Mechanisms Of Enzyme-catalyzed Reactions Research Articles

Characterization of the active site of a germin like protein 1 as an oxidative stress defense enzyme in plants

Glycosylated proteins like germin-like proteins (GLPs) are incredibly diverse inside the kingdom Plantae, and mostly GLPs exhibit superoxide dismutase (SOD) function. Identification of catalytic residues is important for understanding the mechanism of enzyme-catalyzed reactions. The increased bioactivity of SOD was observed when OsRGLP1 was over-expressed in tobacco. The purpose of the current work was to identify and characterize the active site of OsRGLP1. Bioinformatics tools were used to predict the three-dimensional structure of OsRGLP1 and the shape of residues implicated in the substrate and metal ion binding. The role of predicted active site residues (E116, H109, H111, and H157) in the structure-function relationship in OsRGLP1 was investigated by site-directed mutagenesis where each residue was substituted with glycine. These amino acids are highly conserved among GLP family and structural data have implicated these residues in substrate binding at the active site. Transient transformation of tobacco plants was performed to further study these loss-of-function mutants. To investigate the impact of the mutation on SOD activity, these transgenic plants were employed as a source of mutant and native proteins for SOD activity assays. The SOD assay results revealed a complete loss of activity in all mutants, supporting the crucial role of these residues for metal ion binding in the enzyme active site.

Natural Parameter Conditions for Singular Perturbations of Chemical and Biochemical Reaction Networks

We consider reaction networks that admit a singular perturbation reduction in a certain parameter range. The focus of this paper is on deriving "small parameters" (briefly for small perturbation parameters), to gauge the accuracy of the reduction, in a manner that is consistent, amenable to computation and permits an interpretation in chemical or biochemical terms. Our work is based on local timescale estimates via ratios of the real parts of eigenvalues of the Jacobian near critical manifolds. This approach modifies the one introduced by Segel and Slemrod and is familiar from computational singular perturbation theory. While parameters derived by this method cannot provide universal quantitative estimates for the accuracy of a reduction, they represent a critical first step toward this end. Working directly with eigenvalues is generally unfeasible, and at best cumbersome. Therefore we focus on the coefficients of the characteristic polynomial to derive parameters, and relate them to timescales. Thus, we obtain distinguished parameters for systems of arbitrary dimension, with particular emphasis on reduction to dimension one. As a first application, we discuss the Michaelis-Menten reaction mechanism system in various settings, with new and perhaps surprising results. We proceed to investigate more complex enzyme catalyzed reaction mechanisms (uncompetitive, competitive inhibition and cooperativity) of dimension three, with reductions to dimension one and two. The distinguished parameters we derive for these three-dimensional systems are new. In fact, no rigorous derivation of small parameters seems to exist in the literature so far. Numerical simulations are included to illustrate the efficacy of the parameters obtained, but also to show that certain limitations must be observed.

The Origins of Enzyme Catalysis and Reactivity: Further Assessments

Alternatives to conventional mechanisms of enzyme catalyzed reactions, although within the ambit of transition state theory, are explored herein. This is driven by reports of a growing number of enzymes forming covalently linked enzyme-substrate intermediates, which clearly deviate from the conventional Michaelis-complex mechanism. It is argued that the formation of the covalent intermediates can be accommodated within the framework of transition state theory and the original Pauling hypothesis. This also obviates the need to invoke intramolecular reactivity to explain enzymic accelerations. Thus, the covalent binding of a substrate distorted towards the transition state, with the binding being fully manifested in the ensuing transition state, would conform to the traditional endergonic pre-equilibrium mechanism. Intriguingly, an alternative exergonic formation of the covalent intermediate would also lead to catalysis: in this case, any of the three steps–covalent binding, turnover or product release–can be rate limiting. Although the exergonic mode has been dismissed previously as leading to a “thermodynamic pit” (Michaelis complex case), this view now needs to be reassessed as it seems inaccurate. Therefore, it remains for the enzyme to stabilize the various transition states via the multifarious mechanisms available to it. The Pauling hypothesis remains vindicated.

