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PubMed2003

A strategy of plasma protein quantitation by selective reaction monitoring of an intact protein.

Immunoassays are used extensively in the quantitative analysis of proteins in plasma, urine, and other biological matrixes to support preclinical and clinical studies. Although immunoassays are both sensitive and rapid, difficulties during development of these assays are compounded by the need to have a specific antibody or antigen to the protein of interest. Furthermore, calibration curves of immunoassays are inherently nonlinear, and the technique often detects many structurally related components in addition to the analyte of interest. We have developed a novel strategy of analyzing protein concentrations in plasma by utilizing 96-well solid-phase extraction and LC-MS/MS detection of the intact protein. This strategy has been successfully applied in method development and assay validation of quantitatively analyzing protein rK5 concentrations in monkey plasma samples. Additional techniques such as precolumn regeneration and column heating were also incorporated into the assay. Total run time for each sample was approximately 15 min. An LLOQ of 99.2 ng/mL from a sample volume of 50 microL, corresponding to only 380 fmol (3.97 ng) of the rK5 analyte being injected onto the analytical column (assuming 100% extraction recovery), was obtained. The validated linear dynamic range was between 99.2 and 52 920.0 ng/mL, with a correlation coefficient (r(2)) ranging from 0.9972 and 0.9994. The intraassay CV for this assay was between 0.6 and 3.8%, and the interassay CV was between 1.7 and 3.2%. Interassay mean accuracies were between 101.5 and 104.7%. The assay has proven rugged and specific and has been employed to generate data in support of preclinical studies. This strategy for rK5 assay could be used for the development of bioanalytical assays to provide preclinical and clinical support for other protein drug candidates and, furthermore, for the validation of biomarkers discovered from proteomic research.

Amino Acid Sequence↗
PubMed2004

Influence of operating parameters on the retention of chromatographic particles by thermal field-flow fractionation.

We have investigated the retention behavior of chromatographic particles in thermal field-flow fractionation (FFF). Retention time is found to increase with increasing temperature drop across the channel thickness, as expected for species exhibiting a thermophoretic mobility. Experiments have been performed with a vertically oriented channel rather than by using the classical horizontal configuration as this leads to much more reproducible retention data. In acetonitrile, silica-based particles are more retained than octadecyl-bonded silica particles, which confirms our previous finding, by means of a different method, that the thermophoretic mobility of the latter is smaller than that of the former. Whatever the type of particles and the nature of the carrier liquid, the relative retention time is observed to decrease with increasing carrier flow rate. This indicates that a hydrodynamic lift force acts on particles to move them away from the accumulation wall, as is usually observed in all FFF experiments with micrometer-sized particles. However, upward and downward flow directions in the vertical channel lead to similar retention data, indicating that inertial lift forces have a minor influence on retention. In addition, the relative retention time steadily decreases with increasing sample concentration, suggesting that the hydrodynamic lift force increases significantly with sample concentration. Accordingly, we speculate that a new transport phenomenon, called shear-induced hydrodynamic diffusion, not previously accounted for in the modeling of retention in FFF, is controlling the migration of the particles in the FFF channel. Implications of the influence of this phenomenon in other FFF experiments are discussed.

Chemical Fractionation↗
PubMed1998

Routine DNA sequencing of 1000 bases in less than one hour by capillary electrophoresis with replaceable linear polyacrylamide solutions.

Long, accurate reads are an important factor for high-throughput de novo DNA sequencing. In previous work from this laboratory, a separation matrix of high-weight-average molecular mass (HMM) linear polyacrylamide (LPA) at a concentration of 2% (w/w) was used to separate 1000 bases of DNA sequence in 80 min with an accuracy close to 97% (Carrilho, E.; et al. Anal. Chem. 1996, 68, 3305-3313). In the present work, significantly improved speed and sequencing accuracy have been achieved by further optimization of factors affecting electrophoretic separation and data processing. A replaceable matrix containing a mixture of 2.0% (w/w) HMM (9 MDa) and 0.5% (w/w) low-weight-average molecular mass (50 kDa) LPA was employed to enhance the separation of DNA sequencing fragments in CE. Experimental conditions, such as electric field strength and column temperature, as well as internal diameter of the capillary column, have been optimized for this mixed separation matrix. Under these conditions, in combination with energy-transfer (BigDye) dye-labeled primers for high signal-to-noise ratio and a newly developed expert system for base calling, the electrophoretic separation of 1000 DNA sequencing fragments of both standard (M13mp18) and cloned single-stranded templates from human chromosome 17 could be routinely achieved in less than 55 min, with a base-calling accuracy between 98 and 99%. Identical read length, accuracy, and migration time were achieved in more than 300 consecutive runs in a single column.

