Enzyme Chemistry Research Articles

ChemInform Abstract: Molecular Recognition of Caffeine in Solution and Solid State

AbstractReview: 195 refs.

Editorial

Volume 61 of Biographical Memoirs contains 26 accounts of Fellows and Foreign Members who died recently. This is a greater number than has been the case for some years. Of the 26 memoirs, 20 come from the physical and engineering sciences and only 6 from the biomedical sciences, but one of the former group, Michael Fasham, is partly biological. However, the latter group includes two outstanding scientists and Nobel laureates. Fred Sanger, whose memoir was written by George Brownlee, was a committed molecular biologist who uniquely won the Nobel Prize twice, once in 1958 for protein sequencing and again in 1980 for the sequencing of nucleic acids. He stimulated our understanding of the chemistry of many proteins and enzymes and, moreover, his ingenious DNA sequencing method revolutionized molecular biology. Robert Edwards's memoir was written by Richard Gardner, who explains that Edwards was responsible for the most significant advance in the treatment of human fertility, the development of in vitro fertilization (IVF), for which he was awarded the Nobel Prize in 2010. He persisted in his work in spite of vehement opposition from all quarters. However, the first of many IVF successes came in a live birth in 1978. Edwards was also noted for the diagnosis of genetic disease and the use of stem cells in regenerative medicine.

The chemical biology of sirtuins.

The sirtuin family of enzymes are able to catalyze the N(ε)-acyl-lysine deacylation reaction on histone and non-histone protein substrates. Over the past years since the discovery of its founding member (i.e. the yeast silent information regulator 2 (sir2) protein) in 2000, the sirtuin-catalyzed deacylation reaction has been demonstrated to play an important regulatory role in multiple crucial cellular processes such as transcription, DNA damage repair, and metabolism. This reaction has also been regarded as a current therapeutic target for human diseases such as cancer, and metabolic and neurodegenerative diseases. The unique β-nicotinamide adenine dinucleotide (β-NAD(+) or NAD(+))-dependent nature of the sirtuin-catalyzed deacylation reaction has also engendered extensive mechanistic studies, resulting in a mechanistic view of the enzyme chemistry supported by several lines of experimental evidence. On the journey toward these knowledge advances, chemical biological means have constituted an important functional arsenal; technically, a variety of chemical probes and modulators (inhibitors and activators) have been developed and some of them have been employed toward an enhanced mechanistic and functional (pharmacological) understanding of the sirtuin-catalyzed deacylation reaction. On the other hand, an enhanced mechanistic understanding has also facilitated the development of a variety of chemical probes and modulators. This article will review the tremendous accomplishments achieved during the past few years in the field of sirtuin chemical biology. It is hoped that this would also help to set a stage for how outstanding mechanistic and functional questions for the sirtuin-catalyzed deacylation reaction could be addressed in the future from the chemical biology perspective.

Experimental Evidence for a Hydride Transfer Mechanism in Plant Glycolate Oxidase Catalysis

In plants, glycolate oxidase is involved in the photorespiratory cycle, one of the major fluxes at the global scale. To clarify both the nature of the mechanism and possible differences in glycolate oxidase enzyme chemistry from C3 and C4 plant species, we analyzed kinetic parameters of purified recombinant C3 (Arabidopsis thaliana) and C4 (Zea mays) plant enzymes and compared isotope effects using natural and deuterated glycolate in either natural or deuterated solvent. The (12)C/(13)C isotope effect was also investigated for each plant glycolate oxidase protein by measuring the (13)C natural abundance in glycolate using natural or deuterated glycolate as a substrate. Our results suggest that several elemental steps were associated with an hydrogen/deuterium isotope effect and that glycolate α-deprotonation itself was only partially rate-limiting. Calculations of commitment factors from observed kinetic isotope effect values support a hydride transfer mechanism. No significant differences were seen between C3 and C4 enzymes.

The discovery of Mo(III) in FeMoco: reuniting enzyme and model chemistry.

