Reaction Mechanism Of Enzyme Research Articles

Exploring the Minimum-Energy Pathways and Free-Energy Profiles of Enzymatic Reactions with QM/MM Calculations.

Understanding molecular mechanisms of enzymatic reactions is of vital importance in biochemistry and biophysics. Here, we introduce new functions of hybrid quantum mechanical/molecular mechanical (QM/MM) calculations in the GENESIS program to compute the minimum-energy pathways (MEPs) and free-energy profiles of enzymatic reactions. For this purpose, an interface in GENESIS is developed to utilize a highly parallel electronic structure program, QSimulate-QM (https://qsimulate.com), calling it as a shared library from GENESIS. Second, algorithms to search the MEP are implemented, combining the string method (E et al. J. Chem. Phys. 2007, 126, 164103) with the energy minimization of the buffer MM region. The method implemented in GENESIS is applied to an enzyme, triosephosphate isomerase, which converts dihyroxyacetone phosphate to glyceraldehyde 3-phosphate in four proton-transfer processes. QM/MM-molecular dynamics simulations show performances of greater than 1 ns/day with the density functional tight binding (DFTB), and 10-30 ps/day with the hybrid density functional theory, B3LYP-D3. These performances allow us to compute not only MEP but also the potential of mean force (PMF) of the enzymatic reactions using the QM/MM calculations. The barrier height obtained as 13 kcal mol-1 with B3LYP-D3 in the QM/MM calculation is in agreement with the experimental results. The impact of conformational sampling in PMF calculations and the level of electronic structure calculations (DFTB vs B3LYP-D3) suggests reliable computational protocols for enzymatic reactions without high computational costs.

Pillar[5]arene-Derived endo-Functionalized Molecular Tube for Mimicking Protein-Ligand Interactions.

Artificial tubular molecular pockets bearing polar functionalities on their inner surface are useful model systems for understanding the mechanisms of protein-ligand interactions in living systems. We herein report a pillar[5]arene-derived molecular tube, [P4-(OH)BPO], whose endo conformational isomer endo-[P4-(OH)BPO] possesses an inwardly pointing hydrogen-bond (H-bond) donor (OH) in its deep cavity and a strong H-bond acceptor (C═O) on its predominantly hydrophobic inner surface, rendering it a perfect protein binding pocket mimetic. A fragment-based drug design model was established using endo-[P4-(OH)BPO] and a library of various shape-complementary fragment ligands (1-38). On the basis of the binding affinity data for "fragment-pocket" complexes G⊂endo-[P4-(OH)BPO] (G = 1-38), two rationally designed "lead molecules" (39 and 40) were identified as being able to enhance binding affinity significantly by forming H-bonds with both the donor and acceptor of endo-[P4-(OH)BPO]. The described work opens new avenues for developing pillar[n]arene-derived protein binding pocket-mimetic systems for studies of protein-ligand interactions and mechanisms of enzymatic reactions.

Performance of sea sponges micro symbionts as a biomaterial in biodegradation naphthalene waste of modified

The purpose of this research is to understand sponge species, micro symbiont, performance, mechanisms, and types of compounds resulting from biodegradation. The analytical method is applied by selecting the model, results from characterization and morphological identification, phenotype, genotype. Selected of micro symbiont are made as suspensions, interacted with modified naphthalene contaminated waste. The biodegradation process using the Bacillus Sp (BS) isolates sponge Neopetrosia Sp and Acinetobacter Calcoaceticus (AC) isolated from sponge Callyspongia Aerizusa, was carried out by interacting a microscopic suspension of 5,000 mg/L naphthalene waste for 25 days. Micro symbiont biodegradation results by determining the concentration of contaminants and biodegradation products, in the form of pure organic compounds using GC-MS, and the analysis of functional groups of natural components using IR. Destruction of the naphthalene molecule occurs through an enzymatic reaction mechanism, observed based on visible parameters. The performance of BS symbiont biodegradation on naphthalene is in the range of 7.34% - 51.37%, while the AC range is 5.84% -37.26% in w/v, achieved within 5-25 days interaction. Biodegradation products based on functional groups were identified as compounds of aldehyde, ketone, carboxylic acids, esters, alkanes. Observation of biodegradation parameters confirmed pH changes, increased optical density values, gas bubbles formed and the smell of fermentation.

