Radical mechanisms in adenosylcobalamin-dependent enzymes

Adenolsylcobalamin-dependent enzymes catalyze free radical mediated reactions of their substrates. Stereochemical methods have been used to establish the nature of the primary radical initiation step in ribonucleoside triphosphate reductase. Kinetic isotope effects have been used to establish a kinetic coupling between cobalt-carbon bond cleavage and hydrogen atom abstraction from the substrate. Isotope effects have also been used to identify rate-limiting steps with wild type and mutant forms of the enzymes and in model reactions to assess tunneling contributions to hydrogen atom transfer steps. Computational methods have been employed to explore the pathways for functional group migration in the radical pathways. Analogs of substrates and of adenosylcobalamin have been used to explore the fidelity of the enzyme active sites and the radical pathways.     

Interactions in enzymatic reactions

The paper deals with interactions of substances via an enzymatic reaction (Bull. Math. Biophysics,25, 141–154, 1963). The substances are the activators, inhibitors and/or substrates of the reaction. Due to the bimolecularity of the processes in the reaction, the quantitative relation between the steady state amount of complexes and the amounts of the substances assumes a typical form. In multiple enzymatic reactions this form is more complicated, though basically similar. Because the substances may influence the steady state amounts of the complexes in opposite directions, the compensation and blocking effects are the properties of enzymatic reactions. The substances with the same direction of influence may potentiate each other. In the enzymatic reaction here considered, the potentiation is always non-negative.     

Integrated enzymatic reactions and analysis

Summary Enzymatic reactions were performed in a modified auto-injector unit of a Shimadzu HPLC system. The reactions were analyzed by automated injections directly into the HPLC separation system. Two reactions were studied, and the enzymes mandelonitrile lyase and α-chymotrypsin were immobilized by adsorption onto a solid support, e.g., Celite and Chromosorb. The reactions were performed in various organic solvents e.g., diisopropyl ether, heptane/ethyl acetate mixtures and acetonitrile.     

Glycosyl fluorides in enzymatic reactions

Glycosyl fluorides have considerable importance as substrates and inhibitors in enzymatic reactions. Their good combination of stability and reactivity has enabled their use as glycosyl donors with a variety of carbohydrate processing enzymes. Moreover, the installation of fluorine elsewhere on the carbohydrate scaffold commonly modifies the properties of the glycosyl fluoride such that the resultant compounds act as slow substrates or even inhibitors of enzyme action. This review covers the use of glycosyl fluorides as substrates for wild-type and mutant glycosidases and other enzymes that catalyze glycosyl transfer. The use of substituted glycosyl fluorides as inhibitors of enzymes that catalyze glycosyl transfer and as tools for investigation of their mechanism is discussed, including the labeling of active site residues. Synthetic applications in which glycosyl fluorides are used as glycosyl donors in enzymatic transglycosylation reactions for the synthesis of oligo- and polysaccharides are then covered, including the use of mutant glycosidases, the so-called glycosynthases, which are able to catalyze the formation of glycosides without competing hydrolysis. Finally, a short overview of the use of glycosyl fluorides as substrates and inhibitors of phosphorylases and phosphoglucomutase is given.     

Multifractality in intracellular enzymatic reactions

Enzymatic kinetics adjust well to the Michaelis-Menten paradigm in homogeneous media with dilute, perfectly mixed reactants. These conditions are quite different from the highly structured cell plasm, so applications of the classic kinetics theory to this environment are rather limited. Cytoplasmic structure produces molecular crowding and anomalous diffusion of substances, modifying the mass action kinetic laws. The reaction coefficients are no longer constant but time-variant, as stated in the fractal kinetics theory. Fractal kinetics assumes that enzymatic reactions on such heterogeneous media occur within a non-Euclidian space characterized by a certain fractal dimension, this fractal dimension gives the dependence on time of the kinetic coefficients. In this work, stochastic simulations of enzymatic reactions under molecular crowding have been completed, and kinetic coefficients for the reactions, including the Michaelis-Menten parameter KM, were calculated. The simulations results led us to confirm the time dependence of michaelian kinetic parameter for the enzymatic catalysis. Besides, other chaos related phenomena were pointed out from the obtained KM time series, such as the emergence of strange attractors and multifractality.     

