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PubMed2005

Development of 2D band-target entropy minimization and application to the deconvolution of multicomponent 2D nuclear magnetic resonance spectra.

Spectral reconstruction from multicomponent spectroscopic data is the frequent primary goal in chemical system identification and exploratory chemometric studies. Various methods and techniques have been reported in the literature. However, few algorithms/methods have been devised for spectral recovery without the use of any a priori information. In the present studies, a higher dimensional entropy minimization method based on the BTEM algorithm (Widjaja, E.; Li, C.; Garland, M. Organometallics 2002, 21, 1991-1997.) and related techniques were extended to large-scale arrays, namely, 2D NMR spectroscopy. The performance of this novel method had been successfully verified on various real experimental mixture spectra from a series of randomized 2D NMR mixtures (COSY NMR and HSQC NMR). With the new algorithm and raw multicomponent NMR alone, it was possible to reconstruct the pure spectroscopic patterns and calculate the relative concentration of each species without recourse to any libraries or any other a priori information. The potential advantages of this novel algorithm and its implications for general chemical system identification of unknown mixtures are discussed.

Journal Article↗
PubMed2005

Deconvolution and quantification of hydrocarbon-like and oxygenated organic aerosols based on aerosol mass spectrometry.

A new technique has been developed to deconvolve and quantify the mass concentrations of hydrocarbon-like and oxygenated organic aerosols (HOA and OOA) using highly time-resolved organic mass spectra obtained with an Aerodyne Aerosol Mass Spectrometer (AMS). This technique involves a series of multivariate linear regressions that use mass-to-charge ratios (ml/s) 57 (mostly C4H9+) and 44 (mostly CO2+)-the identified AMS mass spectral tracers for HOA and OOA, respectively-as the initial principal components. Two algorithms have been developed: algorithm 1 is based solely on m/z 44 and m/z 57, and algorithm 2 is an iterative procedure expanded from algorithm 1. This technique was applied to the AMS organic aerosol data acquired at the EPA Pittsburgh Supersite during September 2002. The reconstructed organic concentrations (= HOA + OOA) agree well with the measured values (r2 = 0.997, slope = 0.998), and the reconstructed organic data matrix (size = 3199 time steps x 300 m/z's) explains 99% of the variance in the measured time series. In addition, the extracted mass spectrum of HOA shows high similarity to those of diesel exhaust, lubricating oil, and freshly emitted traffic aerosols observed in urban areas, while the spectrum of OOA closely resembles those of aged organic aerosols sampled in rural areas and also shows similarity with the spectrum of fulvic acid- a humic-like substance that is ubiquitous in the environment and has previously been used as an analogue to represent polyacid components found in highly processed and oxidized atmospheric organic aerosols. There is evidence for the presence of a third component, although its contribution to the total organic signal appears to be small in this study. The most important result is that m/z 44 and m/z 57 are reliable AMS mass spectral "markers" that provide the "first guess" for algorithm 2 which allows the quantitative description of the organic aerosol concentration and mass spectra over a period of 16 days in a major urban area and allows the extraction of mass spectra of OOA and HOA that can be interpreted chemically. These findings indicate the potential of performing organic source apportionment on the basis of total particle mass, rather than on the basis of organic tracer compounds that contribute a small fraction of this mass.

Aerosols↗
PubMed2001

Deconvolution and assignment of different optical transitions of the blue copper protein azurin from optically detected electron paramagnetic resonance spectroscopy.

Magnetic circular dichroism is a powerful spectroscopic tool for the assignment of optical resonance lines. An extension of this technique, microwave-modulated circular dichroism, provides additional details, in particular information about the orientation of optical transition moments. It arises from magnetization precessing around the static magnetic field, excited by a microwave field, in close analogy to electron paramagnetic resonance (EPR). In this paper we investigate the visible and near-infrared spectrum of the blue copper protein Pseudomonas aeruginosa azurin. Using a nonoriented sample (frozen solution), we apply this technique to measure the variation of the optical anisotropy with the wavelength. A comparison with the optical anisotropies of the possible ligand-field and charge-transfer transitions allows us to identify individual resonance lines in the strongly overlapping spectrum and assign them to specific electronic transitions. The technique is readily applicable to other proteins with transition metal centers.

Anisotropy↗
PubMed2006

Deconvoluting the structural and drug-recognition complexity of the G-quadruplex-forming region upstream of the bcl-2 P1 promoter.

