly absorbed by mammals, and little information is available on the toxicokinetics of BDE209 and its metabolites in fish. In the present study, rainbow trout (Oncorhynchus mykiss) were administered to 100 ng/g and 500 ng/g body wet weight of BDE209 via a single intraperitoneal injection and parent BDE209 and its metabolites were sequentially monitored for 28 days. The results showed that toxicokinetic profiles of BDE209 could be described by the one-compartment model. In the higher dose group (500 ng/g wet weight), the calculated half-life (t _1/2) and elimination rate (k _e) were 17.7 d and 0.039/d in the liver, and 100.3 d and 0.007/d in the muscle, respectively. Three major methoxylated brominated diphenyl ethers (MeO-BDEs) were detected with 2,2′,4,4′-tetrabromo-5-methoxydiphenyl ether (5-MeO-BDE47) being detected in all tissue samples. There was no significant temporal change of 5-MeO-BDE47 concentration in the muscle, whereas an exponential increase was observed in the liver. Therefore, the metabolism rate of BDE209 depended on the administered dose. BDE209 was hardly accumulated in the muscle of rainbow trout, while the liver was a primary metabolic organ. MeO-BDEs were formed via metabolism of BDE209, which probably played a significant role in fish toxicology as a potential indicator.     

Chemical composition and antifungal activity of essential oils of Thuja sutchuenensis, a critically endangered species endemic to China

The essential oils from leaves, twigs and stems of large trees and shrub-like trees of Thuja sutchuenensis were extracted by hydrodistillation and supercritical fluid extraction, and analyzed by GC and GC-MS. The essential oil composition differed significantly among the three organs, as well as between large trees and shrub-like trees. Furthermore, consistent with the eastern Asia-North American disjunct distribution of the genus, many differences in the essential oil composition between T. sutchuenensis and other Thuja species were apparent. The essential oils exhibited a certain degree of antifungal activity against six strains of human pathogenic fungi.     

New observation on a class of old reactions: Chemoselectivity for the solvent-free reaction of aromatic aldehydes with alkylketones catalyzed by a double-component inorganic base system

Solvent-free reactions of aromatic aldehydes with three representative ketones, including acetophenone, acetone and cyclohexanone, have been examined under the catalysis of a low-cost inorganic base system consisting of NaOH and K₂CO₃. It was found that the chemoselectivity of the reactions is in close relationship with the composition of the reactants and the doublecomponent catalyst. Under the optimized experimental conditions, 1,2,3,4,5-pentasubstituted cyclohexanols, α,β-unsaturated ketones and Claisen-Schmidt bicondensation products were obtained in high yields. Two Kostanecki’s triketones were separated, The composition and structure were affirmed by X-ray crystallographic analysis.     

Assessment of linear finite‐difference Poisson–Boltzmann solvers

CPU time and memory usage are two vital issues that any numerical solvers for the Poisson–Boltzmann equation have to face in biomolecular applications. In this study, we systematically analyzed the CPU time and memory usage of five commonly used finite‐difference solvers with a large and diversified set of biomolecular structures. Our comparative analysis shows that modified incomplete Cholesky conjugate gradient and geometric multigrid are the most efficient in the diversified test set. For the two efficient solvers, our test shows that their CPU times increase approximately linearly with the numbers of grids. Their CPU times also increase almost linearly with the negative logarithm of the convergence criterion at very similar rate. Our comparison further shows that geometric multigrid performs better in the large set of tested biomolecules. However, modified incomplete Cholesky conjugate gradient is superior to geometric multigrid in molecular dynamics simulations of tested molecules. We also investigated other significant components in numerical solutions of the Poisson–Boltzmann equation. It turns out that the time‐limiting step is the free boundary condition setup for the linear systems for the selected proteins if the electrostatic focusing is not used. Thus, development of future numerical solvers for the Poisson–Boltzmann equation should balance all aspects of the numerical procedures in realistic biomolecular applications. © 2010 Wiley Periodicals, Inc. J Comput Chem, 2010     

Measurement of neutron-induced activation cross sections of lanthanum at 14.8 MeV