Xanthine Oxidoreductase-Mediated Superoxide Production Is Not Involved in the Age-Related Pathologies in Sod1-Deficient Mice.

Reactive oxygen species (ROS) metabolism is regulated by the oxygen-mediated enzyme reaction and antioxidant mechanism within cells under physiological conditions. Xanthine oxidoreductase (XOR) exhibits two inter-convertible forms (xanthine oxidase (XO) and xanthine dehydrogenase (XDH)), depending on the substrates. XO uses oxygen as a substrate and generates superoxide (O2•−) in the catalytic pathway of hypoxanthine. We previously showed that superoxide dismutase 1 (SOD1) loss induced various aging-like pathologies via oxidative damage due to the accumulation of O2•− in mice. However, the pathological contribution of XO-derived O2•− production to aging-like tissue damage induced by SOD1 loss remains unclear. To investigate the pathological significance of O2•− derived from XOR in Sod1−/− mice, we generated Sod1-null and XO-type- or XDH-type-knock-in (KI) double-mutant mice. Neither XO-type- nor XDH-type KI mutants altered aging-like phenotypes, such as anemia, fatty liver, muscle atrophy, and bone loss, in Sod1−/− mice. Furthermore, allopurinol, an XO inhibitor, or apocynin, a nicotinamide adenine dinucleotide phosphate oxidase (NOX) inhibitor, failed to improve aging-like tissue degeneration and ROS accumulation in Sod1−/− mice. These results showed that XOR-mediated O2•− production is relatively uninvolved in the age-related pathologies in Sod1−/− mice.

An overview of the cytochrome P450 enzymes that catalyze the same-site multistep oxidation reactions in biotechnologically relevant selected actinomycete strains.

Cytochrome P450 enzymes (P450s) are one of the major factors responsible for the diversity of metabolites produced through many biosynthetic and biodegradative processes in actinomycetes. P450s typically catalyze a single oxidative modification; however, several P450s have been identified with the unique ability to iteratively oxidize the same-site of the substrate. These P450s are capable of forming diverse compounds that affect biological processes, including alcohols, ketones, aldehydes, and carboxylic acids. Although further structural and functional studies are needed to elucidate the mechanisms that allow multistep oxidative modification, recent studies have revealed the enzymatic properties and reaction mechanisms of these P450s. This mini-review covers the current knowledge of P450s that catalyze the multistep oxidation reactions and contribute to the production of a wide variety of metabolites by selected actinomycete strains, along with insights into their application and utility. Understanding the characteristics of these remarkable enzymes will facilitate their utilization in biotechnological applications to create biologically active and other high-value compounds. KEY POINTS: • The multistep oxidation by P450s plays a key role in the diversity of metabolites. • The mechanisms that enable P450s to catalyze iterative oxidation remains unknown. • The effective use of P450s that iteratively oxidize the same-site is discussed.

Innovative Preparation of Biopharmaceuticals Using Transglycosylation Activity of Microbial Endoglycosidases.

Most functional biopharmaceuticals such as antibodies are glycoproteins carrying N-linked oligosaccharides (N-glycans). In animal cells, these glycans are generally expressed as heterogeneous glycoforms that are difficult to separate into a pure form. The structure of these glycans directly affects several biological aspects of the glycoproteins, especially binding affinity. Therefore, the preparation of glycoproteins with well-defined and homogeneous glycoforms is necessary for functional studies and improved efficacy, particularly for biopharmaceuticals. This review describes the recent remarkable progress in the development and production of biopharmaceutical glycan-modified antibodies, through the use of glycan remodeling using microbial endoglycosidases and sophisticated glycoengineering techniques utilizing microbial enzymatic reaction mechanisms.

