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PubMed1999

Use of evolutionary factor analysis in the spectroelectrochemistry of Escherichia coli sulfite reductase hemoprotein and a Mo/Fe/S cluster.

The deconvolution of spectroelectrochemical data is often quite difficult if the spectra of intermediates are not known. Factor analysis, however, has been shown to be a powerful technique which can make it possible to deconvolute overlapping spectra. In this work, evolving factor analysis will be used to determine the number of intermediates and the spectra of those species for two typical spectroelectrochemical experiments: linear scan voltammetry and chronoabsorptometry in a thin-layer cell. The first system was the reduction of E. coli sulfite reductase hemoprotein (SiR-HP). Principal factor analysis indicated that three species were present. By using evolving factor analysis, the potential regions where each of the species were present were identified, and their concentrations and spectra were determined by the use of the mass balance equation. The spectra of the one-electron (SiR-HP1-) and two-electron (SiR-HP2-) reduced product were compared with previous work. The second experiment was the chronoabsorptometry of Cl2FeS2MoS2FeCl2(2-) in methylene chloride. This experiment indicated that five species were present during the experiment. The entire set of 61 spectra were fit by assuming that there were 4 species present during the electrolysis. The rate constant for the appearance of subsequent species fit quite well with the rate constant for the disappearance of previous species. The spectra of the intermediates and final product were obtained using evolving factor analysis and a mass balance equation. Identification of the fifth species, which was probably the initial reduction product, Cl2FeS2MoS2FeCl2(3-), was difficult due to its low concentration and the fact that it was present in the same time region as the starting material.

Bacterial Proteins↗
PubMed1991

Differential scanning calorimetry study of reversible, partial unfolding transitions in dodecameric glutamine synthetase from Escherichia coli.

Partial unfolding of dodecameric glutamine synthetase (GS) from Escherichia coli has been studied by differential scanning calorimetry (DSC). A single endotherm (tm = 51.6 +/- 0.1 degrees C and delta Hcal = 211 +/- 4 kcal/mol of enzyme) was observed in DSC experiments with Mn.GS in the presence of 1.0 mM free Mn2+ and 100 mM KCl at pH 7. The dodecameric structure of Mn.GS was retained throughout heating cycles, and thermal transitions were reversible as shown by rescans [with 6-18 mg of GS (Mr 622,000) from 15 to 68 degrees C at 20-60 degrees C/h] and by greater than 93% recovery of activity. A cooperative ratio delta Hcal/delta HvH of 1.6 +/- 0.1 and deconvolution analysis show two cooperative units (two-state transitions): t1 = 50.4 and t2 = 51.7 degrees C; the ratio of the relative sizes of thermally labile domains is approximately 1:2 as judged by delta H2/delta H1 approximately equal to 2. However, the thermally induced overall enthalpy change (0.34 cal/g) for GS dodecamer is only 5-10% of that for thermal unfolding of small globular proteins at 50 degrees C. The t1 and t2 values from deconvolutions of DSC data agree with t0.5 values previously calculated from spectral measurements of temperature-induced exposures of approximately 0.7 of 2 Trp and approximately 2 of 17 Tyr per subunit, respectively [Shrake et al. (1989) Biochemistry 28, 6281-6294], over a 14 degrees C temperature range using both stabilizing and destabilizing conditions for Mn.GS.(ABSTRACT TRUNCATED AT 250 WORDS)

Calorimetry, Differential Scanning↗
PubMed1994

Secondary structure of the nicotinic acetylcholine receptor: implications for structural models of a ligand-gated ion channel.

