Determination of total proteins in several tissues of rat: a comparative study among spectrophotometric methods

In the present paper, five spectrophotometric methods — biuret, Lowry modified by Hartree (Lowry/Hartree), p-chloranil, ultraviolet at 280 nm (UV-280 nm), and ultraviolet at 260/280 nm (UV-260/280 nm) — were used for protein determination in several rat tissues and the results were compared. The Lowry/Hartree method showed the highest sensitivity (0.9 μg/ml) and the biuret method the lowest sensitivity (55.7 μg/ml). The results were not statistically different for the following methods and tissues: Lowry/Hartree was compared to biuret for five tissues (adrenal, spleen, whole brain, liver and small intestine), to p-chloranil for two tissues (liver and epididymal fat pad), and to UV-260/280 nm for three tissues (whole brain, liver and pancreas). Since the Lowry/Hartree method needs a larger period of time for a whole assay to be carried out, we recommend for determination of total protein the following methods: UV-260/280 nm for whole brain, liver, and pancreas, p-chloranil for epididymal fat pad, and biuret for other tissues. We do not recommend the UV-280 nm method because there are many interfering substances in the tissues.     

Reduction of the concentration difference of proteins in biological liquids using a library of combinatorial ligands

The discovery of polypeptides and proteins with relevance to a particular biological state is complicated by their vast number and concentration range in most biological mixtures. Depletion methodologies are frequently used to remove the most abundant species; however, this removal not only fails significantly to enrich trace proteins, it may also nonspecifically deplete them due to their interactions with the removed high-abundance proteins. Here we report a simple-to-use methodology that reduces the protein concentration range of a complex mixture like whole serum through the simultaneous dilution of high-abundance proteins and the concentration of low-abundance proteins. This methodology utilizes solid-phase ligand libraries of immense diversity, generated by "split, couple, recombine" combinatorial chemistry, that are used for affinity-based binding to the proteins of a given mixture. With a controlled sample-to-ligand ratio it is possible to modulate the relative concentration of proteins such that many peptides or proteins that are undetectable by classical analytical methods become easily accessible. The reduction in the dynamic range of unfractionated serum is specifically described along with treatment of other proteomes such as extracts from Escherichia coli, chicken egg white and cell culture supernatant. Mono- and bi-dimensional electrophoresis (1-DE and 2-DE respectively) and surface-enhanced laser desorption/ionization-mass spectrometry (SELDI-TOF-MS) technology demonstrate the reduction in protein concentration range. Combining this approach with additional fractionation methods further increased the number of detectable species.     

Green synthesis of banana flavor using different catalysts: a comparative study of different methods

ABSTRACT

Esterification of isoamyl alcohol with acetic acid was studied using different ion-exchange resins, namely Amberlyst 15 dry, Amberlyst 16 wet, Amberlite 120-IR. Esterification was carried out using different esterification methods that are quite new (ohmic, ultrasonic probe, and ultrasonic bath) and the results were compared with microwave-assisted esterification (MAE). The highest isoamyl acetate yield (99%) was obtained by MAE, using a mixture of acetic acid and isoamyl alcohol (mole ratio of 1:2) after 2?h of reaction time. In this process, 2% Amberlyst 15 dry was used. MAE had the least specific energy consumption (0.42?kWh/g isoamyl acetate) and specific CO₂ emission (34?g/g isoamyl acetate). According to the images obtained by scanning electron microscopy, lower amounts of Amberlyst 15 dry beads were destroyed by MAE method compared to other esterification methods. In conclusion, MAE proved to be an economic and environmentally-friendly method for esterification of different flavoring compounds.     

Typical aromatic noncovalent interactions in proteins: A theoretical study using phenylalanine