Insights into the Catalytic Mechanism of Domains CD1 and CD2 in Histone Deacetylase 6 from Quantum Calculations

The histone deacetylase 6 enzyme, HDAC6, is a metalloprotein with multiple pathophysiological roles and, as such, is the subject of intense research and drug discovery efforts. Different from the HDAC family, HDAC6 is constituted by a heterodimeric structure with two different catalytic domains, namely CD1 and CD2. Intriguingly, the specific biological relevance of each domain is not fully understood yet. However, a wealth of structural and biochemical data collected on HDAC, and in particular more recently on HDAC6, has revealed that the active sites in both CD1 and CD2 conserve a similar structural architecture. In the present work, we have performed a detailed investigation on the mechanistic aspects of catalysis of HDAC6, comparatively analyzing the enzymatic reaction mechanism in CD1 and CD2. Using density functional theory-based computations, we found that the rate-limiting step of the reaction is the nucleophilic attack of the catalytic water for peptide bond hydrolysis in both domains. Remarkably, the transition state for such a step presents a penta-coordinated metal center. In this regard, we have further validated the crucial contribution to catalysis of Tyr residues (Tyr363 in CD1 and Tyr745 in CD2) for the activation of the substrate, in line with kinetics measures. Importantly, we have quantified the effect on catalysis by the positively charged Lys330 residue in CD1. An analogous contribution is missing in CD2. Our calculations also evidence the contribution of distal residues from the reaction center, such as Gly201/582 and Phe202/583. Taken together, our quantum calculations dissect the catalytic mechanism in HDAC6. These findings may help future experimental studies and drug design efforts for selective HDAC6 targeting.

The importance of exact exchange-A methodological investigation of NO reduction in heme-copper oxidases.

Significant improvements of the density functional theory (DFT) methodology during the past few decades have made DFT calculations a powerful tool in studies of enzymatic reaction mechanisms. For metalloenzymes, however, there are still concerns about the reliability in the DFT-results. Therefore, a systematic study is performed where the fraction of exact exchange in a hybrid DFT functional is used as a parameter. By varying this parameter, a set of different but related functionals are obtained. The various functionals are applied to one of the reactions occurring in the enzyme family heme-copper oxidases, the reduction of nitric oxide (NO) to nitrous oxide (N2O) and water. The results show that, even though certain parts of the calculated energetics exhibit large variations, the qualitative pictures of the reaction mechanisms are quite stable. Furthermore, it is found that the functional with 15% exact exchange (B3LYP*) gives the best agreement with experimental data for the particular reactions studied. An important aspect of the procedure used is that the computational results are carefully combined with a few more general experimental data to obtain a complete description of the entire catalytic cycle of the reactions studied.

Catalytic mechanism of the colistin resistance protein MCR-1.

The mcr-1 gene encodes a membrane-bound Zn2+-metalloenzyme, MCR-1, which catalyses phosphoethanolamine transfer onto bacterial lipid A, making bacteria resistant to colistin, a last-resort antibiotic. Mechanistic understanding of this process remains incomplete. Here, we investigate possible catalytic pathways using DFT and ab initio calculations on cluster models and identify a complete two-step reaction mechanism. The first step, formation of a covalent phosphointermediate via transfer of phosphoethanolamine from a membrane phospholipid donor to the acceptor Thr285, is rate-limiting and proceeds with a single Zn2+ ion. The second step, transfer of the phosphoethanolamine group to lipid A, requires an additional Zn2+. The calculations suggest the involvement of the Zn2+ orbitals directly in the reaction is limited, with the second Zn2+ acting to bind incoming lipid A and direct phosphoethanolamine addition. The new level of mechanistic detail obtained here, which distinguishes these enzymes from other phosphotransferases, will aid in the development of inhibitors specific to MCR-1 and related bacterial phosphoethanolamine transferases.

Kinetic model for the enzymolysis of Paphia undulate by marine low-temperature alkaline proteinase

The kinetics of enzymatic hydrolysis of paphia sinensis was studied. The molecular weight distribution of the small peptide mixture was determined by liquid and mass spectrometry. The effects of initial substrate concentration on enzymatic hydrolysis reaction, the effects of initial enzyme concentration on enzymatic hydrolysis reaction, the effects of enzymatic hydrolysis time on enzymatic hydrolysis reaction and the mechanism of enzymatic hydrolysis reaction were investigated. In this experiment, the basic kinetic model of enzymatic hydrolysis of protein was derived, and the kinetic parameters and enzyme inactivation constant were determined.