Cross-sections for (n,p), (n,α), (n,n′α), (n,t) and (n,2p) reactions have been measured on ¹³⁹La isotope at the neutron energy 14.8 MeV using the activation technique in combination with high-resolution gamma-ray spectroscopy. Neutrons were produced via the ³H(d,n)⁴He reaction using a solid tritium–titanium target. The neutron fluences were determined using the monitor reaction ²⁷Al(n,α)²⁴Na. The neutron energy in this measurement was determined by cross section ratios for the ⁹⁰Zr(n,2n)^89m+gZr and ⁹³Nb(n,2n)^92mNb reactions. Data are reported for the following reactions: ¹³⁹La(n,p)¹³⁹Ba, ¹³⁹La(n,α)¹³⁶Cs, ¹³⁹La(n,n′α)^135mCs, ¹³⁹La (n,t)^137mBa, and ¹³⁹La(n,2p)¹³⁸Cs. The cross sections were discussed and compared with experimental data found in the literature, and with the comprehensive evaluation data in ENDF/B-VII.0, JENDL-3.3, JEFF-3.1/A, and TENDL-2008 libraries.     

Rapid magnetic solid-phase extraction based on magnetite/silica/poly(methacrylic acid–co–ethylene glycol dimethacrylate) composite microspheres for the determination of sulfonamide in milk samples

A novel magnetic solid-phase extraction (MSPE) sorbent, magnetite/silica/poly (methacrylic acid–co-ethylene glycol dimethacrylate) (Fe₃O₄/SiO₂/P(MAA-co-EGDMA)), was developed. This MSPE material was prepared by distillation–precipitation polymerization of MAA and EGDMA in the presence of Fe₃O₄/SiO₂ microspheres with the surface containing abundant reactive double bonds. The resultant sorbent material was characterized by elemental analysis, electron microscopy, X-ray diffraction and Fourier-transformed infrared spectroscopy. In this work, eleven sulfonamides (SAs) were selected as model analytes to validate the extraction performance of this new MSPE sorbent. Noticeably, the extraction can be carried out quickly, the extraction time for the SAs onto Fe₃O₄/SiO₂/P(MAA-co-EGDMA) sorbent can be clearly shortened to 0.5 min. The desorption solution of SAs was analyzed by LC–MS/MS, and the results showed that the recoveries of these compounds were in the range of 87.6–115.6%, with relative standard deviations ranging between 0.9% and 10.8%; the limit of detection were in the range of 0.5–49.5 ng/L.     

Calculating critical relative humidity from solubility according to Pitzer ion interaction model

The solubility and the critical relative humidity (H(cr)) of 14 drugs and inorganic salts were determined, the relationship between the H(cr) and the solubility was explored theoretically, and the H(cr) was calculated in the light of Raoult's law and Pitzer ion interaction model from their solubility. The results indicate that the H(cr) values calculated by Raoult's law in high humidity (H(cr)>80%) and by Pitzer ion interaction model in low humidity (H(cr)<80%) are comparable to the measured ones.     

Synthesis, self-assembly, and charge transporting property of contorted tetrabenzocoronenes

A facile route has been developed for the preparation of a new family of contorted 1.2,3.4,7.8,9.10-tetrabenzocoronenes (TBCs). A two-step cyclization reaction, i.e., oxidative photocyclization followed by FeCl(3)-mediated intramolecular cyclodehydrogenation, was carried out on the olefin precursors to obtain the final TBC compounds. These new TBC molecules have contorted conformation due to steric overcrowding as disclosed by single-crystal crystallographic analysis. Nevertheless, they showed extended π-conjugation compared with coronene and exhibited strong aggregation in solution. The thermal behavior and self-assembly of TBC-C8 in solid were studied by a combination of thermogravimetric analysis (TGA), differential scanning calorimetry (DSC), powder X-ray diffraction (XRD), scanning electron microscope (SEM), and transmission electron microscope (TEM). Compound TBC-C8 showed very good thermal and photostability and exhibited long-range ordered π-stacking in the bulk state. Moreover, uniform nanofibers with tens of micrometer length are formed in the drop-casted thin films. TBC-C8 also possesses a desirable HOMO energy level (-5.10 eV), which allows efficient charge injection from electrodes such as gold electrode. The charge carrier mobilities were determined by using the space-charge limited-current (SCLC) technique and high average hole mobility of 0.61 cm(2) V(-1) s(-1) was obtained for TBC-C8.