Radical reactions in aqueous disulphide-thiol systems

Absolute rate constants have been measured for the reaction of (CH3SSCH3)+. and sulphur centred radical cations of lipoic acid, lip (SS)+., with various thiols including penicillamine, cysteamine and cysteine. Under pulse radiolysis conditions no reactions was observed between the disulphide radical cations and the neutral thiols, RSH, i.e. kappa less than or equal to 10(7) M-1 s-1. Rate constants in the order of 10(9) M-1 s-1, i.e. close to the diffusion controlled limit, were, however, found for the corresponding reactions with the thiolates, RS-. In systems containing lipoate and cysteamine the lip (S therefore S)+. induced oxidation of CyaS- proceeds via CyaS., (CyaS therefore SCya)- and lip (S S)- as intermediates, i.e. results in a cysteamine mediated conversion of an oxidizing lip (S therefore S)+. radical cation to a reducing lip (S S)- radical anion along the reaction route. In other cases the reaction of disulphide radical cations with thiolate anions was found to proceed via an optically absorbing transient (lambda max approximately 380 nm) which is suggested to be an adduct radical. The mechanism of the (RSSR)+. induced oxidation of thiolate appears to depend on the stability of the 3-electron bonded disulphide radical anion.     

Transition state variation in enzymatic reactions

Experimental analysis of enzymatic transition states by kinetic isotope effect methods has established geometric variation in related transition state structures. Differences are apparent in development of the reaction coordinate, in solvolytic transition states relative to those in enzymatic catalytic sites, in the stereochemistry of related substrates at the transition state, and in reactions catalyzed by related enzymes.     

Radical reactions in vivo - an overview

Summary Generation of radicals in vivo depends on metabolic activities. The reactions are usually influenced by(i) the presence and concentration of oxygen;(ii) the availability of transition metals (effects of binding and compartimentalization);(iii) the level of reductants and antioxidants (e.g. nutritional effects). The effects of radicals are thought to be due to(i) membrane damage (affecting passive or active transport through altered fluidity/function interrelationships, intercellular messenging through modifications in the synthesis of prostaglandins and leukotrienes);(ii) protein damage (e.g. affecting membrane transporters, channel proteins, receptor or regulatory proteins, immunomodulators);(iii) damage to DNA. Defense mechanisms consist of(i) prevention of the spreading of primary damage by low molecular weight antioxidants (e.g. vitamin E, GSH, vitamin C,-carotene, uric acid);(ii) prevention or limitation of secondary damage by enzymes (e.g. GSH-peroxidase, catalase, superoxide dismutase, DT-diaphorase) and/or chelators;(iii) repair processes, e.g. lipid degradation/membrane repair enzymes (phospholipases, peroxidases, some transferases and reductases), protein disposal or repair enzymes (proteases, GSSG-reductase), DNA degradation repair enzymes (exonuclease III, endonucleases III and IV, glycosylases, polymerases). Recent hypotheses on a messenging function of the superoxide anion O ₂ ^– are discussed and possible implications of cross-reactions between O ₂ ^– and nitric oxide (endothelium-derived relaxing factor EDRF) are shortly mentioned.Paper given at the workshop Molecular Radiation Biology. German Section of the DNA Repair Network, München-Neuherberg, 21.–23.3.90     

NAD hydrolysis: Chemical and enzymatic mechanisms

The pyridine nucleotide have important non-redox activities as cellular effectors and metabolic regulators [1–3]. The enzyme-catalyzed cleavage of the nicotinamide-ribosyl bond of NAD⁺ and the attendant delivery of the ADPRibosyl moiety to acceptors is central to these many diverse biological activities. Included are the medically important NAD-dependent toxins associated with cholera, diphtheria, pertussis, and related disease [4]; the reversible ADPRibosylation-mediated biological regulatory systems [5,6]; the synthesis of poly (ADPRibose) in response to DNA damage or cellular, division [7]; and the synthesis of cyclic ADPRibose as part of an independent, calcium-mediated regulatory system[8]. As will be presented in this chapter, all evidence points to both the chemical and enzyme-catalyzed cleavage of the nicotinamide-ribosyl bond being dissociative in character via an oxocarbenium intermediate.     