Elucidation of Enzymatic Reaction Mechanism by Neutron Crystallography

Elucidation of Enzymatic Reaction Mechanism by Neutron Crystallography

Microbial nitroreductases: A versatile tool for biomedical and environmental applications.

Nitroreductases, enzymes found mostly in bacteria and also in few eukaryotes, use nicotinamide adenine dinucleotide (NADH) or nicotinamide adenine dinucleotide phosphate (NADPH) as a cofactor for their activity and metabolize an enormous list of a diverse nitro group-containing compounds. Nitroreductases that are capable of metabolizing nitroaromatic and nitro heterocyclic compounds have drawn great attention in recent years owing to their biotechnological, biomedical, environmental, and human impact. These enzymes attracted medicinal chemists and pharmacologists because of their prodrug selectivity for activation/reduction of nitro compounds that wipe out pathogens/cancer cells, leaving the host/normal cells unharmed. It is applied in diverse fields of study like prodrug activation in treating cancer and leishmaniasis, designing fluorescent probes for hypoxia detection, cell imaging, ablation of specific cell types, biodegradation of nitro-pollutants, and interpretation of mutagenicity of nitro compounds. Keeping in view the immense prospects of these enzymes and a large number of research contributions in this area, the present review encompasses the enzymatic reaction mechanism, their role in antibiotic resistance, hypoxia sensing, cell imaging, cancer therapy, reduction of recalcitrant nitro chemicals, enzyme variants, and their specificity to substrates, reaction products, and their applications.

Structural analysis and reaction mechanism of the disproportionating enzyme (D-enzyme) from potato.

Starch produced by plants is a stored form of energy and is an important dietary source of calories for humans and domestic animals. Disproportionating enzyme (D-enzyme) catalyzes intramolecular and intermolecular transglycosylation reactions of α-1, 4-glucan. D-enzyme is essential in starch metabolism in the potato. We present the crystal structures of potato D-enzyme, including two different types of complex structures: a primary Michaelis complex (substrate binding mode) for 26-meric cycloamylose (CA26) and a covalent intermediate for acarbose. Our study revealed that the acarbose and CA26 reactions catalyzed by potato D-enzyme involve the formation of a covalent intermediate with the donor substrate. HPAEC of reaction substrates and products revealed the activity of the potato D-enzyme on acarbose and CA26 as donor substrates. The structural and chromatography analyses provide insight into the mechanism of the coupling reaction of CA and glucose catalyzed by the potato D-enzyme. The enzymatic reaction mechanism does not involve residual hydrolysis. This could be particularly useful in preventing unnecessary starch degradation leading to reduced crop productivity. Optimization of this mechanism would be important for improvements of starch storage and productivity in crops.

Metabolic incorporation of H218 O into specific glucose-6-phosphate oxygens by red-blood-cell lysates as observed by 13 C isotope-shifted NMR signals.

Water enriched with oxygen-18 (H218 O) is a potential tracer for evaluating the sources of glucose and glycogen synthesis since it is incorporated into specific sites of glucose-6-phosphate via specific enzyme-mediated exchange/addition mechanisms. Unlike 2 H, 18 O does not experience significant isotope effects for any of these processes. Therefore, H218 O might provide more precise estimates of endogenous carbohydrate synthesis compared with deuterated water provided that positional 18 O enrichments of glucose can be measured. As a proof of concept, H218 O was incorporated into a well characterized hemolysate model of sugar phosphate metabolism and 13 C NMR was applied to quantify positional 18 O enrichment of glucose-6-phosphate oxygens. Human erythrocyte hemolysate preparations were incubated overnight at 37 °C with a buffer containing sugar phosphate precursors and 20% (n = 5) and 80% (n = 1) H218 O. Enrichment of glucose-6-phosphate was analyzed by 13 C NMR analysis of 18 O-shifted versus unshifted signals following derivatization to monoacetone glucose (MAG). 13 C NMR MAG spectra from hemolysate revealed resolved 18 O-shifted signals in Positions 1-5. Mean 18 O enrichments were 16.4 ± 1.6% (Position 1), 13.3 ± 1.3% (Position 2), 4.1 ± 1.1% (Position 3), 12.6 ± 0.8% (Position 4), 10.7 ± 1.4% (Position 5), and no detectable enrichment of Position 6. No 18 O-shifted glucose-6-phosphate signals were detected in preparations containing sugar phosphate precursors only. H218 O is incorporated into Positions 1-5 of glucose-6-phosphate in accordance with spontaneous aldose hydration and specific enzymatic reaction mechanisms. This provides a basis for its deployment as a tracer for glucose and glycogen biosynthesis.