The secondary structure and effects of two ligands, carbamylcholine and tetracaine, on the secondary structure of affinity-purified nicotinic acetylcholine receptor (nAChR) from Torpedo has been studied using Fourier transform infrared spectroscopy (FTIR). FTIR spectra of the nAChR were acquired in both 1H2O and 2H2O buffer and exhibit spectral features indicative of a substantial alpha-helical content with lesser amounts of beta-sheet and random coil structures. The resolution enhancement techniques of Fourier self-deconvolution and Fourier derivation reveal seven component bands contributing to both the amide I band and amide I' band contours in 1H2O and 2H2O, respectively. Curve-fitting estimates of the nAChR secondary structure are consistent with the qualitative analysis of the FTIR spectra as follows: 39% alpha-helix, 35% beta-sheet, 6% turn, and 20% random coil. Of particular interest is the estimated alpha-helical content as this value places restrictions on models of the nAChR transmembrane topology and on the types of secondary structures that may contribute to functional domains, such as the ligand-binding site. The estimated alpha-helical content is sufficient to account for four transmembrane alpha-helices in each nAChR subunit as well as a substantial portion of the extracellular and/or the cytoplasmic domains. FTIR spectra were also acquired in the presence and absence of 1 mM carbamylcholine and 5 mM tetracaine to examine the effects of ligand binding on the secondary structure of the nAChR. The similarity of the spectra, even after spectral deconvolution, indicates that the secondary structure of the nAChR is essentially unaffected by desensitization.(ABSTRACT TRUNCATED AT 250 WORDS)

Animals↗
PubMed1987

Phage phi X174 probed by laser Raman spectroscopy: evidence for capsid-imposed constraint on DNA secondary structure.

The Raman spectrum of the isometric bacteriophage phi X174 contains a number of well-resolved bands which have been assigned unambiguously to proteins of the capsid or to the single-stranded DNA (ssDNA) genome. Additional Raman bands of protein and DNA, which are partially overlapped in the spectrum of virus, have been resolution enhanced by Fourier deconvolution to permit improved semiquantitative measurement of spectral intensities and frequencies for structural conclusions. Raman conformation markers indicate that the ssDNA molecule within the capsid contains nucleosides of C2'-endo sugar pucker and anti-glycoside bond orientation, but the nucleic acid backbone lacks the geometry characteristic of B-form DNA. The Raman profile of encapsidated phi X DNA indicates a backbone more similar to heat-denatured DNA than to DNA containing hairpinlike secondary structure. This finding suggests limited interbase interactions in the packaged genome, which is presumably the result of constraints imposed by the viral capsid. Thus, the extensive pairing and stacking of bases indicated by Raman profiles from ssRNA viruses are not evident for the phi X174 chromosome. Overall, the proteins of the virion contain extensive beta-sheet and irregular secondary structures. Fourier deconvolution of the Raman amide I band provides an estimate of the percentage of total beta-sheet structure (approximately 60%) in all proteins of the virion. The amide III region of the spectrum confirms that beta-sheet and irregular domains are the predominant protein secondary structures. Samples of phi X174 concentrated for Raman spectroscopy by either ultracentrifugation or ultrafiltration exhibit nearly identical Raman spectra, indicating that either method can be employed to prepare intact virus without significant loss of DNA or protein components.

Bacteriophage phi X 174↗
PubMed1996

Redox dependent interactions of the metal sites in carbon monoxide-bound cytochrome c oxidase monitored by infrared and UV/visible spectroelectrochemical methods.

Spectroelectrochemical titration studies involving the binding of the infrared-active probe ligand carbon monoxide (CO) to the heme alpha 3/CuB site of bovine heart cytochrome c oxidase (CcO) have been reexamined. The spectroelectrochemical cell employed was constructed to monitor both the infrared (IR) and visible/Soret spectra of the CcO-CO complex as a function of the overall oxidation state of the enzyme. A number of commonly used electron transfer mediators were employed to shuttle electrons between the redox active sites within the enzyme and the electrode surface. The well-documented shift in the CO infrared stretch band maximum from 1963.3 cm-1 (CcO fully reduced) to 1965.5 cm-1 (CcO partially oxidized) was carefully titrated electrochemically. Deconvolution of the asymmetric CO stretches indicates the existence of two different states of CO vibrators within the enzyme, presumably due to two conformers which are present in a ratio of approximately 5:1. Upon incrementally stepping the potential from the fully reduced state to the partially oxidized state, we found it possible to follow the decrease in the intensity of the original pair of these conformers and the concomitant increase of a resultant pair while maintaining this 5:1 ratio between the conformers. By plotting the change in the deconvoluted CO peak intensities vs the redox potential, as well as the absorbance changes in the visible/Soret spectra vs the redox potential, we found not only that both fit an n = 1 electron process but also that the spectral changes tracked each other identically with experimental error. Furthermore, analysis of the second derivative of the Soret spectra allowed for the qualitative monitoring of the oxidation state of the Fe alpha site which again tracked identically to that of the CO shift in the IR region. These results would seem to confirm earlier suggestions that perturbing the oxidation state of Fe alpha causes a conformational change in the enzyme which affects the binding site for CO, namely heme alpha 3. As a consequence of the CO IR stretching frequencies changing by only 2 cm-1 during this redox titration, with no accompanying changes in half band width, we suggest that it is impossible that this small but significant change seen in the CO stretching frequencies could be due to an oxidation state change in CuB, given the known sensitivity of the CO stretching frequency to perturbations and the close proximity of Cu(B) to the CO binding site at heme alpha 3 (4.5 A). Therefore, it would appear that Cu(B) must remain reduced as long as CO is bound to the heme alpha 3 site. This is consistent with earlier proposals that Fe alpha 3 and Cu(B) are acting together as a two-electron donor to dioxygen.