Acrylic Resins↗
PubMedDate not supplied

Evaluation of computational chemistry methods: crystallographic and cheminformatics analysis of aminothiazole methoximes.

Cheminformatics is used to validate the capabilities of widely used quantum chemistry and molecular mechanics methods. Among the quantum methods examined are the semiempirical MNDO, AM1, and PM3 methods, Hartree-Fock (ab initio) at a range of basis set levels, density functional theory (DFT) at a range of basis sets, and a post-Hartree-Fock method, local Moller-Plesset second-order perturbation theory (LMP2). Among the force fields compared are AMBER, MMFF94, MMFF94s, OPLS/A, OPLS-AA, Sybyl, and Tripos. Programs used are Spartan, MacroModel, SYBYL, and Jaguar. The test molecule is (2-amino-5-thiazolyl)-alpha-(methoxyimino)-N-methylacetamide, a model of the aminothiazole methoxime (ATMO) side chain of third-generation cephalosporin antibacterial agents. The Ward hierarchical clustering technique yields an insightful comparison of experimental (X-ray) and calculated (energy optimized) bond lengths and bond angles. The computational chemistry methods are also compared in terms of the potential energy curves they predict for internal rotation. Clustering analysis and regression analysis are compared. The MMFF94 force field such as implemented in MacroModel is the best overall computational chemistry method at reproducing crystallographic data and conformational properties of the ATMO moiety. This work demonstrates that going to a higher level of quantum theory does not necessarily give better results and that quantum mechanical results are not necessarily better than molecular mechanics results.

Journal Article↗
PubMed2002

Thermodynamics of carbon dioxide hydrate formation in media with broad pore-size distributions.

Equilibrium pressures for the dissociation of carbon dioxide hydrates confined in silica gel pores of nominal radii 7.5, 5.0, and 3.0 nm were measured over a wide temperature range and were observed to be higher than those for bulk carbon dioxide hydrate. Models that have been previously reported in the literature are used to determine the pore radius involved in each equilibrium associated with these data, exactly reproducing the experimental equilibrium pressure. Based on these models, pore volume distributions are reconstructed and compared to those obtained from nitrogen desorption isotherms. This comparison indicates that in the nominal 7.5 nm pores the hydrate formed nearly uniformly in the available pores, while in the nominal 5.0 and 3.0 nm pores it did not.

Carbon Dioxide↗
PubMed2002

Competing interactions in the tetranuclear spin cluster [Ni[(OH)(2)Cr(bispictn)](3)]I(5).5H(2)O. An inelastic neutron scattering and magnetic study.

The properties of the spin state manifold of the tetranuclear cluster Ni[(OH)(2)Cr(bispictn)](3)]I(5).5H(2)O (bispictn = N,N'-bis(2-pyridylmethyl)-1,3-propanediamine) are investigated by combining magnetic susceptibility and magnetization measurements with an inelastic neutron scattering (INS) study on an undeuterated sample of Ni[(OH)(2)Cr(bispictn)](3)]I(5).5H(2)O. The temperature dependence of the magnetic susceptibility indicates an S = (1)/(2) ground state, which requires antiferromagnetic interactions both between Cr(3+) and Ni(2+) ions and among the Cr(3+) ions. INS reveals potential single-ion anisotropies to be negligibly small and enables an accurate determination of the exchange parameters. The best fit to the experimental energy level diagram is obtained by an isotropic spin Hamiltonian H = J(CrNi)(S(1)().S(4)() + S(2)().S(4)() + S(3)().S(4)()) + J(CrCr)(S(1)().S(2)() + S(1)().S(3)() + S(2)().S(3)()) with J(CrNi) = 1.47 cm(-)(1) and J(CrCr) = 1.25 cm(-)(1). With this model, the experimental intensities of the observed INS transitions as well as the temperature dependence of the magnetic data are reproduced. The resulting overall antiferromagnetic exchange is rationalized in terms of orbital exchange pathways and compared to the situation in oxalato-bridged clusters.

