A comparative study of ruthenium(III) catalysed oxidation of L-leucine and L-isoleucine by alkaline permanganate. A kinetic and mechanistic approach

The kinetics of the Ru^III-catalysed oxidation of L-leucine and L-isoleucine by alkaline permanganate were studied and compared, spectrophotometrically using a rapid kinetic accessory. The reaction is first order with respect to [oxidant] and [catalyst] with an apparently less than unit order in [substrate] and [alkali] respectively. The results suggest the formation of a complex between the amino acid and the hydroxylated species of ruthenium(III). The complex reacts further with the alkaline permanganate species in a rate-determining step, resulting in the formation of a free radical, which again reacts with the alkaline permanganate species in a subsequent fast step to yield the products. The reaction constants involved in the mechanism were calculated. There is a good agreement between observed and calculated rate constants under different experimental conditions. The activation parameters with respect to the slow step of the mechanism for both the amino acids were calculated and discussed. Of the two amino acids, leucine is oxidised at a faster rate than isoleucine.     

Kinetics and Mechanism of the Condensation of Pyridoxal with Amino Acids

The kinetics and mechanism of the condensation of amino acids with pyridoxal were studied in relation to the amino acid structure, solvent, pH, and temperature. A spectrophotometric study revealed several kinetically discernible reaction steps. The condensation rate as a function of pH passes through a maximum, which is caused by formation of two intermediates of different structures. The final products of the condensation and subsequent hydrolysis are pyridoxamine and α-keto acids. The reaction mechanism was suggested.     

Comparison of various coupling reagents in solid-phase aza-peptide synthesis

Aza-peptides are promising drug leads, however extensive study of their properties is hampered by low yielding aza-peptide bond formation during conventional Fmoc SPPS. The kinetics of aza-peptide bond formation in the model peptide H-Ala-AzAla-Phe-NH₂ was compared with various conventional amino acid activators. The reaction rates and yields were dependent on the activator structure. The reaction time of aza-peptide formation using oxyma-based agents was approximately 30 times longer than in typical peptide synthesis. Therefore, new activators are required to increase the reactivity of the activated amino acid to achieve effective acylation of the semicarbazide moiety during aza-peptide bond formation.     

A kinetic and mechanistic study of the amino acid catalyzed aldol condensation of acetaldehyde in aqueous and salt solutions

The amino acid catalyzed aldol condensation is of great interest in organic synthesis and natural environments such as atmospheric particles. However, kinetic and mechanistic information on these reactions is limited. In this work the kinetics of the aldol condensation of acetaldehyde in water and aqueous salt solutions (NaCl, CaCl2, Na2SO4, MgSO4) catalyzed by five amino acids (glycine, alanine, serine, arginine, and proline) at room temperature (295 +/- 2 K) has been studied. Monitoring the formation of three products, crotonaldehyde, 2,4-hexadienal, and 2,4,6-octatrienal, by UV-vis absorption over 200-1100 nm revealed two distinct kinetic regimes: at low amino acid concentrations (in all cases, below 0.1 M), the overall reaction was first-order with respect to acetaldehyde and kinetically limited by the formation of the enamine intermediate. At larger amino acid concentrations (at least 0.3 M), the kinetics was second order and controlled by the C-C bond-forming step. The first-order rate constants increased linearly with amino acid concentration consistent with the enamine formation. Inorganic salts further accelerated the enamine formation according to their pKb plausibly by facilitating the iminium or enamine formation. The rate constant of the C-C bond-forming step varied with the square of amino acid concentration suggesting the involvement of two amino acid molecules. Thus, the reaction proceeded via a Mannich pathway. However, the contribution of an aldol pathway, first-order in amino acid, could not be excluded. Our results show that the rate constant for the self-condensation of acetaldehyde in aqueous atmospheric aerosols (up to 10 mM of amino acids) is identical to that in sulfuric acid 10-15 M (kI approximately 10-7-10-6 s-1) clearly illustrating the potential importance of amino acid catalysis in natural environments. This work also demonstrates that under usual laboratory conditions and in natural environments aldol condensation is likely to be kinetically controlled by the enamine formation. Notably, kinetic investigations of the C-C bond-forming addition step would only be possible with high concentrations of amino acids.     