Animals↗
PubMed1996

Helical and reverse turn changes in the BR->N transition of bacteriorhodopsin.

Fourier transform infrared deconvoluted spectra of bacteriorhodopsin and the N intermediate were compared with the N/BR infrared difference spectrum. In the amide I, clear changes in the bands at 1666 cm-1, assigned to alpha II helices, 1659 cm-1, assigned to alpha I and alpha II helices, and 1652 cm-1, assigned to both alpha I helices and unordered structures, were found. These changes could arise from conversion of some alpha II and alpha I helices. Variations in the bands at 1692 and 1683 cm-1, corresponding to reverse turns, were also detected. The side chains of Tyr (band at 1517 cm-1) and Phe (band at 1498 cm-1) were found to change in going from BR to N. In the carboxylate region, no band was detected at 1737 cm-1 in the deconvoluted spectra that could correspond to the peak observed in the difference spectrum. It is argued that resolution-enhancement methods used along with difference spectra provide more detailed insights into the conformational changes occurring between photocycle intermediates.

Amides↗
PubMed1998

Identification and characterization of kinetically competent carbinolamine and alpha-iminoglutarate complexes in the glutamate dehydrogenase-catalyzed oxidation of L-glutamate using a multiwavelength transient state approach.

A highly constrained and heavily overdetermined multiwavelength transient state kinetic approach has been used to study the oxidative deamination of L-glutamate catalyzed by beef liver glutamate dehydrogenase. Spectra generated using the known enzyme-reduced coenzyme-substrate spectrum served as models for deconvolution of kinetic scan data. Deconvolution of the multiwavelength time course array shows formation of three distinguishable intermediates in the reaction sequence, an ultrablue-shifted complex, an ultrared-shifted complex, and a blue-shifted complex. The ultrablue-shifted entity is identified as the enzyme-NADPH-alpha-iminoglutarate complex (ERI) and the ultrared as the enzyme-NADPH-alpha-carbinolamine complex (ERC). The blue-shifted complex is characterized as the E-NADPH-ketoglutarate species (ERK). The location of these species along the reaction coordinate has been determined and their kinetic competency in the reaction sequence has been established by fitting the concentration time courses of the components for both the alpha-deuterio- and the alpha-protio-L-glutamate reactions to the now highly constrained differential equations derived from a kinetic scheme involving the sequential formation of alpha-iminoglutarate, alpha-carbinolamine, and alpha-ketoglutarate-reduced coenzyme complexes, following the formation of two prehydride transfer complexes.

Algorithms↗
PubMedDate not supplied

A combinatorial approach toward the discovery of non-peptide, subtype-selective somatostatin receptor ligands.