A systematic study of CH ··· π, OH ··· π, NH ··· π, and cation ··· π interactions has been done using complexes of phenylalanine in its cationic, anionic, neutral, and zwitterionic forms with CH₄, H₂O, NH₃, and NH at B3LYP, MP2, MPWB1K, and M06‐2X levels of theory. All noncovalent interactions are identified by the presence of bond critical points (bcps) of electron density (ρ( r )) and the values of ρ( r ) showed linear relationship to the binding energies (E_total). The estimated E_total from supermolecule, fragmentation, and ρ( r ) approaches suggest that cation ··· π interactions are in the range of 36 to 46 kcal/mol, whereas OH ··· π, and NH ··· π interactions have comparable strengths of 6 to 27 kcal/mol and CH ··· π interactions are the weakest (0.62–2.55 kcal/mol). Among different forms of phenylalanine, cationic form generally showed the highest noncovalent interactions at all levels of theory. Cooperativity of multiple interactions is analyzed on the basis of ρ( r ) at bcps which suggests that OH ··· π and NH ··· π interactions show positive, whereas CH ··· π and cation ··· π interactions exhibit negative cooperativity with respect to the side chain hydrogen bond interactions. In general, side chain interactions are strengthened as a result of aromatic interaction. Solvation has no significant effect on the overall geometry of the complex though slight weakening of noncovalent interactions by 1–2 kcal/mol is observed. An assessment of the four levels of theory studied herein suggests that both MPWB1K and M06‐2X give better performance for noncovalent interactions. The results also support the fact that B3LYP is inadequate for the study of weak interactions. © 2008 Wiley Periodicals, Inc. J Comput Chem 2009     

Antibody-scanning and epitope-tagging methods; molecular mapping of proteins using antibodies

Because synthetic short peptides bearing critical binding residues, can chemically mimic the folded antigenic determinants on proteins, short synthetic peptides can generate antibodies that react with cognate sequences in intact folded proteins. According to this mimotope theory, we produced site-specific antibodies by immunization with short peptides which overlapped each other and covered the entire protein, and used them for domain mapping of influenza virus RNA polymerase (antibody-scanning method). We also used a tagged-epitope and its monoclonal antibodies for topology mapping of clathrin light chains in clathrin triskelions by electron microscopy. Both methods using specific epitopes in combination with their antibodies enable us to determine the domains of interesting proteins systematically without the need to generate monoclonal antibodies or mutant proteins.     

Determination of cyclosporine A in whole blood: comparison of a chromatographic method with three different immunological methods

Cyclosporine A is potent immunosuppressive agent characterized by a narrow therapeutic range, inter- and intra-individual variability and a lack of correlation between drug dosage and blood levels. In view of these facts, blood levels of CyA should be routinely monitored to assess organ rejection and toxicity.

We evaluated CyA as well as its metabolites (AM9, AM19, AMl, and AM4N) in whole blood samples from 117 patients using commercially available immunological assays (AxSYM, EMIT, Dimension) and HPLC.

Cross-reactivity of the immunological assays was evaluated using different concentrations of the CyA metabolites (in vitro cross-reactivity) and by statistical analysis of patient data (in vivo cross-reactivity). Cross-reactivity was seen in all immunological assays, with differences in in vitro and in vivo cross-reactivity.

The statistical analysis showed a classical correlation between HPLC and AxSYM of r² = 0.89, HPLC versus EMIT of r² = 0.93, and HPLC versus Dimension of r² = 0.93.

The percentage metabolite cross-reactivity (%) by immunological assays for four metabolites at two concentrations each (250 and 1000 ng ml⁻¹) was lowest with the Dimension assay.

Of the immunological methods examined, the new Dimension for CyA determination can be relied on to produce results comparable to HPLC; other advantages are its simplicity, practicability and ease of handling.     

Determination of total proteins: a study of reaction between quinones and proteins

A previous study was undertaken to test the reaction of several quinones (p-benzoquinone; 2,5-dichloro and 2,6-dichloro p-benzoquinone; tetrachloro-p-benzoquinone; tetrachloro-o-benzoquinone; 2,5-dichloro-3,6-dihydroxy-p-benzoquinone; benz[a]anthracene-7,12-dione) with bovine serum albumin (BSA). From this study, we have devised a spectrophotometric method for determination of total proteins. The quinone, tetrachloro-p-benzoquinone (p-chloranil), showed the best result. The product of reaction between proteins and p-chloranil absorbed at 360 nm and Beer's law was followed up to 200 mug ml(-1) of BSA. The product of reaction of BSA/p-chloranil was stable for 30 min, after that the absorbance increased 16% and kept stable for 24 h. The p-chloranil method showed a limit of detection (1.25 mug ml(-1)) lower than the biuret method (52.0 mug ml(-1)) or p-benzoquinone (PBQ) method (2.6-4.0 mug ml(-1)). The method was applied to spectrophotometric determination of total proteins in blood plasma; the results were compared with the biuret method that is widely used in clinical analysis.     

