Pyridoxamine traps intermediates in lipid peroxidation reactions in vivo: evidence on the role of lipids in chemical modification of protein and development of diabetic complications

Maillard or browning reactions between reducing sugars and protein lead to formation of advanced glycation end products (AGEs) and are thought to contribute to the pathogenesis of diabetic complications. AGE inhibitors such as aminoguanidine and pyridoxamine (PM) inhibit both the formation of AGEs and development of complications in animal models of diabetes. PM also inhibits the chemical modification of protein by advanced lipoxidation end products (ALEs) during lipid peroxidation reactions in vitro. We show here that several PM adducts, formed in incubations of PM with linoleate and arachidonate in vitro, are also excreted in the urine of PM-treated animals. The PM adducts N-nonanedioyl-PM (derived from linoleate), N-pentanedioyl-PM, N-pyrrolo-PM, and N-(2-formyl)-pyrrolo-PM (derived from arachidonate), and N-formyl-PM and N-hexanoyl-PM (derived from both fatty acids) were quantified by liquid chromatography-mass spectrometry analysis of rat urine. Levels of these adducts were increased 5-10-fold in the urine of PM-treated diabetic and hyperlipidemic rats, compared with control animals. We conclude that the PM functions, at least in part, by trapping intermediates in AGE/ALE formation and propose a mechanism for PM inhibition of AGE/ALE formation involving cleavage of alpha-dicarbonyl intermediates in glycoxidation and lipoxidation reactions. We also conclude that ALEs derived from polyunsaturated fatty acids are increased in diabetes and hyperlipidemia and may contribute to development of long term renal and vascular pathology in these diseases.     

Capillary isoelectric focusing with laser-induced fluorescence whole column imaging detection as a tool to monitor reactions of proteins

Capillary isoelectric focusing (CIEF) with laser-induced fluorescence (LIF) whole column imaging detection (WCID) has the characteristics of high resolution, high speed and high sensitivity for separation of amphoteric biomolecules. These features enable a CIEF-LIF-WCID system to monitor the dynamic process of a protein reaction. The reaction can be a physical change or a chemical reaction, provided that the kinetics of the reaction is slower than the focusing speed or that the intermediates involved have long enough life-span compared to the analysis time. The processes of denaturation (a physical reaction), reduction and carbamylation (both chemical reactions) were dynamically monitored. The CIEF profiles at successive reaction times clearly displayed the formation of different products at different stages. At incomplete denaturation, intermediates with higher apparent pI values relative to the products at complete denaturation were detected. Carbamylation products of a protein were detected when the protein reacted with a urea solution that had prepared three months earlier, exhibiting gradually decreased pI values. Mechanisms involved in these reactions were rationalized. A combined mechanism of denaturation and reduction was suggested to explain the denaturing process under high concentrations of urea. Potential applications and critical factors to manipulate these reactions were also discussed.     

Revisiting the dissimilatory sulfate reduction pathway

Sulfur isotopes in the geological record integrate a combination of biological and diagenetic influences, but a key control on the ratio of sulfur isotopes in sedimentary materials is the magnitude of isotope fractionation imparted during dissimilatory sulfate reduction. This fractionation is controlled by the flux of sulfur through the network of chemical reactions involved in sulfate reduction and by the isotope effect associated with each of these chemical reactions. Despite its importance, the network of reactions constituting sulfate reduction is not fully understood, with two principle networks underpinning most isotope models. In this study, we build on biochemical data and recently solved crystal structures of enzymes to propose a revised network topology for the flow of sulfur through the sulfate reduction metabolism. This network is highly branched and under certain conditions produces results consistent with the observations that motivated previous sulfate reduction models. Our revised network suggests that there are two main paths to sulfide production: one that involves the production of thionate intermediates, and one that does not. We suggest that a key factor in determining sulfur isotope fractionation associated with sulfate reduction is the ratio of the rate at which electrons are supplied to subunits of Dsr vs. the rate of sulfite delivery to the active site of Dsr. This reaction network may help geochemists to better understand the relationship between the physiology of sulfate reduction and the isotopic record it produces.     