The tetradecapeptide somatostatin is widely distributed throughout the body and is thought to be involved with a variety of regulatory functions. Recently, five human somatostatin receptors (hSSTR1-5) have been cloned and characterized. Several selective peptidal agonists of the hSSTR receptors are known, and we sought to apply this information to the design of novel non-peptide small molecule ligands for each receptor. Initial computational methods identified a 200 nM murine SSTR2 active compound via a database search of our sample collection. A combinatorial library was designed around the structural class of the compound with the goal of rapidly developing this initial lead into the desired subtype-selective small molecules in order to characterize the pharmacology of each of the receptor subtypes. The library was synthesized using the resin-archive, iterative deconvolution format. The total number of unique compounds in the library was expected to be 131,670, present in 79 mixtures of 1330 or 2660 compounds per mixture. Through sequences of screening and mixture deconvolution, the components of selective and highly active (Ki = 50 pM to 200 nM) non-peptide small molecule ligands for somatostatin subtypes 1, 2, 4, and 5 were identified. In addition to discovering compounds with the desired activity and selectivity, useful structure/activity information was generated which can be used in the design of new compounds and second-generation combinatorial libraries.

Combinatorial Chemistry Techniques↗
PubMedDate not supplied

Prediction of biological targets for compounds using multiple-category Bayesian models trained on chemogenomics databases.

Target identification is a critical step following the discovery of small molecules that elicit a biological phenotype. The present work seeks to provide an in silico correlate of experimental target fishing technologies in order to rapidly fish out potential targets for compounds on the basis of chemical structure alone. A multiple-category Laplacian-modified naïve Bayesian model was trained on extended-connectivity fingerprints of compounds from 964 target classes in the WOMBAT (World Of Molecular BioAcTivity) chemogenomics database. The model was employed to predict the top three most likely protein targets for all MDDR (MDL Drug Database Report) database compounds. On average, the correct target was found 77% of the time for compounds from 10 MDDR activity classes with known targets. For MDDR compounds annotated with only therapeutic or generic activities such as "antineoplastic", "kinase inhibitor", or "anti-inflammatory", the model was able to systematically deconvolute the generic activities to specific targets associated with the therapeutic effect. Examples of successful deconvolution are given, demonstrating the usefulness of the tool for improving knowledge in chemogenomics databases and for predicting new targets for orphan compounds.

Bayes Theorem↗
PubMed2003

Use of multiwavelength transmission spectroscopy for the characterization of Cryptosporidium parvum oocysts: quantitative interpretation.

Combined scattering and absorption properties of suspended particles can be obtained as a function of wavelength by measuring the complete ultraviolet-visible (UV-vis) spectrum. This research reports on the quantitative interpretation of measured UV-vis spectra of Cryptosporidium parvum oocyst suspensions obtained from several commercial sources and evaluated using two different purification techniques. The reproducibility of the measured spectral data was assessed, and the quantitative interpretation of the oocyst spectra in terms of the particle size and the chemical composition of the particles are reported herein. The interpretation model of the spectra is based on light scattering theory, spectral deconvolution techniques, and on the approximation of the wavelength-dependent optical properties of the basic constituents of living organisms. A characteristic set of optical properties for C. parvum oocysts has been determined as a function of wavelength and used for the quantitative interpretation of UV-vis spectra. The results from the spectral deconvolution show quantitative differences among oocyst preparations. These results represent the first step in establishing a set of critical parameters (e.g., oocyst size and chemical composition) necessary for the detection and identification of C. parvum oocysts in water using spectroscopy.

Animals↗
PubMed2005

Cryogenic laser induced U(VI) fluorescence studies of a U(VI) substituted natural calcite: implications to U(VI) speciation in contaminated Hanford sediments.

Time-resolved laser-induced fluorescence spectroscopy (TRLFS) and imaging spectromicroscopy (TRLFISM) were used to examine the chemical speciation of uranyl in contaminated subsurface sediments from the U.S. Department of Energy (U.S. DOE) Hanford Site, Washington. Spectroscopic measurements for contaminant U(VI) were compared to those from a natural, uranyl-bearing calcite (NUC) that had been found via X-ray absorption spectroscopy (XAS) to include uranyl in the same coordination environment as calcium. Spectral deconvolution of TRLFS measurements on the NUC revealed the unexpected presence of two distinct chemical environments consistent with published spectra of U(VI)-substituted synthetic calcite and aragonite. Apparently, some U(VI) substitution sites in calcite distorted to exhibit a local, more energetically favorable aragonite structure. TRLFS measurements of the Hanford sediments NP4-1 and NP1-6 were similar to the NUC in terms of peak positions and intensity, despite a small CaCO3 content (1.0 to 3.2 mass %). Spectral deconvolution of the sediments revealed the presence of U(VI) in calcite and aragonite structural environments. A third, unidentified U(VI) species was also present in the NP1-6 sediment. TRLFISM measurements at multiple locations in the different sediments displayed only minor variation, indicating a uniform speciation pattern. Collectively, the measurements implied that waste U(VI), long-resident beneath the sampled disposal pond (32 y), had coprecipitated within carbonates. These findings have major implications for the solubility and fate of contaminant U(VI).