Biological nitrogen fixation is enabled by molybdenum-dependent nitrogenase enzymes, which effect the reduction of dinitrogen to ammonia using an Fe7MoS9C active site, referred to as the iron molybdenum cofactor or FeMoco. In this mini-review, we summarize the current understanding of the molecular and electronic structure of FeMoco. The advances in our understanding of the active site structure are placed in context with the parallel evolution of synthetic model studies. The recent discovery of Mo(III) in the FeMoco active site is highlighted with an emphasis placed on the important role that model studies have played in this finding. In addition, the reactivities of synthetic models are discussed in terms of their relevance to the enzymatic system.

ChemInform Abstract: H2 and O2 Activation — A Remarkable Insight into Hydrogenase

AbstractReview: [51 refs.

Evaluation of a semiquantitative SNAP test for measurement of bile acids in dogs.

Background. Serum bile acids (SBA) are used as a routine screening tool of liver function in dogs. Serum samples are usually shipped to a referral laboratory for quantitative analysis with an enzymatic chemistry analyzer. The canine SNAP Bile Acids Test (SNAP-BAT) provides an immediate, semi-quantitative measurement of bile acid concentrations in-house. With the SNAP-BAT, bile acids concentrations of 5–30 µmol/L are quantified, and results outside of that range are classified as <5 or >30 µmol/L. Agreement of the SNAP-BAT with the enzymatic method has not been extensively investigated.Objectives. The purposes of this prospective clinical study were to assess the precision of the SNAP-BAT and determine agreement of SNAP-BAT with results from an in-house chemistry analyzer.Methods. After verifying intra-assay precision of the SNAP-BAT, a prospective analysis was performed using blood samples collected from 56 dogs suspected to have liver disease. Each sample was analyzed with an enzymatic, in-house chemistry analyzer and the SNAP-BAT. Agreement between the two methods was statistically assessed using the κ index of agreement.Results. Intra-assay variability was minimal. The κ index for agreement between the SNAP-BAT and routine chemistry analyzer was between 0.752 and 0.819, indicating substantial to near perfect agreement.Conclusions. The SNAP-BAT is a highly accurate, semi-quantitative test that yields immediate results, and has very little intra-assay variability, particularly for results >30 µmol/L.

Chemical discovery in the microbial world: Identifying enzymes that construct unusual molecular architecture

Microbes have amazing chemical capabilities, performing chemical reactions unprecedented in organic synthesis and producing complex, biologically active molecules not easily accessed via any other means. My lab is discovering new enzymatic transformations by studying the biosynthesis of secondary metabolites with atypical structures or chemical functionality. Our approach to pathway discovery and characterization takes advantage of the increasing availability of bacterial genome sequencing data. This talk will discuss our recent progress towards deciphering the enzymatic chemistry that mediates unusual C-C and C-N bond forming reactions in multiple natural product biosynthetic pathways. Functional and mechanistic characterization of these enzymes is revealing new chemical reactivity with potential applications in biocatalysis and metabolic engineering.

Characterization of choline trimethylamine-lyase expands the chemistry of glycyl radical enzymes.

The recently identified glycyl radical enzyme (GRE) homologue choline trimethylamine-lyase (CutC) participates in the anaerobic conversion of choline to trimethylamine (TMA), a widely distributed microbial metabolic transformation that occurs in the human gut and is linked to disease. The proposed biochemical function of CutC, C-N bond cleavage, represents new reactivity for the GRE family. Here we describe the in vitro characterization of CutC and its activating protein CutD. We have observed CutD-mediated formation of a glycyl radical on CutC using EPR spectroscopy and have demonstrated that activated CutC processes choline to trimethylamine and acetaldehyde. Surveys of potential alternate CutC substrates uncovered a strict specificity for choline. Homology modeling and mutagenesis experiments revealed essential CutC active site residues. Overall, this work establishes that CutC is a GRE of unique function and a molecular marker for anaerobic choline metabolism.

H2 and O2 activation--a remarkable insight into hydrogenase.

