Resin probe analysis. II. Amino acid coupling reactions.

Resin probe analysis has been employed to evaluate the availability of dicyclohexylcarbodiimide (DCC)-activated amino acids, the relationship between coupling time and reaction yield, and the influence of triethylamine (TEA) concentration on peptide bond formation. Results are presented for five amino acids which indicate that the coupling reactions plateau within 5 min, and no significant increase in yield is observed for longer incubation times. Large decreases in coupling yield (70–90%) were observed at concentrations of TEA above 0.01 m. Inactivation appears to be dependent in part upon amino acid structural features. In the absence of TEA, DCC-activated t-butyloxycarbonyl (Boc)-glycine was stable in the activated state for hours. peptide bond formation showed little or no amino acid concentration-dependence in the range of 0.01–0.04 m. Resin probe experiments provide quantitative data on reaction progress and factors that influence the availability and reactivity of activated amino acids.     

A sensitive SERS quantitative analysis method for Ni2+ by the dimethylglyoxime reaction regulating a graphene oxide nanoribbon catalytic gold nanoreaction

The nanogold reaction between HAuCl₄ and trisodium citrate (TCA) proceeded very slowly at 60°C in a water bath. The as‐prepared graphene oxide nanoribbons (GONRs) exhibited strong catalysis during the reaction to form gold nanoparticles (Au NPs) and appeared as a strong surface‐enhanced Raman scattering (SERS) peak at 1616 cm^?1 in the presence of the molecular probe Victoria blue 4R (VB4r). With increase in GONR concentration, the SERS peak increased due to increased formation of Au NPs. Upon addition of dimethylglyoxime (DMG) ligand, which was adsorbed onto the GONR surface to inhibit GONR catalysis, the SERS peak decreased. When Ni²⁺ was added, a coordination reaction between DMG and Ni²⁺ took place to form stable complexes of [Ni (DMG)₂]²⁺ and the release of free GONR catalyst that resulted in the SERS peak increasing linearly. A SERS quantitative analysis method for Ni²⁺ was therefore established, with a linear range of 0.07–2.8 μM, and a detection limit of 0.036 μM Ni²⁺.     

A simple gold nanoplasmonic SERS method for trace Hg2+ based on aptamer‐regulating graphene oxide catalysis

The as‐prepared graphene oxide (GO) exhibited a strong catalytic effect on reduction of HAuCl₄ by trisodium citrate to form gold nanoplasmons (AuNPs) with a strong surface‐enhanced Raman scattering (SERS) effect at 1615 cm^?1 in the presence of molecular probe Victoria blue 4R (VB4r). SERS intensity increased with nanocatalyst GO concentration due to the formation of more AuNP substrates. The aptamer (Apt) of Hg²⁺ can bind to GO to form Apt–GO complexes, which can strongly inhibit nanocatalysis. When target Hg²⁺ is present, the formed stable Hg²⁺–Apt complexes are separated from the GO surface, which leads to GO catalysis recovery. The enhanced SERS signal was linear to Hg²⁺ concentration in the range 0.25–10 nmol/L, with a detection limit of 0.08 nmol/L Hg²⁺. Thus, a new gold nanoplasmon molecular spectral analysis platform was established for detecting Hg²⁺, based on Apt regulation of GO nanocatalysis.     

The Efficient Ionization Reaction of DTBA Achieved by Surface Plasmon Catalysis Effect

4,4’-Dithiobisbenzoic acid (DTBA) is equivalent to two 4-mercaptobenzoic acid (pMBA) molecules connected together after losing H⁺, and this bimolecular mechanism of DTBA efficiently promotes the ionization reaction. Under the irradiation of laser light, DTBA molecules are broken to form bimolecules similar to pMBA, and this kind of bimolecular coupling greatly increases the probability of binding with Ag NPs. Also, this molecule has the carboxylic acid group, which leads to a certain sensitivity to pH. In this article, through the comparison of DTBA and pMBA parallel experiments, it is clear that DTBA has better Raman activity, higher reaction efficiency, and more stable reaction than pMBA. The occurrence of this highly efficient ionization reaction under the monitoring of surface-enhanced Raman spectroscopy (SERS) provides a certain value for the progress of further related reactions, and it also has a wide range of applications in pH sensors and intracellular pH monitoring.