Journal Article↗
PubMed2002

Mechanism of C[bond]H bond activation/C[bond]C bond formation reaction between diazo compound and alkane catalyzed by dirhodium tetracarboxylate.

The B3LYP density functional studies on the dirhodium tetracarboxylate-catalyzed C-H bond activation/C-C bond formation reaction of a diazo compound with an alkane revealed the energetics and the geometry of important intermediates and transition states in the catalytic cycle. The reaction is initiated by complexation between the rhodium catalyst and the diazo compound. Driven by the back-donation from the Rh 4d(xz) orbital to the C[bond]N sigma*-orbital, nitrogen extrusion takes place to afford a rhodium[bond]carbene complex. The carbene carbon of the complex is strongly electrophilic because of its vacant 2p orbital. The C[bond]H activation/C[bond]C formation proceeds in a single step through a three-centered hydride transfer-like transition state with a small activation energy. Only one of the two rhodium atoms works as a carbene binding site throughout the reaction, and the other rhodium atom assists the C[bond]H insertion reaction. The second Rh atom acts as a mobile ligand for the first one to enhance the electrophilicity of the carbene moiety and to facilitate the cleavage of the rhodium[bond]carbon bond. The calculations reproduce experimental data including the activation enthalpy of the nitrogen extrusion, the kinetic isotope effect of the C[bond]H insertion, and the reactivity order of the C[bond]H bond.

Journal Article↗
PubMed2003

Thermochemistry of arylselanyl radicals and the pertinent ions in acetonitrile.

Reduction and oxidation potentials of a series of parasubstituted phenylselanyl radicals, XC(6)H(4)Se(*), have been measured using photomodulated voltammetry in acetonitrile. The thermodynamic significance of these data was substantiated through a study of the oxidation process of the pertinent selenolates in linear sweep voltammetry. Both the reduction and the oxidation potentials correlate linearly with the Hammett substituent coefficients sigma and sigma(+) leading in the latter case to slopes, rho(+), of 2.5 and 3.8, respectively. Through comparison of these slopes with those published previously for the O- and S-centered analogues, it is revealed that the pi-interaction becomes progressively smaller as the size of the radical center increases in the order O, S, and Se. Solvation energies of the pertinent selenolates and selanylium ions have been extracted from thermochemical cycles incorporating the measured electrode potentials for XC(6)H(4)Se(*) as well as electron affinities and ionization potentials obtained from theoretical calculations at the B3LYP/6-31+G(d) level. The extracted data show the expected overall substituent dependency for both kinds of ions; that is, the absolute value of the solvation energy decreases as the charge becomes more delocalized. The data have also been compared with solvation energies computed using the polarizable continuum model (PCM). Interestingly, we find that, while the model seems to work well for selenolates, it underestimates the solvation of selanylium ions in acetonitrile by as much as 25 kcal mol(-)(1). These large deviations are ascribed to the fact that the PCM method does not take specific solvent effects into account as it treats the solvent as a continuum described solely by its dielectric constant. Gas-phase calculations show that the arylselanylium ions can coordinate covalently to one or two molecules of acetonitrile in strong Ritter-type adducts. When this strong interaction is included in the solvation energy calculations by means of a combined supermolecule and PCM approach, the experimental data are reproduced within a few kcal mol(-)(1). Although the energy difference of the singlet and triplet spin states of the arylselanylium ions is small for the gas-phase structures, the singlet cation is undoubtedly the dominating species in solution because the triplet cation lacks the ability to form covalent bonds.

Acetonitriles↗
PubMed2004

Mechanisms of HNO and NO production from Angeli's salt: density functional and CBS-QB3 theory predictions.