Calcium Carbonate↗
PubMed2003

On the stability of a single-turn alpha-helix: the single versus multiconformation problem.

The pentapeptide Ac-HAAAH-NH2, cyclized through its imidazoles by PdII to give [Pd(en)(peptide)]2+, has recently been evaluated by 2-D NMR and simulated annealing as a single alpha-helix conformation in solution. In the present work, we have questioned this assumption by developing Pd2+ parameters for AMBER*, performing an extensive conformational search for the [Pd(en)(peptide)]2+, and deconvoluting the averaged NMR data into eight rapidly equilibrating conformations with populations ranging from 2 to 55%. None of the latter correspond to the alpha-helix, although a 3% form possesses a related structure. As a critical component of interpreting an averaged NMR spectrum in terms of a single conformation, we advise testing this assumption with a method that permits conformational deconvolution.

Histidine↗
PubMed2000

Two comparisons of the performance of positional scanning and deletion synthesis for the identification of active constituents in mixture combinatorial libraries.

Two libraries of 120 compounds each were prepared as individual compounds and as full mixtures. The corresponding scanning and deletion synthesis deconvolution libraries were prepared and tested (L-1210, IC(50)) alongside the individual compounds and mixture libraries. This testing, where the properties of each compound in the mixtures were known, was used to compare the performance of scanning and deletion deconvolution libraries. Each has its own intrinsic strengths, with the former being capable of identifying multiple hits at the expense of accurately identifying the most potent library member, while the latter typically is more sensitive to identifying the most potent hit but at the expense of differentiating weaker activities. The protocols complement one another and together more thoroughly identify potent library members.

Animals↗
PubMed2004

Adsorption of cobalt ions on the "electrolytic solution/gamma-alumina" interface studied by diffuse reflectance spectroscopy (DRS).

Diffuse reflectance spectroscopy was used for the first time to investigate the adsorption of the [Co(H2O)6]2+ ions on the interface developed between the surface of the gamma-alumina particles and the electrolytic aqueous solutions used for the preparation of cobalt-supported gamma-alumina catalysts by equilibrium deposition filtration. The formation of inner-sphere Co(II) surface complexes in which Co(II) is in octahedral symmetry was confirmed. A deconvolution peak centered at approximately 585 nm was attributed to the exchange of one aqua ligand with one AlxOHy (x = 1, 2, or 3; y = 0 or 1) negatively charged surface group resulting in the formation of mononuclear monosubstituted inner-sphere Co(II) complexes at a Co(II) surface concentration equal to 0.02 micromol of Co(II)/m2. It was inferred that as the surface Co(II) concentration increases the formation of disubstituted and/or trisubstituted surface complexes is favored with respect to the formation of monosubstituted Co(II) surface complexes. A deconvolution peak centered at approximately 640 nm was attributed to the exchange of one or more aqua ligands with bridging hydroxo ligands (Co-O-H). The relative magnitude of this peak increases with the Co(II) surface concentration, reflecting the increasing formation of binuclear, oligonuclear, and multinuclear Co(II) surface complexes and then the formation of the Co(II) surface precipitate.

Adsorption↗
PubMed2005

Pore size distribution analysis of selected hexagonal mesoporous silicas by grand canonical Monte Carlo simulations.