The study of efficient ionization reaction of 4,4’-dithiobisbenzoic acid with bimolecular structure

     

A Sensitive SERS Quantitative Analysis Method for Amino Acids Using Ruhemann’s Purple as Molecular Probe in Triangle Nanosilver Sol Substrate

The stable silver nanotriangle (AgNT) sol was prepared by reduction of silver ions with sodium borohydride in the presence of H₂O₂ and sodium citrate. Under the action of NaCl, AgNTs were aggregated to a highly surface-enhanced Raman scattering (SERS) active substrate. In pH 6.0 Na₂HPO₄-NaH₂PO₄ buffer solution (PBS) at 80 °C water bath, ninhydrin reacted with amino acids to form blue-violet complex Ruhemann’s purple (RP), and the RP molecules adsorbed on the aggregated AgNT surfaces that exhibited a strong SERS peak at 657 cm^?1. The peak was linear to amino acid concentration in the range of 0.7–99.8 μmol/L, with a detection limit (DL) of 0.5 μmol/L. This SERS method was applied to detect amino acid in samples, with satisfactory results. In addition, the analytical system was also investigated by resonance Rayleigh scattering (RRS), absorption, and electron microscope techniques.     

Iron Autoxidation in Mops and Hepes Buffers

Iron autoxidation in Mops and Hepes buffers is characterized by a lag phase that becomes shorter with increasing FeCl₂ concentration and pH. During iron oxidation in these buffers a yellow colour develops in the solution. When the reaction is conducted in the presence of nitro blue tetrazolium (NBT), blue formazan is formed. Of the many OH' scavengers tested, mannitol and sorbitol are most effective in inhibiting Fe²⁺ oxidation, yellow colour development and NBT reduction. Some inhibition was also noted with catalase. The iron product of the oxidative reaction differs from Fe³⁺ in its absorption spectrum and its low reactivity with thiocyanate. Similar results are obtained when iron autoxidation is studied in unbuffered solutions brought to alkaline pH with NaOH. In phosphate buffer, no lag phase is evident and the absorption spectrum of the final solution is identical to that of Fe³⁺ in this buffer. The iron product reacts immediately with thiocyanate. When iron oxidation is conducted in the presence of NBT the formation of formazan is almost undetectable. Of the many compounds tested only catalase inhibits iron autoxidation in this buffer. The sequence of reactions leading to iron autoxidation in Good-type buffers¹ thus resembles that occurring in unbuffered solutions brought to alkaline pH with NaOH and greatly differs from that occurring in phosphate buffer. These results are in agreement with the observation that these buffers have very low affinity for iron.¹ The data presented define experimental conditions where Fe²⁺ is substantially stable for a considerable length of time in Mops buffer.     

Modulation of the Primary Electron Transfer Rate in Photosynthetic Reaction Centers by Reduction of a Secondary Acceptor

Photosynthetic application of picosecond spectroscopic techniques to bacterial reaction centers has led to a much greater understanding of the chemical nature of the initial steps of photosynthesis. Within 10 ps after excitation, a charge transfer complex is formed between the primary donor, a “special pair” of bacteriochlorophyll molecules, and a transient acceptor involving bacteriopheophytin. This complex subsequently decays in about 120 ps by donating the electron to a metastable acceptor, a tightly bound quinone.

Recent experiments with conventional optical and ESR techniques have shown that when reaction centers are illuminated by a series of single turnover flashes in the presence of excess electron donors and acceptors, a stable, anionic ubisemiquinone is formed on odd flashes and destroyed on even flashes, suggesting that the acceptor region contains a second quinone that acts as a two-electron gate between the reaction center and subsequent electron transport events involving the quinone pool.

Utilizing standard picosecond techniques, we have examined the decay of the charge transfer complex in reaction centers in the presence of the stable semiquinone, formed by flash illumination with a dye laser 10 s before excitation by a picosecond pulse. In this state the decay rate for the charge transfer complex is considerably slower than when no electron is present in the quinone acceptor region. This indicates fairly strong coupling between constituents of the reaction center-quinone acceptor complex and may provide a probe into the relative positions of the various components.