The mechanism of decomposition of Angeli's salt, Na(2)N(2)O(3), was explored with B3LYP and CBS-QB3 computational methods. Angeli's salt produces both nitroxyl (HNO) and nitric oxide (NO), depending upon the pH of the solution. These calculations show that protonation on N(2), while less favorable than O protonation, leads spontaneously to HNO production, while diprotonation at O(3) leads to NO generation. K(a) values for protonation at different centers and rate constants have been found which reproduce experimental data satisfactorily.

Models, Chemical↗
PubMed2000

A capillary electrophoresis laser-induced fluorescence method for analysis of potato glycoalkaloids based on a solution-phase immunoassay. 1. Separation and quantification of immunoassay products.

Solution-phase immunoassays are typically faster and more precise than ELISAs. This research developed a solution-phase for the immunoassay of potato glycoalkaloids (GAs) based on quantification by capillary electrophoresis (CE) with laser-induced fluorescence (LIF) detection. Solanidine coupled to 4'-(aminomethyl)fluorescein and a polyclonal antibody solution were used as the immunoreagents. Unbound fluorescent solanidine was detected by CE-LIF (excitation 488 nm, emission 520 nm). Optimum resolution of immunoassay products was achieved with a buffer consisting of 50 mM phosphate, 10% (v/v) methanol, and 1.5 mM SDS, pH 7.5. A plot of signal vs log [GA] produced a sigmoidal curve typical of immunoassays. Analysis of extracts of sprouted Yukon Gold potato tubers and nonsprouted Yukon Gold tubers resulted in total [GA] of 98 microg/g (RSD 9%) and 55 microg/g (RSD 9%), respectively. The findings indicated that CE-LIF coupled with a solution-phase immunoassay can be used to quantify total GA in potatoes.

Carbohydrate Sequence↗
PubMed2002

Planar transition structures in the epoxidation of alkenes. A DFT study on the reaction of peroxyformic acid with norbornene derivatives.

We studied, with the RB3LYP/6-311+G(d,p) method, the mechanism of peroxyformic acid epoxidation of norbornene, norbornadiene, tetramethylethene, and anti- and syn-sesquinorbornenes. The transition structures (TSs) for the reaction of tetramethylethene and norbornene show a perfect spiro geometry (the peroxy acid plane is perpendicular to the C=C bond axis) with synchronous bond formation. Also three out of the four TSs of the norbornadiene reaction are spiro-like, but the highly asynchronous syn,endo-TS has a planar-like geometry. anti- and syn-sesquinorbornenes are substrates that, because of steric constraints, cannot easily accommodate spiro-like TSs. In fact, we managed to locate only a planar-like TS and a planar TS (the peroxy acid plane contains the C=C bond axis), respectively, for these substrates. These planar TSs are "nonconcerted" since they are strongly unsymmetrical and only one of the C-O bonds of the oxirane ring is significantly formed. IRC analysis, while confirming that formation of one C-O bond fully precedes that of the other, also suggests that all this can take place without formation of intermediates, that is, within a "nonconcerted one-step process". Our theoretical data correctly reproduce the experimental facial syn selectivity of norbornene and norbornadiene epoxidations and compare well with the experimental activation free energies of the peroxy acid epoxidation of all the olefins reported here. This accord validates the method used as adequate to deal with the reactivity of these systems.

Journal Article↗
PubMed2005

Polarizable empirical force field for alkanes based on the classical Drude oscillator model.

Recent extensions of potential energy functions used in empirical force field calculations have involved the inclusion of electronic polarizability. To properly include this extension into a potential energy function it is necessary to systematically and rigorously optimize the associated parameters based on model compounds for which extensive experimental data are available. In the present work, optimization of parameters for alkanes in a polarizable empirical force field based on a classical Drude oscillator is presented. Emphasis is placed on the development of parameters for CH3, CH2, and CH moieties that are directly transferable to long chain alkanes, as required for lipids and other biomolecules. It is shown that a variety of quantum mechanical and experimental target data are reproduced by the polarizable model. Notable is the proper treatment of the dielectric constant of pure alkanes by the polarizable force field, a property essential for the accurate treatment of, for example, hydrophobic solvation in lipid bilayers. The present alkane force field will act as the basis for the aliphatic moieties in an extensive empirical force field for biomolecules that includes the explicit treatment of electronic polarizability.