A Kinetic Analysis of the Reaction Catalysed by (Hydroxymethyl)bilane Synthase

(Hydroxymethyl)bilane synthase (HMBS) catalyses the conversion of porphobilinogen ( 2 ) into the (hydroxymethyl)bilane derivative 3 , a linear tetrapyrrolic intermediate in the biosynthesis of haem, chlorophyll, and related pigments. The conversion involves the sequential formation of four intermediate covalent enzyme-substrate complexes, before the product is released. We analysed the pre-steady-state kinetics of the formation of the complexes, taking advantage of their remarkable chemical stability allowing chromatographic separation. The experimental approach involved the generation of the complexes while HMBS was immobilised on an anion-exchange column. A solution being 0.2 K_m in substrate was pumped through the column during a time interval which was varied to sample the pre-steady-state period. Then, the enzyme and enzyme-substrate complexes were eluted and their proportions evaluated. A computer simulation of the pre-steady-state time course, in combination with a χ² fitting to the experimental data, allowed the specificity constants k_cat/K_m for the individual steps of the process to be derived. By repeating the analysis with variants of HMBS in which specific amino acids were replaced by others, we demonstrated that it is possible to trace the consequences of amino-acid replacements down to the individual steps of the reaction sequence. Since the positions of the amino acids concerned in the three-dimensional structure were known, detailed structure-function relationships become evident in this way.     

Homocyclic o-dicarboxaldehydes: Derivatization reagents for sensitive analysis of amino acids and related compounds by capillary and microchip electrophoresis

Amino acids are essential compounds for living organisms, and their determination in biological fluids is crucial for the clinical analysis and diagnosis of many diseases. However, the detection of most amino acids is hindered by the lack of a strong chromophore/fluorophore or electrochemically active group in their chemical structures. The highly sensitive determination of amino acids often requires derivatization. Capillary electrophoresis is a separation technique with excellent characteristics for the analysis of amino acids in biological fluids. Moreover, it offers the possibility of precapillary, on-capillary, or postcapillary derivatization. Each derivatization approach has specific demands in terms of the chemistry involved in the derivatization, which is discussed in this review. The family of homocyclic o-dicarboxaldehyde compounds, namely o-phthalaldehyde, naphthalene-2,3-dicarboxaldehyde, and anthracene-2,3-dicarboxaldehyde, are powerful derivatization reagents for the determination of amino acids and related compounds. In the presence of suitable nucleophiles they react with the primary amino group to form both fluorescent and electroactive derivatives. Moreover, the reaction rate enables all of the derivatization approaches mentioned above. This review focuses on articles that deal with using these reagents for the derivatization of amino acids and related compounds for ultraviolet-visible spectrometry, fluorescence, or electrochemical detection. Applications in capillary and microchip electrophoresis are summarized and discussed.     

Peptide bond formation by aminolysin-A catalysis: a simple approach to enzymatic synthesis of diverse short oligopeptides and biologically active puromycins

A new S9 family aminopeptidase derived from the actinobacterial thermophile Acidothermus cellulolyticus was cloned and engineered into a transaminopeptidase by site-directed mutagenesis of catalytic Ser(491) into Cys. The engineered biocatalyst, designated aminolysin-A, can catalyze the formation of peptide bonds to give linear homo-oligopeptides, hetero-dipeptides, and cyclic dipeptides using cost-effective substrates in a one-pot reaction. Aminolysin-A can recognize several C-terminal-modified amino acids, including the l- and d-forms, as acyl donors as well as free amines, including amino acids and puromycin aminonucleoside, as acyl acceptors. The absence of amino acid esters prevents the formation of peptides; therefore, the reaction mechanism involves aminolysis and not a reverse reaction of hydrolysis. The aminolysin system will be a beneficial tool for the preparation of structurally diverse peptide mimetics by a simple approach.     

Changes in trace element concentrations in human serum after parenteral application of amino acids

The concentrations of ten trace elements were assayed up to 3 hours after an infusion of an amino acid mixture. The changes in metabolism induced by the administered amino acids led to characteristic alterations of the trace element concentrations. These characteristic alterations could be explained by a mechanism which seems to compensate for membraneous charge alterations caused by the metabolic reaction. Obviously, non essential trace elements are involved in this mechanism.     