Characterization of covalent Ene adduct intermediates in "hydride equivalent" transfers in a dihydropyridine model for NADH reduction reactions

A study of the reactions of an NADH model, 1,4-di(trimethylsilyl)-1,4-dihydropyridine, 7, with a series of α,β-unsaturated cyano and carbonyl compounds has produced the first direct evidence for an obligatory covalent adduct between a dihydropyridine and substrate in a reduction reaction. The reactions were monitored by NMR spectroscopy. In all reactions studied, the covalent adduct was the first new species detected and its decomposition to form products could be observed. Concentrations of adducts were sufficiently high at steady-state that their structures could be determined directly from NMR spectra of the reaction mixtures; adduct structures are those expected from an Ene reaction between 7 and the substrate. This first reaction step results in transfer of the C(4) hydrogen nucleus of 7 to the substrate and formation of a covalent bond between C(2) of the dihydropyridine ring and the substrate α-atom. Discovery of these Ene-adduct intermediates completes the spectrum of mechanisms observed in NADH model reactions to span those with free radical intermediates, no detectable intermediates and now covalent intermediates. The geometry of the transition state for formation of the Ene adduct is compared with those of theoretical transition state models and crystal structures of enzyme-substrate/inhibitor complexes to suggest a relative orientation for the dihydropyridine ring and the substrate in an initial cyclic transition state that is flexible enough to accommodate all observed mechanistic outcomes.     

Experimental study of the protein folding landscape: unfolding reactions in cytochrome c.

Hydrogen exchange results for cytochrome c have been interpreted in terms of transient hydrogen bond-breaking reactions that include large unfolding reactions and small fluctuational distortions. The differential sensitivity of these opening reactions to denaturant, temperature, and protein stability makes it possible to distinguish the different opening reactions and to characterize their structural and thermodynamic parameters. The partially unfolded forms (PUFs) observed are few and discrete, evidently because they are produced by the reversible unfolding of the protein's several intrinsically cooperative secondary structural elements. The PUFs are robust, evidently because the structural elements do not change over a wide range of conditions. The discrete nature of the PUFs and their small number is as expected for classical folding intermediates but not for theoretically derived folding models apparently because the simplified non-protein models usually analyzed in theoretical studies encompass only a single cooperative unit rather than multiple separable units.     

The hemoglobin cyanomet ligation analogue and carbon monoxide induce similar allosteric mechanisms

Current thermodynamic models of protein cooperativity predicting sigmoidal ligand equilibrium curves differ in the assumptions regarding the structural/functional properties of the intermediate ligation states. Quantitative information on the intermediates cannot be extracted from the equilibrium curves, but must be obtained from direct studies of the intermediates. Since the intermediates are intrinsically unstable species, ligation analogues with reduced mobility are indispensable tools for cooperativity studies provided that the tertiary/quaternary changes triggered by the ligation analogue are similar to those observed using the physiological ligands. We demonstrate that the valency exchange reactions occurring in mixtures of deoxy and cyanomethemoglobin yield non-random distributions of deoxy/cyanomet intermediates that resemble those observed in the equilibrium with carbon monoxide. Previous and new data using the analogue, in agreement with the studies of the CO intermediates, indicate that the mechanism of hemoglobin cooperativity is neither purely concerted nor sequential nor combinatorial, but contains some elements of each of these models.     

Navigating molecular space for reaction mechanisms: an efficient,automated procedure

Mechanism is a core chemical concept that has vital implications for reaction rate, efficiency and selectivity. The discovery of mechanism is not easy due to the great diversity of possible chemical rearrangements in even relatively simple systems. For this reason, mechanisms involving bond breaking and forming are usually proposed via chemical intuition – which limits the scope of considered possibilities – and these hypotheses are then tested using simulation or experiment. This article discusses an automated simulation strategy for investigating multiple elementary step reaction mechanisms in chemical systems. The method starts from a single input structure and seeks out nearby intermediates, optimises the proposed structures and then determines the kinetic viability of each elementary step. The kinetically accessible intermediates are catalogued and new searches are performed on each unique structure. This process is repeated for an arbitrary number of steps without human intervention, and massively parallel computation enables fast searches in chemical space. Importantly, this strategy can be empirically shown to lead to a finite number of accessible structures, not a combinatorial explosion of intermediates. Therefore, the method should be able to predict multi-step reaction pathways in many interesting chemical systems. Demonstrations on organic reactions and a hydrogen storage material, ammonia borane, show that the herein proposed strategy can uncover complex reactivity without relying on existing chemical intuition.     