Use of isotopically labeled substrates reveals kinetic differences between human and bacterial serine palmitoyltransferase

Isotope labels are frequently used tools to track metabolites through complex biochemical pathways and to discern the mechanisms of enzyme-catalyzed reactions. Isotopically labeled l-serine is often used to monitor the activity of the first enzyme in sphingolipid biosynthesis, serine palmitoyltransferase (SPT), as well as labeling downstream cellular metabolites. Intrigued by the effect that isotope labels may be having on SPT catalysis, we characterized the impact of different l-serine isotopologues on the catalytic activity of recombinant SPT isozymes from humans and the bacterium Sphingomonas paucimobilis Our data show that S. paucimobilis SPT activity displays a clear isotope effect with [2,3,3-D]l-serine, whereas the human SPT isoform does not. This suggests that although both human and S. paucimobilis SPT catalyze the same chemical reaction, there may well be underlying subtle differences in their catalytic mechanisms. Our results suggest that it is the activating small subunits of human SPT that play a key role in these mechanistic variations. This study also highlights that it is important to consider the type and location of isotope labels on a substrate when they are to be used in in vitro and in vivo studies.

Phase-plane geometries in coupled enzyme assays

The determination of a substrate or enzyme activity by coupling one enzymatic reaction with another easily detectable (indicator) reaction is a common practice in the biochemical sciences. Usually, the kinetics of enzyme reactions is simplified with singular perturbation analysis to derive rate or time course expressions valid under the quasi-steady-state and reactant stationary state assumptions. In this paper, the dynamical behavior of coupled enzyme catalyzed reaction mechanisms is studied by analysis of the phase-plane. We analyze two types of time-dependent slow manifolds – Sisyphus and Laelaps manifolds – that occur in the asymptotically autonomous vector fields that arise from enzyme coupled reactions. Projection onto slow manifolds yields various reduced models, and we present a geometric interpretation of the slow/fast dynamics that occur in the phase–planes of these reactions.

Measurement of Kinetic Isotope Effects in an Enzyme-Catalyzed Reaction by Continuous-Flow Mass Spectrometry.

Kinetic isotope effects (KIEs) provide powerful probes of the mechanisms of enzyme-catalyzed reactions. In this chapter, we describe the use of continuous-flow mass spectrometry to determine the deuterium KIE for the enzyme N-acetylpolyamine oxidase based on the ratio of labeled and unlabeled products in mass spectra of whole reaction mixtures.

Measurement of oxygen isotope ratios ((18)O/(16)O) of aqueous O2 in small samples by gas chromatography/isotope ratio mass spectrometry.

Oxygen isotope fractionation of molecular O2 is an important process for the study of aerobic metabolism, photosynthesis, and formation of reactive oxygen species. The latter is of particular interest for investigating the mechanism of enzyme-catalyzed reactions, such as the oxygenation of organic pollutants, which is an important detoxification mechanism. We developed a simple method to measure the δ(18) O values of dissolved O2 in small samples using automated split injection for gas chromatography coupled to isotope ratio mass spectrometry (GC/IRMS). After creating a N2 headspace, the dissolved O2 partitions from aqueous solution to the headspace, from which it can be injected into the gas chromatograph. In aqueous samples of 10 mL and in diluted air samples, we quantified the δ(18) O values at O2 concentrations of 16 μM and 86 μM, respectively. The chromatographic separation of O2 and N2 with a molecular sieve column made it possible to use N2 as the headspace gas for the extraction of dissolved O2 from water. We were therefore able to apply a rigorous δ(18) O blank correction for the quantification of (18) O/(16) O ratios in 20 nmol of injected O2 . The successful quantification of (18) O-kinetic isotope effects associated with enzymatic and chemical reduction of dissolved O2 illustrates how the proposed method can be applied for studying enzymatic O2 activation mechanisms in a variety of (bio)chemical processes.