The human bcl-2 gene contains a GC-rich region upstream of the P1 promoter that has been shown to be critically involved in the regulation of bcl-2 gene expression. We have demonstrated that the guanine-rich strand of the DNA in this region can form any one of three distinct intramolecular G-quadruplex structures. Mutation and deletion analysis permitted isolation and identification of three overlapping DNA sequences within this element that formed the three individual G-quadruplexes. Each of these was characterized using nondenaturing gel analysis, DMS footprinting, and circular dichroism. The central G-quadruplex, which is the most stable, forms a mixed parallel/antiparallel structure consisting of three tetrads connected by loops of one, seven, and three bases. Three different G-quadruplex-interactive agents were found to further stabilize these structures, with individual selectivity toward one or more of these G-quadruplexes. Collectively, these results suggest that the multiple G-quadruplexes identified in the promoter region of the bcl-2 gene are likely to play a similar role to the G-quadruplexes in the c-myc promoter in that their formation could serve to modulate gene transcription. Last, we demonstrate that the complexity of the G-quadruplexes in the bcl-2 promoter extends beyond the ability to form any one of three separate G-quadruplexes to each having the capacity to form either three or six different loop isomers. These results are discussed in relation to the biological significance of this G-quadruplex-forming element in modulation of bcl-2 gene expression and the inherent complexity of the system where different G-quadruplexes and loop isomers are possible.

Base Sequence↗
PubMed2000

Cross-referenced combinatorial libraries for the discovery of metal-complexing ligands: library deconvolution by LC-MS.

N-Acylthioureas are excellent ligands for a variety of heavy metals, but their metal selectivity is highly dependent on the precise nature of the substituents present. In this paper we show how combinatorial chemistry techniques can be used to establish relative affinities for copper within a mixture of 100 such thioureas. Following a straightforward synthesis, and copper extraction using standard liquid-liquid extraction techniques, LC-MS was used to identify the ligands which bind most strongly to the copper ions. Among the 100 ligands XC(O)N(Z)C(S)NHY, the most important substituent is the Y group bound to the NH: only aromatic Y substituents give strong binding to copper. The acyl X substituents are invariably aromatic, and an electron-rich X group is best; the affinity for copper seems to be less dependent on the Z substituent, although a large group such as benzyl disfavours copper binding. The five ligands from the library which bind copper most strongly have been clearly identified by a series of experiments: they all have aromatic groups in the Y position, but the X and Z substituents can be more varied. This is a very convincing demonstration of the power of combinatorial methods: to have found the same information by conventional methods would have required a lengthy and repetitive series of syntheses and investigations. In addition, our results give some preliminary evidence for synergistic binding of two different ligands, but this requires further investigation.

Journal Article↗
PubMed2006

CYP121, CYP51 and associated redox systems in Mycobacterium tuberculosis: towards deconvoluting enzymology of P450 systems in a human pathogen.

An extraordinary array of P450 (cytochrome P450) enzymes are encoded on the genome of the human pathogen Mycobacterium tuberculosis (Mtb) and in related mycobacteria and actinobacteria. These include the first characterized sterol 14alpha-demethylase P450 (CYP51), a known target for azole and triazole drugs in yeasts and fungi. To date, only two Mtb P450s have been characterized in detail: CYP51 and CYP121. The CYP121 P450 shows structural relationships with P450 enzymes involved in synthesis of polyketide antibiotics. Both P450s exhibit tight binding to a range of azole drugs (e.g. clotrimazole and fluconazole) and the same drugs also have potent effects on growth of mycobacteria (but not of e.g. Escherichia coli). Atomic structures are available for both Mtb CYP51 and CYP121, revealing modes of azole binding and intriguing mechanistic and structural aspects. This paper reviews our current knowledge of these and the other P450 systems in Mtb including recent data relating to the reversible conversion of the CYP51 enzyme between P450 (thiolate-co-ordinated) and P420 (thiol-co-ordinated) species on reduction of the haem iron in the absence of a P450 substrate. The accessory flavoprotein and iron-sulfur proteins required to drive P450 catalysis are also discussed, providing an overview of the current state of knowledge of Mtb P450 redox systems.

Azoles↗
PubMed1980

The reproducibility of double-isotope deconvolution measurements of intestinal calcium absorption.