     

SERS quantitative detection of trace human chorionic gonadotropin using a label‐free Victoria blue B as probe in the aggregated immunonanogold sol substrate

Nanogold particles (NG) were modified by anti‐rabbit antibody (RAb) against human chorionic gonadotropin to obtain an immunonanogold probe (ING). In pH 7.0 Na₂HPO₄‐citrate buffer solution containing KCl, ING probes formed large aggregates in which Victoria blue B (VBB) molecules were adsorbed on the surface and which exhibited strong surface‐enhanced Raman scattering (SERS) at a peak of 1612 cm^–1. After addition of human chorionic gonadotropin (hCG) an immune reaction with the ING probe occurred to form dispersive ING–hCG complexes with non‐SERS activity that led to a decreased SERS peak at 1612 cm^–1. The decreased SERS intensity was linear to the concentration of hCG over 2.4–73.2 ng/mL. The ING reaction was studied in detail by SERS, scanning electron microscope (SEM), resonance Rayleigh scattering (RRS), surface plasmon resonance (SPR) absorption and laser scattering techniques. SERS quenching was observed and discussed. Copyright © 2014 John Wiley & Sons, Ltd.     

Comparison of metal-amino acid interaction in Phe-Ag and Tyr-Ag complexes by spectroscopic measurements

In this article, we have compared the metal–amino acid interactions in Tyr–Ag and Phe–Ag complexes through pH dependent SERS measurements. By analyzing the variation in relative intensities of SERS bands with the pH of the amino acid solution, we have obtained the orientation and conformation of the amino acid molecules on the Ag surface. The results obtained from our experimental studies are supported by the energy minimized structures and the observed charge distributions in different terminals of the molecules. This, in a way, shows that SERS measurements not only exhibit the interaction of the amino acid molecules with Ag clusters but also demonstrate their orientation around it. We have addressed a long standing query on whether the amine group is directly attached to the Ag surface along with the carboxylate group and π-electrons in these systems. In addition, pH dependent optical absorption and transmission electron microscopy measurements have been performed to understand the required conditions for the appearance of the SERS spectra in the light of the aggregation of metal particles and the number of hot sites in the sol. Our results confirm that the formation of hot sites in the sol plays a direct role in forming a stable Ag–ligand complex. Furthermore, the interaction kinetics of metal–amino acid complexes have been analyzed via both Raman and absorption measurements.     

Synthesis and Biological Activity of (±)2′,3′-Dihydroabscisic Acid

An enzyme which catalyzes the oxidation of poly(vinyl alcohol) (PVA) has been purified from a fraction adsorbed to DEAE-Sephadex at pH 7.0 from PVA-degrading enzyme activities produced by a bacterial symbiotic mixed culture in a culture broth when the culture was grown in a minimal medium where PVA served as a sole source of carbon and energy. The enzyme was separated from a coexisting oxidized PVA hydrolase by dye-ligand chromatography on Matrex Gel Blue A. The purified enzyme was homogeneous as judged by polyacrylamide gel electrophoreses in the absence and presence of SDS.

The enzyme is a single polypeptide with a molecular weight of about 40,000 and has an isoelectric point of 4.5. The amino acid composition of the enzyme has been determined and found to have no histidine. The N- and C-terminal amino acid residues are both alanine. The enzyme solution is pink and shows absorption maxima at 276, 364, and 469 nm. One atom of non-heme iron has been detected per molecule in the enzyme.

The enzyme catalyzes the oxidation of PVA and also of various low molecular weight secondary alcohols to the corresponding ketones with the production of H₂0₂ and the consumption of 0₂. The molar ratio of these ketones, H₂0₂ and 0₂ is 1:1:1. The most effective electron acceptor is 0₂, while 2,6-dichlorophenolindophenol and nitro blue tetrazolium also serve as the acceptor with efficiencies to 0₂ of about 31 and 16%, respectively. The enzyme is, therefore, considered to be a secondary alcohol oxidase.