以三种非极性氨基酸为例探讨氨基酸合成代谢的化学原理

由于氨基酸代谢的多样性和相对独立性,在基础教学中对相关内容的讨论和推广对培养21世纪新型跨学科人才是极其重要的。本文将以三种基本的非极性天然氨基酸——缬氨酸、异亮氨酸和亮氨酸为例,从氨基酸合成代谢的内容和方式等方面做教学模式的探索,并尝试归纳与总结自然界采取这样代谢路径的原因和逻辑。同时,其中相关的生物化学过程也体现出生命体系所采取的不同寻常的合成路径和反应机制。这对于本科生而言不仅是具有趣味性与启发性的良好的素材,也是了解目前研究热点和积累知识的有效渠道,期望对其后续深入的学习和研究有帮助。     

Kinetics of reactions of aquacobalamin with aspartic and glutamic acids and their amides in water solutions

The kinetics of aquacobalamin reaction with aspartic and glutamic acids, and with their amides in water solutions, is studied via spectrophotometry. The kinetic and activation parameters of the process are determined. It is shown that the reaction product is cobalamin–amino acid complex. The data are compared to results on the reaction between aquacobalamin and primary amines.     

Effect of amino acids on the interaction between cobalamin(II) and dehydroascorbic acid

The kinetics of the reaction between one-electron-reduced cobalamin (cobalamin(II), Cb(II)) and the two-electron-oxidized form of vitamin C (dehydroascorbic acid, DHA) with amino acids in an acidic medium is studied by conventional UV–Vis spectroscopy. It is shown that the oxidation of Cbl(II) by dehydroascorbic acid proceeds only in the presence of sulfur-containing amino acids (cysteine, acetylcysteine). A proposed reaction mechanism includes the step of amino acid coordination on the Co(II)-center through the sulfur atom, along with that of the interaction between this complex and DHA molecules, which results in the formation of ascorbyl radical and the corresponding Co(III) thiolate complex.     

Rate constants for the reaction of OH radicals with some amino polycarboxylic acids

Rate constants of OH radical reaction with some amino polycarboxylic acids (APCAs) such as EDTA, DTPA, HEDTA, NTA, and HIDA have been determined at different pHs using pulse radiolysis competition kinetics method with thiocyanate as the reference solute. The rate constants varied with pH (possibly due to their various pKs) and the plots of rate constants vs. pH are given. Rate constants for OH radical reaction with the various acid–base forms of these amino polycarboxylic acids are estimated from the plateau values in the plots. © 2000 John Wiley & Sons, Inc. Int J Chem Kinet 32: 99–104, 2000     

Kinetics and mechanism of the condensation of pyridoxal hydrochloride with L-tryptophan and D-tryptophan,and the chemical transformation of their products

The kinetics and mechanism of interaction between pyridoxal and L-tryptophan, D-tryptophan, and their derivatives are studied. It is found that condensation reactions proceed via three kinetically distinguishable stages: (1) the rapid intraplanar addition of the NH₂ groups of the amino acids to pyridoxal with the formation of amino alcohols; (2) the rotational isomerism of amino alcohol fragments with their subsequent dehydration and the formation of a Schiff base with a specific configuration; (3) the abstraction of α-hydrogen in the product of condensation of pyridoxal with L-tryptophan, or the abstraction of СО₂ in the product of condensation of pyridoxal with D-tryptophan with the formation of quinoid structures, hydrolysis of which results in the preparation of pyridoxamine and keto acid or pyridoxal and tryptamine, respectively. Schiff bases resistant to further chemical transformations are formed in the reaction with tryptophan methyl ester.     

Direct measurement of isotopomer of intracellular metabolites using capillary electrophoresis time-of-flight mass spectrometry for efficient metabolic flux analysis

We have developed a metabolic flux analysis method that is based on (13)C-labeling patterns of the intracellular metabolites directly measured by capillary electrophoresis time-of-flight mass spectrometry (CE-TOFMS). The flux distribution of the central carbon metabolism in Escherichia coli was determined by this new approach and the results were compared with findings obtained by conventional GC-MS analysis based on isotopomer of the proteinogenic amino acids. There were some differences in estimation results between new approach using CE-TOFMS and conventional approach using GC-MS. These were thought to be attributable to variations in measured mass distributions between amino acids and the corresponding precursors and to differences in the sensitivity of the exchange coefficients to mass distributions. However, our CE-TOFMS method facilitates high-throughput flux analysis without requiring complicated sample preparation such as hydrolysis of proteins and derivatization of amino acids.     