This article summarizes the development of a range of organometallic, biomimetic analogues of [NiFe]hydrogenases and their employment in a new generation of H2 -O2 fuel cells. It begins with a summary of O2 -sensitive and O2 -tolerant enzyme chemistry before detailing the properties and functionality of our biomimetic complexes, including: the first ever fully functional model, selective H2 and O2 activation, and the first catalyst using only common metals. These systems are centered on Ni-Fe, Ni-Ru, Ir-Ir, and Rh-Rh cores and use a range of ligands that all follow a set of design principles described herein.

The natural history of biocatalytic mechanisms.

Phylogenomic analysis of the occurrence and abundance of protein domains in proteomes has recently showed that the α/β architecture is probably the oldest fold design. This holds important implications for the origins of biochemistry. Here we explore structure-function relationships addressing the use of chemical mechanisms by ancestral enzymes. We test the hypothesis that the oldest folds used the most mechanisms. We start by tracing biocatalytic mechanisms operating in metabolic enzymes along a phylogenetic timeline of the first appearance of homologous superfamilies of protein domain structures from CATH. A total of 335 enzyme reactions were retrieved from MACiE and were mapped over fold age. We define a mechanistic step type as one of the 51 mechanistic annotations given in MACiE, and each step of each of the 335 mechanisms was described using one or more of these annotations. We find that the first two folds, the P-loop containing nucleotide triphosphate hydrolase and the NAD(P)-binding Rossmann-like homologous superfamilies, were α/β architectures responsible for introducing 35% (18/51) of the known mechanistic step types. We find that these two oldest structures in the phylogenomic analysis of protein domains introduced many mechanistic step types that were later combinatorially spread in catalytic history. The most common mechanistic step types included fundamental building blocks of enzyme chemistry: “Proton transfer,” “Bimolecular nucleophilic addition,” “Bimolecular nucleophilic substitution,” and “Unimolecular elimination by the conjugate base.” They were associated with the most ancestral fold structure typical of P-loop containing nucleotide triphosphate hydrolases. Over half of the mechanistic step types were introduced in the evolutionary timeline before the appearance of structures specific to diversified organisms, during a period of architectural diversification. The other half unfolded gradually after organismal diversification and during a period that spanned ∼2 billion years of evolutionary history.

Ordered-Mesoporous-Carbon-Bonded Cobalt Phthalocyanine: A Bioinspired Catalytic System for Controllable Hydrogen Peroxide Activation

The chemistry of enzymes presents a key to understanding the catalysis in the world. In the pursuit of controllable catalytic oxidation, researchers make extensive efforts to discover and develop functional materials that exhibit various properties intrinsic to enzymes. Here we describe a bioinspired catalytic system using ordered-mesoporous-carbon (OMC)-bonded cobalt tetraaminophthalocyanine (CoTAPc-OMC) as a catalyst that could mimic the space environment and reactive processes of metalloporphyrin-based heme enzymes and employing linear dodecylbenzenesulfonate as the fifth ligands to control the activation of H2O2 toward the peroxidase-like oxidation. The generation of nonselective free hydroxyl radicals was obviously inhibited. In addition, functional modification of OMC has been achieved by a moderate method, which can reduce excessive damage to the structure of OMC. Because of its favorable and tunable pore texture, CoTAPc-OMC provides a suitable interface and environment for the accessibility and oxidation of C.I. Acid Red 1, the model compound, and exhibits significantly enhanced catalytic activity and sufficient stability for H2O2 activation. The high-valent cobalt oxo intermediates with high oxidizing ability have been predicted as the acceptable active species, which have been corroborated by the results from the semiempirical quantum-chemical PM6 calculations.