The enzyme is most active at pH 7.0 and at 45°C and is stable between pH 5.0 and 9.0 and at temperatures below 45°C. The activity is inhibited by Hg²⁺ and is restored by the addition of reduced glutathione, although p-chloromercuribenzoate has no effect.

The enzyme shows a common antigenicity in immunodiffusion and neutralization reactions with antisera to a secondary alcohol oxidase previously isolated from another fraction adsorbed on SP-Sephadex at pH 7.0 of the PVA-degrading enzyme activities [Agric. Biol. Chem., 43, 1225 (1979)]. The relations between these two secondary alcohol oxidases are discussed.     

Single base extension reaction-based surface enhanced Raman spectroscopy for DNA methylation assay

DNA methylation is a key diagnostic maker for genetic disease, cancer progression and pharmcogenomics. So far various techniques have been developed for DNA methylation assay, but most of them are laborious and time-consuming. Here we develop a simple and highly sensitive DNA methylation assay based on single base extension reaction and surface enhanced Raman spectroscopy (SERS). In the presence of methylated DNA, gold nanoparticle-modified capture probe can couple with a cyanine 5-deoxyribonucleoside triphosphate (cy5-dGTP) through single base extension reaction, and generates a high SERS signal after further addition of gold nanoparticles to increase the local electromagnetic field. While in the presence of unmethylated DNA, gold nanoparticle-modified capture probe cannot couple with cy5-dGTP due to the presence of a mismatch base, and no SERS signal is observed. This single base extension reaction-based SERS can determine methylated DNA with a detection limit of 3 pM, and can even distinguish as low as 1% methylation level in tumor suppressor gene CDKN2/p16/MTS1 (p16) from the mixtures. Notably, the sensitivity of this assay has improved by 5 orders of magnitude as compared to reported gold nanoparticle-based colorimetric assay, and by 2 orders of magnitude as compared to microarray-based methylation-sensitive single nucleotide primer extension assay (Ms-SNuPE). This method might be further applied to detect the methylation status in tumor-linked genes for cancer diagnosis.     

Folding and stability of trp aporepressor from Escherichia coli

Equilibrium and kinetic studies of the urea-induced unfolding of trp aporepressor from Escherichia coli were performed to probe the folding mechanism of this intertwined, dimeric protein. The equilibrium unfolding transitions at pH 7.6 and 25 degrees C monitored by difference absorbance, fluorescence, and circular dichroism spectroscopy are coincident within experimental error. All three transitions are well described by a two-state model involving the native dimer and the unfolded monomer; the free energy of folding in the absence of denaturant and under standard-state conditions is estimated to be 23.3 +/- 0.9 kcal/mol of dimer. The midpoint of the equilibrium unfolding transition increases with increasing protein concentration in the manner expected from the law of mass action for the two-state model. We find no evidence for stable folding intermediates. Kinetic studies reveal that unfolding is governed by a single first-order reaction whose relaxation time decreases exponentially with increasing urea concentration and also decreases with increasing protein concentration in the transition zone. Refolding involves at least three phases that depend on both the protein concentration and the final urea concentration in a complex manner. The relaxation time of the slowest of these refolding phases is identical with that for the single phase in unfolding in the transition zone, consistent with the results expected for a reaction that is kinetically reversible. The two faster refolding phases are presumed to arise from slow isomerization reactions in the unfolded form and reflect parallel folding channels.     

Modeling of a Catalyzed Reaction Using Lipase Immobilized in a Poly(vinyl alcohol) Membrane

A mathematical model for the hydrolysis reaction of p‐nitro phenol laurate catalyzed by a lipase immobilized in a membrane was developed. In an earlier study this model reaction was found to show very different reaction rates when it was performed in aqueous micellar solution with free enzyme and with membrane immobilized enzyme. It was assumed that a local accumulation of substrate in the membrane is responsible for the observed rate enhancement. The conversion of p‐nitro phenol ester within the membrane was modeled by considering a combination of the convective flow through poly(vinyl alcohol) membrane pores, concentration polarization of substrate containing micelles at the membrane surface and the kinetics of the reaction with free enzymes. It was demonstrated that the model offered a comprehensive understanding of the interaction of the involved phenomena. The modeling results are in good agreement with the experimental data from 10 runs with different enzyme and substrate concentrations. The substrate concentration at the membrane surface increased by up to a factor of 3 compared to the feed concentration. This effect explains the observed rate enhancement. Moreover, the model was used to determine the unknown parameters, i.e., the intrinsic retention and the mass transfer coefficient, by fitting the model to the experimental data. The model may also be used to calculate the optimum operating conditions and design parameters of such a reactor.     