Alkanes↗
PubMed2006

X- (X = O, S) ions in alkali halide lattices through density functional calculations. 1. Substitutional defect models.

Monoatomic X- (X = O, S) chalcogen centers in MZ (M = Na, K, Rb and Z = Cl, Br, I) alkali halide lattices are investigated within the framework of density functional theory with the principal aim to establish defect models. In electron paramagnetic resonance (EPR) experiments, X- defects with tetragonal, orthorhombic, and monoclinic g-tensor symmetry have been observed. In this paper, models in which X- replaces a single halide ion, with a next nearest neighbor and a nearest neighbor halide vacancy, are validated for the X- centers with tetragonal and orthorhombic symmetry, respectively. As such defect models are extended, the ability to reproduce experimental data is a stringent test for various computational approaches. Cluster in vacuo and embedded cluster schemes are used to calculate energy and EPR parameters for the two vacancy configurations. The final assignment of a defect structure is based on the qualitative and quantitative reproduction of experimental g and (super)hyperfine tensors.

Journal Article↗
PubMedDate not supplied

Identification and quantification of differentially expressed proteins in E-cadherin deficient SCC9 cells and SCC9 transfectants expressing E-cadherin by dimethyl isotope labeling, LC-MALDI MS and MS/MS.

A strategy based on isotope labeling of peptides and liquid chromatography matrix-assisted laser desorption ionization mass spectrometry (LC-MALDI MS) has been employed to accurately quantify and confidently identify differentially expressed proteins between an E-cadherin-deficient human carcinoma cell line (SCC9) and its transfectants expressing E-cadherin (SCC9-E). Proteins extracted from each cell line were tryptically digested and the resultant peptides were labeled individually with either d(0)- or d(2)-formaldehyde. The labeled peptides were combined and the peptide mixture was separated and fractionated by a strong cation exchange (SCX) column. Peptides from each SCX fraction were further separated by a microbore reversed-phase (RP) LC column. The effluents were then directly spotted onto a MALDI target using a heated droplet LC-MALDI interface. After mixing with a MALDI matrix, individual sample spots were analyzed by MALDI quadrupole time-of-flight MS, using an initial MS scan to quantify the dimethyl labeled peptide pairs. MS/MS analysis was then carried out on the peptide pairs having relative peak intensity changes of greater than 2-fold. The MS/MS spectra were subjected to database searching for protein identification. The search results were further confirmed by comparing the MS/MS spectra of the peptide pairs. Using this strategy, we detected and compared relative peak intensity changes of 5480 peptide pairs. Among them, 320 peptide pairs showed changes of greater than 2-fold. MS/MS analysis of these changing pairs led to the identification of 49 differentially expressed proteins between the parental SCC9 cells and SCC9-E transfectants. These proteins were determined to be involved in different pathways regulating cytoskeletal organization, cell adhesion, epithelial polarity, and cell proliferation. The changes in protein expression were consistent with increased cell-cell and cell-matrix adhesion and decreased proliferation in SCC9-E cells, in line with E-cadherin tumor suppressor activity. Finally, the accuracy of the MS quantification and subcellular localization for 6 differentially expressed proteins were validated by immunoblotting and immunofluorescence assays.

Amino Acid Sequence↗
PubMed1998

DNA methylation patterns of Melandrium album chromosomes.