Kinetic analysis of gluconate phosphorylation by human gluconokinase using isothermal titration calorimetry

Gluconate is a commonly encountered nutrient, which is degraded by the enzyme gluconokinase to generate 6-phosphogluconate. Here we used isothermal titration calorimetry to study the properties of this reaction. ΔH, KM and kcat are reported along with substrate binding data. We propose that the reaction follows a ternary complex mechanism, with ATP binding first. The reaction is inhibited by gluconate, as it binds to an Enzyme–ADP complex forming a dead-end complex. The study exemplifies that ITC can be used to determine mechanisms of enzyme catalyzed reactions, for which it is currently not commonly applied.

Why do Sequence Signatures Predict Enzyme Mechanism? Homology versus Chemistry.

First, we identify InterPro sequence signatures representing evolutionary relatedness and, second, signatures identifying specific chemical machinery. Thus, we predict the chemical mechanisms of enzyme-catalyzed reactions from catalytic and non-catalytic subsets of InterPro signatures. We first scanned our 249 sequences using InterProScan and then used the MACiE database to identify those amino acid residues that are important for catalysis. The sequences were mutated in silico to replace these catalytic residues with glycine and then again scanned using InterProScan. Those signature matches from the original scan that disappeared on mutation were called catalytic. Mechanism was predicted using all signatures, only the 78 “catalytic” signatures, or only the 519 “non-catalytic” signatures. The non-catalytic signatures gave indistinguishable results from those for the whole feature set, with precision of 0.991 and sensitivity of 0.970. The catalytic signatures alone gave less impressive predictivity, with precision and sensitivity of 0.791 and 0.735, respectively. These results show that our successful prediction of enzyme mechanism is mostly by homology rather than by identifying catalytic machinery.

W. W. “Mo” Cleland: A Catalytic Life

Professor W. Wallace Cleland, the architect of modern steady-state enzyme kinetics, died on March 6, 2013, from injuries sustained in a fall outside of his home. He will be most remembered for giving the enzyme community Ping-Pong kinetics and the invention of dithiothreitol (DTT). He pioneered the utilization of heavy atom isotope effects for the elucidation of the chemical mechanisms of enzyme-catalyzed reactions. His favorite research journal was Biochemistry, in which he published more than 135 papers beginning in 1964 with the disclosure of DTT.

The Application of Transient-State Kinetic Isotope Effects to the Resolution of Mechanisms of Enzyme-Catalyzed Reactions

Much of our understanding of the mechanisms of enzyme-catalyzed reactions is based on steady-state kinetic studies. Experimentally, this approach depends solely on the measurement of rates of free product appearance (d[P]/dt), a mechanistically and mathematically complex entity. Despite the ambiguity of this observed parameter, the method’s success is due in part to the elaborate rigorously derived algebraic theory on which it is based. Transient-state kinetics, on the other hand, despite its ability to observe the formation of intermediate steps in real time, has contributed relatively little to the subject due in, some measure, to the lack of such a solid mathematical basis. Here we discuss the current state of existing transient-state theory and the difficulties in its realistic application to experimental data. We describe a basic analytic theory of transient-state kinetic isotope effects in the form of three novel fundamental rules. These rules are adequate to define an extended mechanism, locating the isotope-sensitive step and identifying missing steps from experimental data. We demonstrate the application of these rules to resolved component time courses of the phenylalanine dehydrogenase reaction, extending the previously known reaction by one new prehydride transfer step and two new post hydride transfer steps. We conclude with an assessment of future directions in this area.

Combined Quantum Mechanics/Molecular Mechanics (QM/MM) Methods in Computational Enzymology

Computational enzymology is a rapidly maturing field that is increasingly integral to understanding mechanisms of enzyme-catalyzed reactions and their practical applications. Combined quantum mechanics/molecular mechanics (QM/MM) methods are important in this field. By treating the reacting species with a quantum mechanical method (i.e., a method that calculates the electronic structure of the active site) and including the enzyme environment with simpler molecular mechanical methods, enzyme reactions can be modeled. Here, we review QM/MM methods and their application to enzyme-catalyzed reactions to investigate fundamental and practical problems in enzymology. A range of QM/MM methods is available, from cheaper and more approximate methods, which can be used for molecular dynamics simulations, to highly accurate electronic structure methods. We discuss how modeling of reactions using such methods can provide detailed insight into enzyme mechanisms and illustrate this by reviewing some recent applications. We outline some practical considerations for such simulations. Further, we highlight applications that show how QM/MM methods can contribute to the practical development and application of enzymology, e.g., in the interpretation and prediction of the effects of mutagenesis and in drug and catalyst design.