Selective oxidation and N-coupling by purified laccase of Xylaria polymorpha MTCC-1100

The chemical route of oxidation of methyl group to its aldehyde is inconvenient because once a methyl group is attacked, it is likely to be oxidized to the carboxylic acid and it is very difficult to stop the reaction at the aldehyde stage. Fungal laccases can be used for such oxidation reaction and the reaction can be completed sharply within 1–2 h. Coupling of amines are another important reactions known for fungal laccases; coupling reactions generally take 3–7 h. We have used the purified laccase of molecular weight 63 kDa obtained from the fungal strain Xylaria polymorpha MTCC-1100 with activity of 1.95 IU/mL for selective oxidation of 2-fluorotoluene, 4-fluorotoluene, and 2-chlorotoluene to 2-fluorobenzaldehyde, 4-fluorobenzaldehyde, and 2-chlorobenzaldehyde, respectively, and syntheses of 3-(3, 4-dihydroxyphenyl)-propionic acid derivatives by N-coupling of amines. In each oxidation reactions, ABTS was used as mediator molecule. All the syntheses are ecofriendly and were performed at room temperature.     

Reaction pattern and mechanism of light induced oxidative water splitting in photosynthesis

This mini review is an attempt to briefly summarize our current knowledge on light driven oxidative water splitting in photosynthesis. The reaction leading to molecular oxygen and four protons via photosynthesis comprises thermodynamic and kinetic constraints that require a balanced fine tuning of the reaction coordinates. The mode of coupling between electron (ET) and proton transfer (PT) reactions is shown to be of key mechanistic relevance for the redox turnover of Y_Z and the reactions within the WOC. The WOC is characterized by peculiar energetics of its oxidation steps in the WOC. In all oxygen evolving photosynthetic organisms the redox state S₁ is thermodynamically most stable and therefore this general feature is assumed to be of physiological relevance. Available information on the Gibbs energy differences between the individual redox states S_i+1 and S_i and on the activation energies of their oxidative transitions are used to construct a general reaction coordinate of oxidative water splitting in photosystem II (PS II). Finally, an attempt is presented to cast our current state of knowledge into a mechanism of oxidative water splitting with special emphasis on the formation of the essential O-O bond and the active role of the protein environment in tuning the local proton activity that depends on time and redox state S_i. The O-O linkage is assumed to take place within a multistate equilibrium at the redox level of S₃, comprising both redox isomerism and proton tautomerism. It is proposed that one state, S₃(P), attains an electronic configuration and nuclear geometry that corresponds with a hydrogen bonded peroxide which acts as the entatic state for the generation of complexed molecular oxygen through S₃(P) oxidation by Y_Z^ox.     

Reaction pattern and mechanism of light induced oxidative water splitting in photosynthesis

This mini review is an attempt to briefly summarize our current knowledge on light driven oxidative water splitting in photosynthesis. The reaction leading to molecular oxygen and four protons via photosynthesis comprises thermodynamic and kinetic constraints that require a balanced fine tuning of the reaction coordinates. The mode of coupling between electron (ET) and proton transfer (PT) reactions is shown to be of key mechanistic relevance for the redox turnover of Y(Z) and the reactions within the WOC. The WOC is characterized by peculiar energetics of its oxidation steps in the WOC. In all oxygen evolving photosynthetic organisms the redox state S(1) is thermodynamically most stable and therefore this general feature is assumed to be of physiological relevance. Available information on the Gibbs energy differences between the individual redox states S(i+1) and S(i) and on the activation energies of their oxidative transitions are used to construct a general reaction coordinate of oxidative water splitting in photosystem II (PS II). Finally, an attempt is presented to cast our current state of knowledge into a mechanism of oxidative water splitting with special emphasis on the formation of the essential O-O bond and the active role of the protein environment in tuning the local proton activity that depends on time and redox state S(i). The O-O linkage is assumed to take place within a multistate equilibrium at the redox level of S(3), comprising both redox isomerism and proton tautomerism. It is proposed that one state, S(3)(P), attains an electronic configuration and nuclear geometry that corresponds with a hydrogen bonded peroxide which acts as the entatic state for the generation of complexed molecular oxygen through S(3)(P) oxidation by Y(Z)(ox).     