Characterization of the folding pathway of recombinant human macrophage-colony stimulating-factor β (rhM-CSF β) by bis-cysteinyl modification and mass spectrometry

Melarsen oxide [p-(4,6-diamino-1,3,5-triazin-2-yl)aminophenylarsonous acid (MEL)], which selectively bridges spatially neighboring bis-cysteinyl residues in (reduced) proteins, was used to trap folding intermediates chemically during 1) time-dependent renaturation of recombinant human macrophage colony-stimulating factor (rhM-CSF); by redox refolding in vitro; 2) reductive unfolding in the presence of the trapping reagent; and 3) denaturing unfolding reactions in urea and guanidinium hydrochloride. Characterization of intermediates from folding and unfolding reactions was performed by electrospray ionization mass spectometry (ESI-MS). In all folding and unfolding reactions a characteristic dimeric intermediate with two attached melarsen oxide (MEL) groups was observed, suggesting that these rhM-CSF β species were important refolding intermediates. These intermediates presented a characteristic “charge structure” in ESI spectra with a most abundant 26+ charged molecular ion whereas the mature homodimeric rhM-CSF β showed a most abundant 23+ molecular ion, indicating that the final product was more compact. The major locations of the two MEL groups were identified by mass spectrometric peptide mapping at cysteine residues C157 and C159 from each monomer. Cysteine residues C7 and C90 were minor modification sites. The mass spectrometric results from the in vitro folding reactions of rhM-CSF β are in agreement with intrinsic tryptophan fluorescence measurements and are consistent with the folding pathway that starts with a fully reduced monomer (R), includes partially folded monomeric intermediates (M) and dimeric intermediates (D), and yields a final product with the native tertiary structure (N): 2R ⇒ 2M ⇒ D ⇒ N. Our results show that selective chemical trapping of bis-thiol groups of proteins with MEL permits study of folding pathways by mass spectrometric structure characterization of intermediates with otherwise transient conformations. Proteins Suppl. 2:50–62, 1998. © 1998 Wiley-Liss, Inc.     

Positional isotope exchange

The detection of intermediates in enzyme-catalyzed reactions can be accomplished by several techniques. For those intermediates which do not have easily observed electronic spectra, use can be made of isotope exchange phenomena if the chemistry of the reaction is appropriate. Recently, the technique of positional isotope exchange (intramolecular isotopic scrambling) has been used to study several reactions which have been thought to involve high-energy intermediates in their mechanisms. A review of some of these reactions and the limitations of the method are presented in this article.     

Antagonism and bistability in protein interaction networks

A protein interaction network (PIN) is a set of proteins that modulate one another's activities by regulated synthesis and degradation, by reversible binding to form complexes, and by catalytic reactions (e.g., phosphorylation and dephosphorylation). Most PINs are so complex that their dynamical characteristics cannot be deduced accurately by intuitive reasoning alone. To predict the properties of such networks, many research groups have turned to mathematical models (differential equations based on standard biochemical rate laws, e.g., mass-action, Michaelis-Menten, Hill). When using Michaelis-Menten rate expressions to model PINs, care must be exercised to avoid making inconsistent assumptions about enzyme-substrate complexes. We show that an appealingly simple model of a PIN that functions as a bistable switch is compromised by neglecting enzyme-substrate intermediates. When the neglected intermediates are put back into the model, bistability of the switch is lost. The theory of chemical reaction networks predicts that bistability can be recovered by adding specific reaction channels to the molecular mechanism. We explore two very different routes to recover bistability. In both cases, we show how to convert the original 'phenomenological' model into a consistent set of mass-action rate laws that retains the desired bistability properties. Once an equivalent model is formulated in terms of elementary chemical reactions, it can be simulated accurately either by deterministic differential equations or by Gillespie's stochastic simulation algorithm.     