A practical guide to modelling enzyme-catalysed reactions.

Molecular modelling and simulation methods are increasingly at the forefront of elucidating mechanisms of enzyme-catalysed reactions, and shedding light on the determinants of specificity and efficiency of catalysis. These methods have the potential to assist in drug discovery and the design of novel protein catalysts. This Tutorial Review highlights some of the most widely used modelling methods and some successful applications. Modelling protocols commonly applied in studying enzyme-catalysed reactions are outlined here, and some practical implications are considered, with cytochrome P450 enzymes used as a specific example.

QnAs with Vern L. Schramm

At Albert Einstein College of Medicine of Yeshiva University in New York City, Vern Schramm, a professor of biochemistry, devises ways to block cellular enzymes. Those enzymes, which catalyze a range of reactions at the heart of normal physiology, might hold keys to treating psoriasis, autoimmune disease, and some forms of cancer. Schramm’s studies on the mechanism of enzyme-catalyzed reactions have led to a handful of drugs now being tested in clinical trials. In 2009, he developed a test for ricin, a deadly toxin found in castor beans, which has the potential to be used by bioterrorists. Schramm tells PNAS how his work on enzymes led to a nifty test for ricin and experimental drugs for some human diseases. Vern L. Schramm. PNAS: What makes ricin a potential bioterrorism weapon? Schramm: Ricin contains two protein subunits. One allows the toxin to enter mammalian cells. The other, an enzyme, attacks ribosomes—cells’ protein-making machinery. The enzyme binds to a single nucleotide residue, called adenine, within an RNA molecule inside the ribosome. Once ricin cleaves the adenine, the ribosome becomes nonfunctional. The cell dies because of its inability to make proteins. Each molecule of ricin can inactivate about 1,000 ribosomes within a minute. Therefore, only a few micrograms of this toxin is lethal to humans, and there’s enough ricin in a single castor bean to kill more than 1,000 people. To be truly …

Use of the contour approach for visualizing the dynamic behavior of intermediates during O-nitrophenyl-β- d-galactoside hydrolysis by β-galactosidase

ONPG disappearance and ONP appearance were synchronously measured during ONPG hydrolysis by β-galactosidase using in situ on-line UV–vis spectroscopy. Intermediate formation was determined by the formula d[ONPG]/ dt − d[ONP]/ dt. The combined effects of temperature and time on ν inst and ν inc during the conversion of ONPG to ONP were expressed by the isogram method in which contour plots were used. Based on this approach, new insights were obtained into the irreversible-continuous conversion of ONPG to ONP during hydrolysis. The intermediate was a moving mass that flowed in three-dimensional space from the substrate to the product. The results of this study support the use of the isogram method for understanding the mechanisms of enzyme-catalyzed reactions via the dynamic resolution approach.

Investigations of Enzyme-Catalyzed Reactions Based on Physicochemical Descriptors Applied to Hydrolases

The EC number system for the classification of enzymes uses different criteria such as reaction pattern, the nature of the substrate, the type of transferred groups or the type of acceptor group. These criteria are used with different emphasis for the various enzyme classes and thus do not contribute much to an understanding of the mechanisms of enzyme catalyzed reactions. To explore the reasons for bonds being broken in enzyme catalyzed metabolic reactions, we calculated physicochemical effects for the bonds reacting in the substrate of these enzymatic reactions. These descriptors allow the definition of similarities within these reactions and thus can serve as a method for the classification of enzyme reactions. To foster an understanding of the investigations performed here, we compare the similarities found on the basis of the physicochemical effects with the EC number classification. To allow a reasonable comparison we selected enzymatic reactions where the EC number system is largely built on criteria based on the reaction mechanism. This is true for hydrolysis reactions, falling into the domain of the EC class 3 (EC 3.b.c.d). The comparison is made by a Kohonen neural network based on an unsupervised learning algorithm. For these hydrolysis reactions, the similarity analysis on physicochemical effects produces results that are, by and large, similar to the EC number. However, this similarity analysis reveals finer details of the enzymatic reactions and thus can provide a better basis for the mechanistic comparison of enzymes.