Melandrium album (syn. Silene latifolia) belongs to dioecious plant species possessing heteromorphic sex chromosomes, X and Y. Our previous experiments using in situ nick translation and replication kinetics analysis indicated structural and functional differences between the two X chromosomes in homogametic female cells. Here we show DNA methylation patterns of M. album root tip chromosomes using the indirect immunofluorescence approach with a monoclonal antibody raised against 5-methylcytosine (5-mC). In male cells, a more intensive 5-mC labelling on the shorter arm of the only X chromosome was observed in comparison with the longer X arm. A global hypermethylation of the male Y chromosome was not found, which indicates its prevalent euchromatic character. In female cells, the specific 5-mC pattern of the X chromosome was found on a single X chromosome, whereas the other X displayed an overall higher level of 5-mC labelling. Application of a hypomethylating drug, 5-azacytidine (5-azaC), during seed germination led to a deletion of any specific differences in the 5-mC distribution between the two X chromosomes. Confocal laser scanning microscopy analysis of DNA methylation in interphase nuclei showed hypermethylated domains that were efficiently decondensed and hypomethylated by 5-azaC treatment. The presented data show reproducible differences in the DNA methylation patterns between the two X chromosomes in M. album female somatic cells, which indicate their distinct transcriptional activities as a possible consequence of the negative dosage compensation of X-linked genes.

Azacitidine↗
PubMed2002

A comparison of methods for calculating NMR cross-relaxation rates (NOESY and ROESY intensities) in small peptides.

Three methods for calculating nuclear magnetic resonance cross-relaxation rates from molecular dynamics simulations of small flexible molecules have been compared in terms of their ability to reproduce relaxation data obtained experimentally and to produce consistent descriptions of the system. The importance of the accuracy of the simulation versus the amount of sampling of phase space has also been assessed by comparing different length simulations performed with different time step schemes. A nine-residue peptide from the protein HPr of E. coli was used as a test system. The work shows that, in this case, single conformations or a limited ensemble of configurations are insufficient to properly describe the behavior of the peptide and that different approaches to incorporate molecular motions lead to significant differences in the cross-relaxation rates calculated. The correlation between the cross-relaxation rates calculated from simulations performed with different time step schemes was high and increased with increasing simulation length indicating that the extent of sampling is more important than the details of the atomic motion.

Bacterial Proteins↗
PubMed2004

A cell fractionation approach for the quantitative analysis of subcellular drug disposition.

PURPOSE: The purpose of this work was to develop and validate a method that can be used to quantify drugs associated with intracellular compartments. METHODS: The human leukemic cell line U-937 was used to evaluate the distribution of model compounds with known and different subcellular distribution profiles. Lysotracker Red is a lysosomal vital stain and doxorubicin is an anticancer agent with a strong propensity for nuclear accumulation in U-937 cells. After incubation with compounds, cells were separated into fractions containing nuclei, cytosol, and cytoplasmic organelles (lysosomes, mitochondria, Golgi apparatus). Compounds contained within isolated fractions were subsequently extracted and analyzed by high-performance liquid chromatography. Diffusion of compounds from isolated organelles was also investigated. RESULTS: Using this approach we have shown that the model compounds Lysotracker Red and doxorubicin preferentially accumulated within lysosomes and nuclei, respectively. We have reproducibly determined concentrations of these compounds in each of the cellular fractions. We have also shown that diffusion of these compounds from isolated cellular compartments was minimal during the time required to complete the experimental procedure. CONCLUSIONS: The analytical approach described in this manuscript yielded reproducible quantitative data regarding the intracellular distribution of model compounds in U-937 cells. With the aid of a relatively sensitive analytical assay, this technique should be useful for most drugs that have a specific concentrative mechanism for organelle accumulation similar to Dox and LTR.

Cell Fractionation↗
PubMed2006

Random intercept item factor analysis.

The common factor model assumes that the linear coefficients (intercepts and factor loadings) linking the observed variables to the latent factors are fixed coefficients (i.e., common for all participants). When the observed variables are participants' observed responses to stimuli, such as their responses to the items of a questionnaire, the assumption of common linear coefficients may be too restrictive. For instance, this may occur if participants consistently use the response scale idiosyncratically. To account for this phenomenon, the authors partially relax the fixed coefficients assumption by allowing the intercepts in the factor model to change across participants. The model is attractive when m factors are expected on the basis of substantive theory but m + 1 factors are needed in practice to adequately reproduce the data. Also, this model for single-level data can be fitted with conventional software for structural equation modeling. The authors demonstrate the use of this model with an empirical data set on optimism in which they compare it with competing models such as the bifactor and the correlated trait-correlated method minus 1 models.

Factor Analysis, Statistical↗