Single-molecule enzymatic reaction dynamics and mechanisms of GPX3 and TRXh9 from Arabidopsis thaliana.

Glutathione peroxidases (GPXs) regulate the levels of reactive oxygen species in cells and tissues. During the redox cycling, the plant GPX is regenerated by thioredoxins (TRXs) as reductant rather than glutathione as the electron donor. However, the direct experimental observation on the interaction dynamics between GPXs and TRXs has not been reported, and the redox mechanism is unclear. In this work, the protein interactions between oxidized AtGPX3 and reduced AtTRXh9 have been studied using single-molecule fluorescence resonance energy transfer (smFRET). The obtained results indicate there are four processes in these two protein interaction, including biological recognition, binding, intermediate and unbinding state. Two enzymatic reaction intermediate states have been identified in the dissociation of AtGPX3-AtTRXh9 complex from binding to unbinding state, suggesting two types of interaction pathways and intermediate complexes. In particular, the dynamical study reveals that the redox reaction between oxidized AtGPX3 and reduced AtTRXh9 is realized through the forming and breaking of disulfide bonds via the active sites of Cys4 and Cys57 in AtTRXh9. These findings are of significant for deep understanding the redox reaction and mechanism between GPXs and TRXs enzymes, and studying other protein dynamics at single-molecule level.

Can a quantum mechanical cluster model explain the special stereospecificity of glyoxalase I?

Quantum mechanical (QM) cluster approach is a useful and convenient tool to study mechanisms of enzymatic reactions. Our investigation is to propose a proper QM-cluster that reproduces the special specificity of glyoxalase I (GlxI). GlxI converts S and R enantiomers of hemithioacetal to only S-D enantiomer of its product. It shows this special specificity with two glutamate residues that are symmetrically coordinated to a Zn ion. However, molecular dynamics simulations showed that one of the glutamates, Glu-172 is more flexible than the other one, Glu-99. Results indicate that a QM-cluster with a more flexible model of Glu-172 can reproduce proposed mechanisms for the S-substrate. However, the same cluster can reach to the R-L enantiomer of the product from the R substrate. We propose the necessity of using much more expensive, hybrid QM/MM methods or a very big QM-cluster to model and study reaction mechanisms of stereospecific enzymes like GlxI.

Enzymatic reaction mechanism of cis-aconitate decarboxylase based on the crystal structure of IRG1 from Bacillus subtilis

Itaconate, which is formed by decarboxylation of cis-aconitate—an intermediate metabolite in the tricarboxylic acid cycle—has been used as a building block in polymer synthesis and is an important chemical in several biomedical and industrial applications. Itaconate is an immunometabolite with antibacterial, antiviral, immunoregulatory, and tumor-promoting activities. Recent focus has been on the role of itaconate in the field of immunology, with immune-responsive gene 1 (IRG1) being identified as the cis-aconitate decarboxylase responsible for itaconate production. We solved the structure of IRG1 from Bacillus subtilis (bsIRG1) and showed that IRG1 adopts either a closed or an open conformation; bsIRG1 was in the open form. A1 and A2 loops around the active site are flexible and can control the formation of the open and closed forms of IRG1. An in silico docking simulation showed that only the open form of IRG1 can accommodate the substrate. The most energetically favorable position of cis-aconitate in the active site of bsIRG1 involved the localization of C2 and C5 of cis-aconitate into the H102 region and H151 region of bsIRG1, respectively. Based on the structural study of bsIRG1, compared with IDS epimerase, and in silico docking simulation, we proposed two tentative enzymatic reaction mechanisms of IRG1, a two-base model and a one-base model.