Reduction kinetics of mechanically activated hematite concentrate with hydrogen gas using nonisothermal methods

The reduction kinetics of both non-activated and mechanically activated hematite concentrate in a vibratory mill for different grinding periods have been studied using themogravimetry (TG). Changes in the structure of hematite were studied using X-ray diffraction analysis. The isoconversional method of Kissinger-Akahira-Sunose (KAS) was used to determine the activation energy of the different reactions. The Vyazovkin model-free kinetic method was also used for prediction of kinetic behavior of the samples for a given temperature.Fe₂O₃ was found to reduce to Fe in a two-step via Fe₃O₄. Intensive grinding resulted in improved resolution of overlapping reduction events. It was also established that the mechanical activation had a positive effect on the first step of reduction. With increasing the grinding time, the activation energy at lower extent of conversion (α ≤ 0.11) decreased from 166 to 106 kJ mol⁻¹ range in the initial sample to about 102-70 kJ mol⁻¹ in the sample ground for 9 h. The complexity of the reduction of hematite to magnetite and magnetite to iron was illustrated by the dependence of E on the extent of conversion, α(0.02 ≤ α ≤ 0.95). The values of E decreased sharply with α for 0.02 ≤ α ≤ 0.11 range in the initial sample and mechanically activated samples, followed by a slight decrease in the values of E during further reduction by α ≤ 0.85 in the ground samples up to 3 h. A slight increasing dependence of E on α for mechanically activated sample within 9 h in the second step of reduction was observed due to the finely agglomerated particles during intensive milling and subsequently the formation of a dense layer during the reduction processes. In addition, the dependence of ln A_α on α was detected and it was found that the ln A_α shows the same dependence on α as the apparent activation energies.     

Two-dimensional electrophoresis of liver proteins: characterization of a drug-induced hepatomegaly in rats

Two-dimensional electrophoresis (2-DE) of liver proteins was applied to further characterize an unusual drug-induced increase in hepatocellular rough endoplasmic reticulum (RER) in Sprague-Dawley rats given a substituted pyrimidine derivative. Absolute liver weights of drug-treated rats (9.9 +/- 0.4 g) increased above vehicle-treated controls (7.2 +/- 0.2 g) by 37%. Light microscopy revealed diffuse granular basophilia of the hepatocellular cytoplasm, uncharacteristic of hepatocytes and suggested cells rich in ribosomes, which was confirmed by electron microscopy. Immunostaining for cell proliferation, viz., 5-bromo-2'-deoxyuridine (BrdU) and proliferating cell nuclear antigen (PCNA), indicated marked hepatocellular proliferative activity. 2-DE of solubilized liver using an ISO-DALT gel system indicated significant (p<0.001) quantitative changes in at least 17 liver proteins (12 increased, 5 decreased) compared to controls. The protein with the largest increase was homologous to acute-phase reactant, contrapsin-like protein inhibitor-6. Other markedly upregulated proteins were methionine adenosyltransferase, a catalyst in methionine/ATP metabolism and mitochondrial HMG-CoA synthase, involved in cholesterol synthesis. The complementary strategies of 2-DE coupled either with database spot mapping or protein isolation and amino acid sequencing successfully identified a subset of proteins from xenobiotic-damaged rodent livers, the expression of which differed from controls. However, the current bioinformatics platform for rodent hepatic proteins and limited knowledge of specific protein functionality restricted application of this proteomics profile to further define a mechanistic basis for this unusual hepatotoxicity.     

Near-infrared absorption in symmetric squarylium and croconate dyes: a comparative study using symmetry-adapted cluster-configuration interaction methods

Symmetric croconate (CR) and squarylium dyes (SQ) are well-known near-infrared (NIR) dyes and, in general, are considered to be donor-acceptor-donor type molecules. It is established in the literature that CR dyes absorb in a longer wavelength region than the corresponding SQ dyes. This has been attributed to the CR ring being a better acceptor than the SQ ring. Thus increasing the donor capacity should lead to a bathochromic shift in both SQ and CR. On the other hand, some experiments reported in the literature have revealed that increasing the conjugation in the donor part of the SQ molecule leads first to red shift, which upon a further increase of the conjugation changes to a blue shift. Hence, to understand the role of the central ring and the substitutions in the absorption of these dyes, we carried out high-level symmetry-adapted cluster-configuration interaction (SAC-CI) calculations of some substituted SQ and CR dyes and compare the absorption energy with the existing experimental data. We found that there is very good agreement. We also carried out SAC-CI calculations of some smaller model molecules, which contain the main oxyallyl substructure. We varied the geometry (angle) of the oxyallyl subgroup and the substitution in these model molecules to establish a correlation with the bathochromic shift. We found that the charge transfer is very small and does not play the key role in the red shift, but on the other hand, the perturbation of the HOMO-LUMO gap (HLG) from both the geometry and substitution seems to be responsible for this shift. We suggest as a design principle that increasing the donor capacity of the groups may not help in the red shift, but introducing groups which perturb the HLG and decrease it without changing the MO character should lead to a larger bathochromic shift.     