We combine here a regularization procedure with individual adsorption isotherms obtained from grand canonical Monte Carlo simulations in order to obtain reliable pore size distributions. The methodology is applied to two hexagonal high-ordered silica materials: SBA-15 and PHTS, synthesized in our laboratory. Feasible pore size distributions are calculated through an adaptable procedure of deconvolution over the adsorption integral equation, with two necessary inputs: the experimental adsorption data and individual adsorption isotherms, assuming the validity of the independent pore model. The application of the deconvolution procedure implies an adequate grid size evaluation (i.e., numbers of pores and relative pressures to be considered for the inversion, or kernel size), the fulfillment of the discret Picard condition, and the appropriate choice of the regularization parameter (L-curve criteria). Assuming cylindrical geometry for both porous materials, the same set of individual adsorption isotherms generated from molecular simulations can be used to construct the kernel to obtain the PSD of SBA-15 and PHTS. The PSD robustness is measured imposing random errors over the experimental data. Excellent agreement is found between the calculated and the experimental global adsorption isotherms for both materials. Molecular simulations provide new insights into the studied systems, pointing out the need of high-resolution isotherms to describe the presence of complementary microporosity in these materials.

Adsorption↗
PubMed2001

In vivo-in vitro correlation (IVIVC) modeling incorporating a convolution step.

The purpose of in vivo-in vitro correlation (IVIVC) modeling is described. These models are usually fitted to deconvoluted data rather than the raw plasma drug concentration/time data. Such a two-stage analysis is undesirable because the deconvolution step is unstable and because the fitted model predicts the fraction of a dosage unit dissolved/absorbed in vivo which generally is not the primary focus of our attention. Interest usually centers on the plasma drug concentration or some function of it (e.g., AUC, Cmax). Incorporation of a convolution step into the model overcomes these difficulties. Odds, hazards, and reversed hazards models which include a convolution step are described. The identity model (which states that average in vivo and in vitro dissolution/time curves are coincident or directly superimposable) is a special case of these models. The odds model and the identity model were fitted to data sets for two different products using nonlinear mixed effects model fitting software. Results show that the odds model describes both data sets reasonably well and is a significantly better fit than the identity model in each case.

Cross-Over Studies↗
PubMed2001

Gliadin nanoparticles as carriers for the oral administration of lipophilic drugs. Relationships between bioadhesion and pharmacokinetics.

PURPOSE: The aim of this work was to evaluate the bioadhesive properties of non-hardened gliadin nanoparticles (NPs) and cross-linked gliadin nanoparticles (CL-NP) in the carbazole pharmacokinetic parameters obtained after the oral administration of these carriers. METHODS: A deconvolution model was used to estimate the carbazole absorption when loaded in the different gliadin nanoparticles. In addition, the elimination rates of both adhered and non-adhered nanoparticulate fractions within the stomach were estimated. RESULTS: Nanoparticles dramatically increased the carbazole oral bioavailability up to 49% and provided sustained release properties related to a decrease of the carbazole plasma elimination rate. The carbazole release rates from nanoparticles (NP and CL-NP), calculated by deconvolution, were found to be of the same order as the elimination rates of the adhered fractions of nanoparticles in the stomach mucosa. In addition, good correlation was found between the carbazole plasmatic levels, during the period of time in which the absorption process prevails, and the amount of adhered carriers to the stomach mucosa. CONCLUSION: Gliadin nanoparticles significantly increased the carbazole bioavailability, providing sustained plasma concentrations of this lipophilic molecule. These pharmacokinetic modifications were directly related to the bioadhesive capacity of these carriers with the stomach mucosa.

Administration, Oral↗
PubMed1989

The area function method for assessing the drug absorption rate in linear systems with zero-order input.

A noncompartmental approach for determination of the apparent zero-order absorption rate constant (k0) has been developed. The procedure evolves from the convolution integral and requires individual oral-dose plasma concentrations values and calculation of area intervals under the plasma concentration-time curves after intravenous administration. The proposed method was evaluated and compared with the Wagner-Nelson, Loo-Riegelman, deconvolution, nonlinear regression, and moment methods using errorless and errant simulation data from one- or two-compartment models. The area function method is generally equal to the best of these techniques (nonlinear regression) and superior to the weaker methods (moment, deconvolution, Loo-Riegelman), especially for errant two-compartment data. Coupled with a companion procedure for constructing fraction absorbed versus time plots and assessing first-order absorption rate constants, the area function methods offer direct and accurate means of discerning drug absorption kinetics without the need for assignment of a disposition model for drugs with linear elimination kinetics.

Intestinal Absorption↗