海因酶法制备D-对羟基苯甘氨酸的研究进展

D-对羟基苯甘氨酸(D-HPG)主要用于合成β-内酰胺类半合成抗生素,是国内最紧缺的医药中间体之一。微生物酶法是目前获得光学纯D-HPG的重要途径,微生物中起催化作用的主要是D-海因酶和N-氨甲酰水解酶。文章综述了产酶微生物的来源,酶的理化性质,以及培养条件的优化、基因工程、酶的固定化技术生产D-HPG的研究进展。     

Pyridoxamine, an inhibitor of advanced glycation reactions, also inhibits advanced lipoxidation reactions. Mechanism of action of pyridoxamine

Maillard or browning reactions lead to formation of advanced glycation end products (AGEs) on protein and contribute to the increase in chemical modification of proteins during aging and in diabetes. AGE inhibitors such as aminoguanidine and pyridoxamine (PM) have proven effective in animal model and clinical studies as inhibitors of AGE formation and development of diabetic complications. We report here that PM also inhibits the chemical modification of proteins during lipid peroxidation (lipoxidation) reactions in vitro, and we show that it traps reactive intermediates formed during lipid peroxidation. In reactions of arachidonate with the model protein RNase, PM prevented modification of lysine residues and formation of the advanced lipoxidation end products (ALEs) N(epsilon)-(carboxymethyl)lysine, N(epsilon)-(carboxyethyl)lysine, malondialdehyde-lysine, and 4-hydroxynonenal-lysine. PM also inhibited lysine modification and formation of ALEs during copper-catalyzed oxidation of low density lipoprotein. Hexanoic acid amide and nonanedioic acid monoamide derivatives of PM were identified as major products formed during oxidation of linoleic acid in the presence of PM. We propose a mechanism for formation of these products from the 9- and 13-oxo-decadienoic acid intermediates formed during peroxidation of linoleic acid. PM, as a potent inhibitor of both AGE and ALE formation, may prove useful for limiting the increased chemical modification of tissue proteins and associated pathology in aging and chronic diseases, including both diabetes and atherosclerosis.     

Maillard reaction products in tissue proteins: New products and new perspectives

Summary. The chemical modification of protein by nonenzymatic browning or Maillard reactions increases with age and in disease. Maillard products are formed by reactions of both carbohydrate- and lipid-derived intermediates with proteins, leading to formation of advanced glycation and lipoxidation end-products (AGE/ALEs). These modifications and other oxidative modifications of amino acids increase together in proteins and are indicators of tissue aging and pathology. In this review, we describe the major pathways and characteristic products of chemical modification of proteins by carbohydrates and lipids during the Maillard reactions and identify major intersections between these pathways. We also describe a new class of intracellular sulfhydryl modifications, Cys-AGE/ALEs, that may play an important role in regulatory biology and represent a primitive link between nonenzymatic and enzymatic chemistry in biological systems.     

Electron transfer through DNA and peptides

Electrons can migrate through DNA and peptides over very long distances in a multistep hopping process. Stepping stones, which carry the charges for a short time, are the nucleotide bases of DNA or the aromatic side chains of amino acids in peptides. Chemical reactions of these charged intermediates lead to the formation but also to the repair of DNA lesions. In enzymes, long distance electron transfer can activate the binding pocket, and initiates the chemical transformation of the substrate.     

Free energy transduction in a chemical motor model

Motor enzymes catalyse chemical reactions, like the hydrolysis of ATP, and in the process they also perform work. Recent studies indicate that motor enzymes perform work with specific biochemical steps in their catalysed reactions, challenging the classical view that work can only be performed within a biochemical state. To address these studies an alternative class of models, often referred to as chemical motor models, has emerged in which motors perform work with biochemical transitions. In this paper, I develop a novel, self-consistent framework for chemical motor models, which accommodates multiple pathways for free energy transfer, predicts rich behaviors from the simplest multi-motor systems, and provides important new insights into muscle and motor function.     

Ultrafiltration,a useful method for isolation of intermediates in native chemical ligation exemplified with the total synthesis of Sortase AΔN59

In this paper, ultrafiltration was employed to facilitate the isolation of intermediates in native chemical ligation. Depending on the molecular weight cutoff of the membrane used, molecules with different sizes could be purified, separated, or concentrated by the ultrafiltration process. Total chemical synthesis of the polypeptide chain of the enzyme Sortase A_ΔN59 was used as an example of the application of ultrafiltration in chemical protein synthesis. Sortase A is a ligase that catalyzes transpeptidation reactions between proteins that have C‐terminal LPXTG recognition sequence and Gly5‐ on the peptidoglycan of bacterial cell walls [3]. Ultrafiltration technique facilitated synthesis of Sortase A_ΔN59 and was a promising tool in isolation of intermediates in native chemical ligation. Copyright © 2015 European Peptide Society and John Wiley & Sons, Ltd.     