Chemical methods for degradation of target proteins using designed light-activatable organic molecules

Molecular design, chemical synthesis, and biological evaluation of several designed organic molecules, which target-selectively degrade proteins upon photo-irradiation, are introduced. The designed molecules for protein photo-degradation include 2-phenylquinoline-steroid hormone hybrids and porphyrin derivatives, both of which selectively photo-degrade estrogen receptor-α, and fullerene-sugar and -sulfonic acid hybrids, which selectively photo-degrade HIV-1 protease and amyloid β, respectively. The information will provide a novel and effective way to control specific functions of proteins, and contribute to the molecular design of novel protein photo-degrading agents, which should find wide application in chemistry, biology, and medicine.     

Spectrophotometric titration of ionisable groups in proteins: a theoretical study

A simple theoretical model is proposed for evaluation of the optical titration behaviour of tyrosyl and carboxyl residues in proteins. The pK values involved in the model are computed using the semi-empirical method. The titration curves are calculated using the values of the molar absorption differences for tyrosyl residues in the ultraviolet (UV) region at 245 and 295 nm, and for carboxyl residues in the infrared (IR) region at 1565 and 1707 cm(-1), respectively. The theoretical tyrosyl titration curves are compared with the experimental data for lysozyme, myoglobin and chymotrypsinogen (available in the literature). This approach provides a good tool for distinguishing between the ionisation and the conformational changes in the alkaline range. The quantitative evaluation of the change of molar extinction coefficients as a function of pH in the case of carboxyl titration for lysozyme, trypsin and cytochrome c shows a good agreement with the experimental titration data.     

Hard sphere fluids at a soft repulsive wall: a comparative study using Monte Carlo and density functional methods

Hard-sphere fluids confined between parallel plates at a distance D apart are studied for a wide range of packing fractions including also the onset of crystallization, applying Monte Carlo simulation techniques and density functional theory. The walls repel the hard spheres (of diameter σ) with a Weeks-Chandler-Andersen (WCA) potential V(WCA)(z) = 4ε[(σ(w)/z)(12) - (σ(w)/z)(6) + 1/4], with range σ(w) = σ/2. We vary the strength ε over a wide range and the case of simple hard walls is also treated for comparison. By the variation of ε one can change both the surface excess packing fraction and the wall-fluid (γ(wf)) and wall-crystal (γ(wc)) surface free energies. Several different methods to extract γ(wf) and γ(wc) from Monte Carlo (MC) simulations are implemented, and their accuracy and efficiency is comparatively discussed. The density functional theory (DFT) using fundamental measure functionals is found to be quantitatively accurate over a wide range of packing fractions; small deviations between DFT and MC near the fluid to crystal transition need to be studied further. Our results on density profiles near soft walls could be useful to interpret corresponding experiments with suitable colloidal dispersions.     

Biomimetic interactions of proteins with functionalized nanoparticles: a thermodynamic study

Gold nanoparticles (NPs) functionalized with L-amino acid-terminated monolayers provide an effective platform for the recognition of protein surfaces. Isothermal titration calorimetry (ITC) was used to quantify the binding thermodynamics of these functional NPs with alpha-chymotrypsin (ChT), histone, and cytochrome c (CytC). The enthalpy and entropy changes for the complex formation depend upon the nanoparticle structure and the surface characteristics of the proteins, e.g., distributions of charged and hydrophobic residues on the surface. Enthalpy-entropy compensation studies on these NP-protein systems indicate an excellent linear correlation between DeltaH and TDeltaS with a slope (alpha) of 1.07 and an intercept (TDeltaS0) of 35.2 kJ mol(-1). This behavior is closer to those of native protein-protein systems (alpha = 0.92 and TDeltaS0 = 41.1 kJ mol(-1)) than other protein-ligand and synthetic host-guest systems.     