1. Radiocalcium absorption was measured in duplicate in 10 subjects by the double-isotope method, with calcium as the oral carrier (2.5 mmol). Analysis of variance gave 95% confidence limits for a single measurement of fractional absorption and maximum absorption rate in a given individual of +/- 16.5% of administered dose and +/- 18.2% of dose/h respectively. 2. The size of these within individual variations suggests that alterations in the rate of calcium absorption may contribute to the week-to-week stabilization of some other controlled variable, such as plasma concentration of calcium. 3. In six of the subjects, calcium absorption was also measured with calcium loads at concentrations of 0.5, 5.0 and 20 mmol. Significant falls in fractional absorption, maximum absorption rate and mean transfer rate occurred as the load increased, together with a rise in mean transit time. Although between-individual differences at a given load were considerable, given a single-test result with a known carrier load, it is possible to predict quite accurately the results which would be obtained if a different carrier load were to be given.

Analysis of Variance↗
PubMed2000

Radiolytic studies of trimethylamine dehydrogenase. Spectral deconvolution of the neutral and anionic flavin semiquinone, and determination of rate constants for electron transfer in the one-electron reduced enzyme.

Trimethylamine dehydrogenase from the pseudomonad Methylophilus methylotrophus has been examined using the technique of pulse radiolysis to rapidly introduce a single reducing equivalent into the enzyme. Using enzyme that has had its iron-sulfur center rendered redox-inert by prior reaction with ferricenium hexafluorophosphate, we determined the spectral change associated with formation of both the anionic and neutral forms that were generated at high and low pH, respectively, of the unique 6-cysteinyl-FMN of the enzyme. With native enzyme, electron transfer was observed within the radiolytically generated one-electron reduced enzyme but only at low pH (6.0). The kinetics and thermodynamics of this electron transfer in one-electron reduced enzyme may be compared with that studied previously in the two-electron reduced enzyme. In contrast to previous studies with two-electron reduced enzyme in which a pK(a) of approximately 8 was determined for the flavin semiquinone, in the one-electron reduced enzyme the semiquinone was not substantially protonated even at pH 6. 0. These results indicate that reduction of the iron-sulfur center of the enzyme significantly decreases the pK(a) of the flavin semiquinone of the active site. This provides further evidence, in conjunction with the strong magnetic interaction known to exist between the centers in the two-electron reduced enzyme, that the two redox-active centers in trimethylamine dehydrogenase are in intimate contact with one another in the active site of the enzyme.

Catalysis↗
PubMed2005

Yeast nucleosome DNA pattern: deconvolution from genome sequences of S. cerevisiae.

Positional correlation analysis for the complete genome of Saccharomyces cerevisiae is performed with the aim to reveal possible chromatin-related sequence features. A strong periodicity with the period 10.4 bases is detected in the distance histograms for the dinucleotides AA and TT, with the characteristic decay distance of approximately 50 base pairs. The oscillations are observed as well in the distributions of other dinucleotides. However, the respective amplitudes are small, consistent with secondary effects, due to dominant periodicity of AA and TT. The observations are in accord with earlier data on the chromatin sequence periodicities and nucleosome DNA sequence patterns. The autocorrelations of AA and TT dinucleotides in yeast include also a counter-phase component. A tentative DNA sequence pattern for the yeast nucleosomes is suggested and verified by comparison of its autocorrelation plots with the respective natural autocorrelations. The nucleosome mapping guided by the pattern is in accord with experimental data on the linker length distribution in yeast.

Algorithms↗
PubMed1997

The sleep-inducing lipid oleamide deconvolutes gap junction communication and calcium wave transmission in glial cells.

Oleamide is a sleep-inducing lipid originally isolated from the cerebrospinal fluid of sleep-deprived cats. Oleamide was found to potently and selectively inactivate gap junction-mediated communication between rat glial cells. In contrast, oleamide had no effect on mechanically stimulated calcium wave transmission in this same cell type. Other chemical compounds traditionally used as inhibitors of gap junctional communication, like heptanol and 18beta-glycyrrhetinic acid, blocked not only gap junctional communication but also intercellular calcium signaling. Given the central role for intercellular small molecule and electrical signaling in central nervous system function, oleamide- induced inactivation of glial cell gap junction channels may serve to regulate communication between brain cells, and in doing so, may influence higher order neuronal events like sleep induction.

Animals↗