Metal-catalyzed oxidation reactions and mass spectrometry: the roles of ascorbate and different oxidizing agents in determining Cu-protein-binding sites

Further study has been made of metal-catalyzed oxidation (MCO) reactions and mass spectrometry as a method to determine the binding site of copper in metalloproteins. The role of ascorbate and a variety of oxidizing agents, including O2, H2O2, and S2O8(2-), have been investigated using Cu/Zn superoxide dismutase (SOD) as a model system. Ascorbate is found to play two competing roles in the MCO reactions. It reduces Cu(II), which initiates and maintains the generation of reactive oxygen species, and it scavenges radicals, which helps to localize oxidation products to amino acids near the metal center. An ascorbate concentration of 100 mM is found to be optimal with regard to localizing oxidation products to only the Cu-binding residues (His44, His46, His61, and His118) of Cu/Zn SOD. This concentration of ascorbate is very similar to the optimum concentration found in our previous studies of different Cu-binding proteins. Another notable result from this study is the observation that S2O8(2-) is more effective as an oxidant than O2 or H2O2 in the MCO reactions. Because S2O8(2-) is more stable in solution than H2O2, using it as an oxidizing agent results in much less nonspecific oxidation to the protein. The overall results of this study suggest that general MCO reaction conditions may exist for determining the metal-binding site of a wide range of Cu-binding proteins.     

Reaction of formaldehyde with calf-thymus nucleohistone

The reactions of formaldehyde with calf thymus nucleohistone were analyzed in the following ways: measurement with fluorescamine of the decrease in primary amino groups resulting from hydroxymethylation and crosslinking reactions, measurement with dodecylsulphate-gel electrophoresis of formation of histone oligomers, measurement of fixation of histones to the DNA in nucleohistone, and measurement of changes in the circular dichroism spectrum in the region of 250--300 nm. In the presence of formaldehyde, the primary amino groups of histones decreased very rapidly, attaining an equilibrium within 60 min, and successively intermolecular crosslinks were also formed between histone molecules, the resulting dimers and oligomers being separable by dodecylsulfate-gel electrophoresis. Whereas the fixation reaction proceeded much more slowly. The extent of fixation could be measured more accurately by dodecylsulfate/sucrose centrifugation analysis than by sulfuric acid extraction. After removal of formaldehyde from the reaction mixture, the fraction of masked amino groups decreased, perhaps due to the reverse reaction, but the extent of fixation of histones continued to increase with time. No specificity was observed among five molecular species of histones in the fixation reaction. With increase in formaldehyde concentration, the ellipticity of nucleohistone decreased to a minimum with about 0.4% formaldehyde, and then increased.     

Racemization in the Coupling Reaction with the Several Methods beside the Activated Ester Methods

The degree of racemization in the coupling reaction, Pro-Val + Pro, with the several other methods than the activated ester methods was measured and the results were compared with that in the coupling reaction, Leu-Phe + Val, as well as in the previous paper.¹⁾ In the azide and the mixed anhydride methods, no or almost no racemization was detected, whereas in the other tested methods of peptide synthesis (Pachornik-, DCCD- and phosphazo-methods) the significantly large racemization was observed. It can be attributed to the strong nucleo- philic N-atom in the penultimate amino acids (Pro) and the steric hindrance of C-terminal amino acid (Val), which are favourable to the formation of the oxazolone ring.

This assumption was further systematically confirmed in the synthesis of the other several tripeptides with the DCCD method. The separation of the diastereoisomers (LLL and LDL) of the resulting tripeptides by gas chromatography with a packed column was also here reported.