Energy Landscape of the Michaelis Complex of Lactate Dehydrogenase: Relationship to Catalytic Mechanism

Lactate dehydrogenase (LDH) catalyzes the interconversion between pyruvate and lactate with nicotinamide adenine dinucleotide (NAD) as a cofactor. Using isotope-edited difference Fourier transform infrared spectroscopy on the “live” reaction mixture (LDH·NADH·pyruvate ⇌ LDH·NAD+·lactate) for the wild-type protein and a mutant with an impaired catalytic efficiency, a set of interconverting conformational substates within the pyruvate side of the Michaelis complex tied to chemical activity is revealed. The important structural features of these substates include (1) electronic orbital overlap between pyruvate’s C2=O bond and the nicotinamide ring of NADH, as shown from the observation of a delocalized vibrational mode involving motions from both moieties, and (2) a characteristic hydrogen bond distance between the pyruvate C2=O group and active site residues, as shown by the observation of at least four C2=O stretch bands indicating varying degrees of C2=O bond polarization. These structural features form a critical part of the expected reaction coordinate along the reaction path, and the ability to quantitatively determine them as well as the substate population ratios in the Michaelis complex provides a unique opportunity to probe the structure–activity relationship in LDH catalysis. The various substates have a strong variance in their propensity toward on enzyme chemistry. Our results suggest a physical mechanism for understanding the LDH-catalyzed chemistry in which the bulk of the rate enhancement can be viewed as arising from a stochastic search through an available phase space that, in the enzyme system, involves a restricted ensemble of more reactive conformational substates as compared to the same chemistry in solution.

Prevention of amiodarone-induced cardiac toxicity in male BALB/c mice by a nutrient mixture

Amiodarone (Amio), a potent anti-arrhythmic drug, is associated with life-threatening pulmonary toxicity involving fibroses and inflammation. A unique nutrient mixture (NM) consisting of lysine, proline, ascorbic acid, N-acetyl cysteine and green tea extract has previously been shown to exhibit a broad spectrum of pharmacological, therapeutic, cardiovascular and chemopreventive properties. The present study was undertaken to determine whether the NM exhibits preventive effects on Amio-induced cardiac toxicity. Six-week-old male BALB/c mice were divided into four groups (A–D) of six animals per group. Mice in groups A and C were fed a regular diet for three weeks, while the diets of the mice in groups B and D were supplemented with 1% NM during that period. After three weeks, the mice in groups C and D received daily Amio injections of 50 mg/kg body weight intraperitoneally for 4 days, whilst those in groups A and B received saline alone. At 24 h after the final dose, mice were sacrificed, blood was withdrawn and serum was collected for clinical chemistry of the heart enzymes creatine phosphokinase (CPK) and aspartate aminotransferase (AST). In addition, livers, kidneys, hearts and lungs were excised and weighed. No significant differences in weight gain were identified among the groups and liver, kidney, heart and lung weights were comparable in all four groups. Administration of Amio to group C resulted in a significant increase in serum CPK levels, whereas in NM-fed group D, the CPK levels were comparable to those in the saline injection groups, A and B. Amio administration also resulted in a significant increase in serum AST levels in group C, but not in the group D animals which exhibited similar levels to those of groups A and B. Therefore, the results indicate that NM has the potential to protect against Amio-induced cardiac toxicity.

Looking for Hydrogen Atoms: Neutron Crystallography Provides Novel Insights Into Protein Structure and Function

Neutron crystallography allows direct localization of hydrogen positions in biological macromolecules. Within enzymes, hydrogen atoms play a pivotal role in catalysis. Recent advances in instrumentation and sample preparation have helped to overcome the difficulties of performing neutron diffraction experiments on protein crystals. The application of neutron macromolecular crystallography to a growing number of proteins has yielded novel structural insights. The ability to accurately position water molecules, hydronium ions, and hydrogen atoms within protein structures has helped in the study of low-barrier hydrogen bonds and hydrogen-bonding networks. The determination of protonation states of protein side chains, substrates, and inhibitors in the context of the macromolecule has provided important insights into enzyme chemistry and ligand binding affinities, which can assist in the design of potent therapeutic agents. In this review, we give an overview of the method and highlight advances in knowledge attained through the application of neutron protein crystallography.