Excitation decay pathways of Lhca proteins: a time-resolved fluorescence study

Light-harvesting complex I (LHCI), which serves as a peripheral antenna for photosystem I (PSI) in green plants, consists mainly of four polypeptides, Lhca1-4. We report room temperature emission properties of individual reconstituted monomeric Lhca proteins (Lhca1, -2, -3, and -4) and dimeric Lhca1/4, performed by steady-state and time-resolved fluorescence techniques. The emission quantum yields of the samples are approximately 0.12, 0.085, 0.081, 0.041, and 0.063 for Lhca1, -2, -3, -4, and the -1/4 dimer, respectively, which is considerably lower than the value of 0.22 found for light-harvesting complex II (LHCII), the main peripheral antenna complex of photosystem II in green plants. The decay components of LHCI proteins can be divided in two categories: Lhca1 and Lhca3 have decay times of 1.1-1.6 ns and 3.3-3.6 ns, and Lhca2 and Lhca4 have decay times of 0.7-0.9 ns and 3.1-3.2 ns. These categories seem to correlate with the pigment composition of the samples. All decay times are faster than that observed previously for LHCII. When the absolute emission yields and the lifetimes of the Lhca samples are combined, the overall emission properties of the individual Lhca proteins are expressed in terms of their emitting dipole moment strength. In the samples without extreme red states, that is, Lhca1 and Lhca2, the emitting dipole moment has a value close to unity (relative to monomeric chlorophyll in acetone), which is similar to that for LHCII, whereas, in the samples with the red-most state (F-730), that is, Lhca3, -4, and the -1/4 dimer, the emitting dipole moment has a value less than unity (0.6-0.8), which can be explained by mixing the red-most (exciton) state with a dark charge-transfer state, as suggested in previous PSI red pigment studies. In addition, we find a lifetime component of approximately 50-150 ps in all red-pigment-containing samples, which cannot be due to "slow" energy transfer, but is instead assigned to an unrelaxed state of the pigment-protein, which, on this time-scale, is converted into the final emitting state.     

Determination of dimethylarginine levels in rats using HILIC-MS/MS: an in vivo microdialysis study

Nitric oxide (NO) is one of the most important mediators and neurotransmitters and its levels change under pathological conditions. NO production may be regulated by endogenous nitric oxide synthase (NOS) inhibitors, in particular asymmetric dimethylarginine (ADMA). Most of the interest is focused on ADMA, since this compound is present in plasma and urine and accumulation of ADMA has been described in many disease states but little is known about cerebrospinal fluid (CSF) concentrations of this compound and of its structural isomer symmetric dimethylarginine (SDMA). To determine the levels of methylarginines, we here present a new hydrophilic interaction chromatography (HILIC)-MS/MS method for the precise determination of these substances in CSF from microdialysis samples of rat prefrontal cortex (PFC). The method requires only minimal sample preparation and features isotope-labelled internal standards.     

Charge reduction in a vermiculite by acid and hydrothermal methods: a comparative study

A comparative study on acid and hydrothermal methods as ways to reduce interlamellar charge has been carried out on a vermiculite. This study showed that the application of the hydrothermal treatment as a previous step to pillaring the vermiculites, reported here for the first time, is a new route to obtain the porous material with a particular interest as heterogeneous catalysts, starting from mineral clays with a high density of charge. Modified clays have been characterized by atomic absorption, emission spectrograph, X-ray diffraction, cation-exchange capacity, total acidity, infrared spectroscopy (DRIFT), and nitrogen adsorption. The results have shown that all solids have been structurally modified. However, acid and hydrothermal methods showed different behavior. For the vermiculite, the hydrothermal treatment did not produce major differences in terms of the crystalline structure, whereas the acid method caused severe structural damage. The catalytic properties have been tested over Pt-impregnated samples (1%) using the hydroisomerization of heptane. Important catalytic activity was established for all solids with high selectivity regarding the isomer products.     

Acetylation of a heterocyclic enaminonitrile: Unambiguous structural assignment using NMR methods

Using a combination of nmr techniques, the structure of the acetylation product of methyl 3-[2-amino-3-cyano-9-methoxy-4H-5,6-dihydronaphtho[1,2-b]pyran-4-yl] benzoate 2b has been shown to be the N-acetyl derivative 5a , rather than the rearranged 2-acetoxydihydropyridine 6a.