Bioorganic Chemistry. A Natural Reunion of the Physical and Life Sciences

Organic substances were conceived as those found in living organisms. Although the definition was soon broadened to include all carbon-containing compounds, naturally occurring molecules have always held a special fascination for organic chemists. From these beginnings, molecules from nature were indespensible tools as generations of organic chemists developed new techniques for determining structures, analyzed the mechanisms of reactions, explored the effects conformation and stereochemistry on reactions, and found challenging new targets to synthesize. Only recently have organic chemists harnessed the powerful techniques of organic chemistry to study the functions of organic molecules in their biological hosts, the enzymes that synthesize molecules and the complex processes that occur in a cell. In this Perspective, I present a personal account of my entree into bioorganic chemistry as a physical organic chemist and subsequent work to understand the chemical mechanisms of enzyme-catalyzed reactions, to develop techniques to identify and assign hydrogen bonds in tRNAs through NMR studies with isotopically labeled molecules, and to study how structure determines function in biosynthetic enzymes with proteins obtained by genetic engineering.

Rapid-Equilibrium Enzyme Kinetics

Rapid-equilibrium rate equations for enzyme-catalyzed reactions are especially useful because if experimental data can be fit by these simpler rate equations, the Michaelis constants can be interpreted as equilibrium constants. However, for some reactions it is necessary to use the more complicated steady-state rate equations. Thermodynamics is used in rapid-equilibrium derivations to calculate the equilibrium concentrations of reactants up to the rate-determining reaction, and that means that the reactions in the mechanism have to be independent. This is quite different from steady-state treatments of mechanisms where reactions do not have to be independent. The innovation in this article is the use of half-reactions to construct complete rapid-equilibrium rate equations. Five half-reactions are described. Any forward half-reaction can be combined with any reverse half-reaction. Rapid-equilibrium rate equations are given for fifteen mechanisms of enzyme-catalyzed reactions, but more rate equations can be constructed from these five half-reactions.

Chemical accuracy in QM/MM calculations on enzyme-catalysed reactions

Combined quantum mechanics/molecular mechanics (QM/MM) modelling has the potential to answer fundamental questions about enzyme mechanisms and catalysis. Calculations using QM/MM methods can now predict barriers for enzyme-catalysed reactions with unprecedented, near chemical accuracy, i.e. to within 1 kcal/mol in the best cases. Quantitative predictions from first-principles calculations were only previously possible for very small molecules. At this level, quantitative, reliable predictions can be made about the mechanisms of enzyme-catalysed reactions. This development signals a new era of computational biochemistry.

Synthesis of mono- and di-deuterated (2 S,3 S)-3-methylaspartic acids to facilitate measurement of intrinsic kinetic isotope effects in enzymes

Kinetic isotope effects provide a powerful method to investigate the mechanisms of enzyme-catalyzed reactions, but often other slow steps in the reaction such as substrate binding or product release suppress the isotopically sensitive step. For reactions at methyl groups, this limitation may be overcomed by measuring the isotope effect by an intra-molecular competition experiment. This requires the synthesis of substrates containing regio-specifically mono- or di-deuterated methyl groups. To facilitate the mechanistic investigations of the adenosylcobalamin-dependent enzyme, glutamate mutase, we have developed a synthesis of mono- and di-deuterated (2 S,3 S)-3-methylaspartic acids. Key intermediates are the correspondingly labeled mesaconic acids and their dimethyl esters that potentially provide starting materials for a variety of isotopically labeled molecules.