Use of 31P and 13C NMR to study enzyme mechanisms

A number of complex biochemical problems have been solved recently by application of new techniques in which 31P and 13C NMR spectroscopy is used. Oxygen isotope exchange phenomena were studied by these NMR methods and used to analyze individual mechanistic events in enzymatic reactions. The existence of intermediates in the reactions catalyzed by glutamine synthetase (EC 6.3.1.2) and carbamyl-phosphate synthetase (EC 2.7.2.9) has been established as well as the kinetic competence of these intermediates for each enzyme. The NMR theory and kinetic experiments required to conduct such studies are discussed.     

L-serine analogues form Schiff base and quinonoidal intermediates with Escherichia coli tryptophan synthase

Substrate analogues of L-serine have been found that react with the alpha 2 beta 2 complex of Escherichia coli tryptophan synthase. Upon reaction with alpha 2 beta 2, the analogues glycine, L-histidine, L-alanine, and D-histidine form chemical intermediates derived from reaction with enzyme-bound pyridoxal 5'-phosphate with characteristic UV-visible spectral bands. The spectra of the products of the glycine, L-histidine, and L-alanine reactions with alpha 2 beta 2 contain contributions from the external aldimine, the quinonoid species, and other intermediates along the catalytic pathway. Just as previously reported for the reaction of L-serine with beta 2 [Goldberg, M. E., York, S., & Stryer, L. (1968) Biochemistry 7, 3662-3667], the reactions of glycine, L-histidine, and L-alanine with the beta 2 form of tryptophan synthase yield spectra with no contributions from catalytic intermediates beyond the external aldimine. The kinetics of intermediate formation and comparisons of the time courses for the exchange of alpha-1H for solvent 2H catalyzed by alpha 2 beta 2 or beta 2 were found to be consistent with these assignments. Intermediates further along the tryptophan synthase catalytic pathway are stabilized to a greater degree in the alpha 2 beta 2 complex than in the beta 2 species alone. This observation strongly suggests that the association of alpha and beta subunits to form the native alpha 2 beta 2 species lowers the activation energies for the interconversion of the external aldimine with chemical species further along the catalytic path.(ABSTRACT TRUNCATED AT 250 WORDS)     

Trapping intermediates in the crystal: ligand binding to myoglobin

Crystal structures of the reactive short-lived species that occur in chemical or binding reactions can be determined using X-ray crystallography via time-resolved or kinetic trapping approaches. Recently, various kinetic trapping methods have been used to determine the structure of intermediates in ligand binding to myoglobin.     

Observation of multistate kinetics during the slow folding and unfolding of barstar.

The kinetics of the slow folding and unfolding reactions of barstar, a bacterial ribonuclease inhibitor protein, have been studied at 23(+/-1) degrees C, pH 8, by the use of tryptophan fluorescence, far-UV circular dichroism (CD), near-UV CD, and transient mixing (1)H nuclear magnetic resonance (NMR) spectroscopic measurements in the 0-4 M range of guanidine hydrochloride (GdnHCl) concentration. The denaturant dependences of the rates of folding and unfolding processes, and of the initial and final values of optical signals associated with these kinetic processes, have been determined for each of the four probes of measurement. Values determined for rates as well as amplitudes are shown to be very much probe dependent. Significant differences in the intensities and rates of appearance and disappearance of several resolved resonances in the real-time one-dimensional NMR spectra have been noted. The NMR spectra also show increasing dispersion of chemical shifts during the slow phase of refolding. The denaturant dependences of rates display characteristic folding chevrons with distinct rollovers under strongly native as well as strongly unfolding conditions. Analyses of the data and comparison of the results obtained with different probes of measurement appear to indicate the accumulation of a myriad of intermediates on parallel folding and unfolding pathways, and suggest the existence of an ensemble of transition states. The energetic stabilities of the intermediates estimated from kinetic data suggest that they are approximately half as stable as the fully folded protein. The slowness of the folding and unfolding processes (tau = 10-333 s) and values of 20.5 (+/-1.4) and 18 (+/-0.5) kcal mol(-)(1) for the activation energies of the slow refolding and unfolding reactions suggest that proline isomerization is involved in these reactions, and that the intermediates accumulate and are therefore detectable because the slow proline isomerization reaction serves as a kinetic trap during folding.