Radical reactions of nitric oxide synthases

NOSs (nitric oxide synthases) are flavohaem enzymes that function broadly in human health and disease. We are combining mutagenesis, crystallographic and rapid kinetic methods to understand their mechanism and regulation. The NOSs create a transient tetrahydrobiopterin radical within the enzyme to generate their free radical product (NO). Recent work is revealing how critically important this process is at all levels of catalysis. This article will synthesize four seemingly disparate but related aspects of NOS tetrahydrobiopterin radical formation: (i) how it enables productive O2 activation by providing an electron to the enzyme haem, (ii) what structural features help to regulate this electron transfer, (iii) how it enables NOS to synthesize NO from its diamagnetic substrate and (iv) how it allows NOS to release NO after each catalytic cycle instead of other nitorgen oxide-containing products.     

Low-level chemiluminescence during lipid peroxidations and enzymatic reactions

Low-level chemiluminescence during lipid peroxidation and enzymatic reaction have been analysed by a filter type spectrometer. Tyrosine and tryprophan residues in proteins were found to be emitters in the visible region during their enzymatic oxidation. The natural chemiluminescence from fertilization of sea urchin eggs was found to have originated from tyrosine – cation radical mediated reaction in ovo-peroxidase – membrane protein – H₂O₂ system.     

Enthalpy array analysis of enzymatic and binding reactions

Enthalpy arrays enable label-free, solution-based calorimetric detection of molecular interactions in a 96-detector array format. The combination of the small size of the detectors and the ability to perform measurements in parallel results in a significant reduction of sample volume and measurement time compared with conventional calorimetry. We have made significant improvements in the technology by reducing the temperature noise of the detectors and improving the fabrication materials and methods. In combination with an automated measurement system, the advances in device performance and data analysis have allowed us to develop basic enzyme assays for substrate specificity and inhibitor activity. We have also performed a full titration of 18-crown-6 with barium chloride. These results point to future applications for enthalpy array technology, including fragment-based screening, secondary assays, and thermodynamic characterization of leads in drug discovery.     

Free radical mechanisms in enzyme reactions

Free radicals are formed in prosthetic groups or amino acid residues of certain enzymes. These free radicals are closely related to the activation process in enzyme catalysis, but their formation does not always result in the formation of substrate free radicals as a product of the enzyme reactions. The role of free radicals in enzyme catalysis is discussed.     

Radical reactions of thiamin pyrophosphate in 2-oxoacid oxidoreductases

Thiamin pyrophosphate (TPP) is essential in carbohydrate metabolism in all forms of life. TPP-dependent decarboxylation reactions of 2-oxo-acid substrates result in enamine adducts between the thiazolium moiety of the coenzyme and decarboxylated substrate. These central enamine intermediates experience different fates from protonation in pyruvate decarboxylase to oxidation by the 2-oxoacid dehydrogenase complexes, the pyruvate oxidases, and 2-oxoacid oxidoreductases. Virtually all of the TPP-dependent enzymes, including pyruvate decarboxylase, can be assayed by 1-electron redox reactions linked to ferricyanide. Oxidation of the enamines is thought to occur via a 2-electron process in the 2-oxoacid dehydrogenase complexes, wherein acyl group transfer is associated with reduction of the disulfide of the lipoamide moiety. However, discrete 1-electron steps occur in the oxidoreductases, where one or more [4Fe-4S] clusters mediate the electron transfer reactions to external electron acceptors. These radical intermediates can be detected in the absence of the acyl-group acceptor, coenzyme A (CoASH). The π-electron system of the thiazolium ring stabilizes the radical. The extensively delocalized character of the radical is evidenced by quantitative analysis of nuclear hyperfine splitting tensors as detected by electron paramagnetic resonance (EPR) spectroscopy and by electronic structure calculations. The second electron transfer step is markedly accelerated by the presence of CoASH. While details of the second electron transfer step and its facilitation by CoASH remain elusive, expected redox properties of potential intermediates limit possible scenarios. This article is part of a Special Issue entitled: Radical SAM enzymes and Radical Enzymology.     

Generalized rate equation for one-substrate enzymatic reactions

A generalized rate equation for formally two-step enzymatic reaction has been derived. In this derivation the reaction rate has been regarded as a function of substrate conversion. Applications of this equation to reactor operating parameters and productivity calculations are presented and discussed.