Some aspects of the active transport of amino acids

Active transport is the transport of substances against their activity gradients. In the cell, metabolic processes provide the energy for active transport through the membrane, during which amino acids are coupled with a carrier system located in the membrane. Some of the proteins involved in the translocation of amino acids have now been isolated from E. coli.     

Binary and ternary complexes involving copper(II), glycyl-dl-leucine and amino acids or amino acid esters: hydrolysis and equilibrium studies

Binary and ternary complex formation equilibria of copper(II) with glycyl-dl-leucine and amino acids or their esters were investigated potentiometrically at 25°C and a constant ionic strength. The kinetics of base hydrolysis of amino acid esters in their ternary complexes were monitored using the pH-stat method. The ester groups, with the exception of the histidine methyl ester, undergo rapid promoted hydrolysis. The rate and catalysis constants were evaluated from the experimental data.     

化学衍生用于代谢物异构体质谱分析

内源性代谢物是机体生命活动的中间体和终产物,对其进行定性和定量分析在生命科学研究中具有重要意义.质谱能够同时提供化合物的定性和定量信息,已经成为一种通用的内源性代谢物分析技术.由于质谱是通过检测离子质荷比获取化合物组成信息,区分生物体内复杂多样代谢物同分异构体仍然是质谱分析亟待解决的难题之一.化学衍生通过放大同分异构体...     

Tryptophan in Multicomponent Petasis Reactions for Peptide Stapling and Late-Stage Functionalisation

Peptide stapling is a robust strategy for generating enzymatically stable, macrocyclic peptides. The incorporation of biologically relevant tags (such as cell-penetrating motifs or fluorescent dyes) into peptides, while preserving their binding interactions and enhancing their stability, is highly sought after. Despite the unique opportunities offered by tryptophan‘s indole scaffold for targeted functionalisation, its utilisation in peptide stapling has been limited as compared to other amino acids. Herein, we present an approach for peptide stapling using the tryptophan-mediated Petasis reaction. This method enables the synthesis of both stapled and labelled peptides and is applicable to both solution and solid-phase synthesis. Importantly, the use of the Petasis reaction in combination with tryptophan facilitates the formation of stapled peptides in a straightforward, multicomponent fashion, while circumventing the formation of undesired by-products. Furthermore, this approach allows for efficient and diverse late-stage peptide modifications, thereby enabling rapid production of numerous conjugates for biological and medicinal applications.     

Chemical cross‐linking with NHS esters: a systematic study on amino acid reactivities

Structure elucidation of tertiary or quaternary protein structures by chemical cross‐linking and mass spectrometry (MS) has recently gained importance. To locate the cross‐linker modification, dedicated software is applied to analyze the mass or tandem mass spectra (MS/MS). Such software requires information on target amino acids to limit the data analysis time. The most commonly used homobifunctional N‐hydroxy succinimide (NHS) esters are often described as reactive exclusively towards primary amines, although side reactions with tyrosine and serine have been reported. Our goal was to systematically study the reactivity of NHS esters and derive some general rules for their attack of nucleophilic amino acid side chains in peptides. We therefore studied the cross‐linking reactions of synthesized and commercial model peptides with disuccinimidyl suberate (DSS). The first reaction site in all cases was expectedly the α‐NH₂‐group of the N‐terminus or the ε‐NH₂‐group of lysine. As soon as additional cross‐linkers were attached or loops were formed, other amino acids were also involved in the reaction. In addition to the primary amino groups, serine, threonine and tyrosine showed significant reactivity due to the effect of neighboring amino acids by intermediate or permanent Type‐1 cross‐link formation. The reactivity is highly dependent on the pH and on adjacent amino acids. Copyright © 2009 John Wiley & Sons, Ltd.