Digital PCR as a Novel Technology and Its Potential Implications for Molecular Diagnostics

The latest incarnation of PCR, digital PCR (dPCR),2 takes 2 decades of development in enzyme chemistry and assay design and applies them with formidable precision and sensitivity. dPCR is achieved by performing a limiting dilution of DNA into a succession of individual PCR reactions (or partitions). Limiting dilution, made practical by advances in partitioning with nanofluidics and emulsion chemistries, capitalizes on the random distribution of the DNA template and the fact that Poisson statistics can be used to measure the quantities of DNA present for a given proportion of positive partitions. And what is more, it appears to work; results obtained with the technique are linear, and it is capable of detecting and quantifying miniscule amounts of template (1, 2). All of these features are achievable without the calibration curve required with almost all other molecular methods for accurately quantifying DNA. Compared with real-time quantitative PCR (qPCR), dPCR has already been heralded as more precise (3), better at detecting rare genetic variants (4), and less susceptible to inhibitors (5, 6). Recognition of these advantages has naturally led to speculation as to the potential of dPCR for molecular diagnostics. This issue of Clinical Chemistry presents the reports of 2 studies that have demonstrated the unique clinical application of dPCR for measuring circulating cell-free nucleic acids. Taly et al. (7) build on their group's leading research in the application of dPCR to investigating the detection of rare tumor-associated mutations in cell-free DNA (cfDNA) in the plasma of cancer patients, and Beck et al. (8) report that the cfDNA of transplantation patients contains detectable quantities of DNA from donor organs and that monitoring of such DNA may serve as a surrogate marker of graft injury and rejection. The articles demonstrate the clinical application of 2 aspects of dPCR, namely …

Use of ω-Transaminase Enzyme Chemistry in the Synthesis of a JAK2 Kinase Inhibitor

ω-Transaminase enzyme chemistry provides an excellent methodology to build synthetically useful chiral amines from their corresponding ketones. An application of this methodology, providing a long-term commercial manufacturing route to a JAK2 kinase inhibitor, is reported herein.

Introduction to enzyme and coenzyme chemistry

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Changes in Protein Architecture and Subpicosecond Protein Dynamics Impact the Reaction Catalyzed by Lactate Dehydrogenase

We have previously established the importance of a promoting vibration, a subpicosecond protein motion that propagates through a specific axis of residues, in the reaction coordinate of lactate dehydrogenase (LDH). To test the effect that perturbation of this motion would have on the enzymatic reaction, we employ transition path sampling to obtain transition path ensembles for four independent LDH enzymatic systems: the wild type enzyme, a version of the enzyme expressing heavy isotopic substitution, and two enzymes with mutations in the promoting vibration axis. We show that even slight changes in the promoting vibration of LDH result in dramatic changes in enzymatic chemistry. In the "heavy" version of the enzyme, we find that the dampening of the subpicosecond dynamics from heavy isotopic substitution leads to a drastic increase in the time of barrier crossing. Furthermore, we see that mutation of the promoting vibration axis causes a decrease in the variability of transition paths available to the enzymatic reaction. The combined results reveal the importance of the protein architecture of LDH in enzymatic catalysis by establishing how the promoting vibration is finely tuned to facilitate chemistry.

Fast protein motions are coupled to enzyme H-transfer reactions.

Coupling of fast protein dynamics to enzyme chemistry is controversial and has ignited considerable debate, especially over the past 15 years in relation to enzyme-catalyzed H-transfer. H-transfer can occur by quantum tunneling, and the temperature dependence of kinetic isotope effects (KIEs) has emerged as the "gold standard" descriptor of these reactions. The anomalous temperature dependence of KIEs is often rationalized by invoking fast motions to facilitate H-transfer, yet crucially, direct evidence for coupled motions is lacking. The fast motions hypothesis underpinning the temperature dependence of KIEs is based on inference. Here, we have perturbed vibrational motions in pentaerythritol tetranitrate reductase (PETNR) by isotopic substitution where all non-exchangeable atoms were replaced with the corresponding heavy isotope ((13)C, (15)N, and (2)H). The KIE temperature dependence is perturbed by heavy isotope labeling, demonstrating a direct link between (promoting) vibrations in the protein and the observed KIE. Further we show that temperature-independent KIEs do not necessarily rule out a role for fast dynamics coupled to reaction chemistry. We show causality between fast motions and enzyme chemistry and demonstrate how this impacts on experimental KIEs for enzyme reactions.