Electronic structure benchmark calculations of CO2 fixing elementary chemical steps in RuBisCO using the projector-based embedding approach.

Ribulose 1,5-bisphosphate carboxylase-oxygenase (RuBisCO) is the main enzyme involved in atmospheric carbon dioxide (CO2 ) fixation in the biosphere. This enzyme catalyzes a set of five chemical steps that take place in the same active-site within magnesium (II) coordination sphere. Here, a set of electronic structure benchmark calculations have been carried out on a reaction path proposed by Gready et al. by means of the projector-based embedding approach. Activation and reaction energies for all main steps catalyzed by RuBisCO have been calculated at the MP2, SCS-MP2, CCSD, and CCSD(T)/aug-cc-pVDZ and cc-pVDZ levels of theory. The treatment of the magnesium cation with post-HF methods is explored to determine the nature of its involvement in the mechanism. With the high-level ab initio values as a reference, we tested the performance of a set of density functional theory (DFT) exchange-correlation (xc) functionals in reproducing the reaction energetics of RuBisCO carboxylase activity on a set of model fragments. Different DFT xc-functionals show large variation in activation and reaction energies. Activation and reaction energies computed at the B3LYP level are close to the reference SCS-MP2 results for carboxylation, hydration and protonation reactions. However, for the carbon-carbon bond dissociation reaction, B3LYP and other functionals give results that differ significantly from the ab initio reference values. The results show the applicability of the projector-based embedding approach to metalloenzymes. This technique removes the uncertainty associated with the selection of different DFT xc-functionals and so can overcome some of inherent limitations of DFT calculations, complementing, and potentially adding to modeling of enzyme reaction mechanisms with DFT methods.

Modelling Enzymatic Mechanisms with QM/MM Approaches: Current Status and Future Challenges

AbstractQuantum mechanics/molecular mechanics (QM/MM) methods are presently a well‐established alternative for the study of enzymatic reaction mechanisms. They enable the description of a small part of the enzyme, where reactions take place through QM, while the majority of the thousands of atoms that comprise these biomolecules are handled through MM. While different “flavors” and variations in the QM/MM field exist, this review will focus more on the application of the ONIOM methodology, presenting a fresh perspective on the application of this popular method in light of the growth in computational power and level of sophistication of the different methodologies that it can combine. In addition to a brief presentation of the basic principles behind these methods, this review will discuss different examples of applicability, common choices, practical considerations, and main problems involved, stemming from our experience in this field. Finally, a reflection on the future challenges for the next decade in the QM/MM modeling of enzymatic mechanisms is presented.

Elucidating the unusual reaction kinetics of D-glucuronyl C5-epimerase.

The chemoenzymatic synthesis of heparin, through a multienzyme process, represents a critical challenge in providing a safe and effective substitute for this animal-sourced anticoagulant drug. D-glucuronyl C5-epimerase (C5-epi) is an enzyme acting on a heparin precursor, N-sulfoheparosan, catalyzing the reversible epimerization of D-glucuronic acid (GlcA) to L-iduronic acid (IdoA). The absence of reliable assays for C5-epi has limited elucidation of the enzymatic reaction and kinetic mechanisms. Real time and offline assays are described that rely on 1D 1H NMR to study the activity of C5-epi. Apparent steady-state kinetic parameters for both the forward and the pseudo-reverse reactions of C5-epi are determined for the first time using polysaccharide substrates directly relevant to the chemoenzymatic synthesis and biosynthesis of heparin. The forward reaction shows unusual sigmoidal kinetic behavior, and the pseudo-reverse reaction displays nonsaturating kinetic behavior. The atypical sigmoidal behavior of the forward reaction was probed using a range of buffer additives. Surprisingly, the addition of 25mM each of CaCl2 and MgCl2 resulted in a forward reaction exhibiting more conventional Michaelis-Menten kinetics. The addition of 2-O-sulfotransferase, the next enzyme involved in heparin synthesis, in the absence of 3'-phosphoadenosine 5'-phosphosulfate, also resulted in C5-epi exhibiting a more conventional Michaelis-Menten kinetic behavior in the forward reaction accompanied by a significant increase in apparent Vmax. This study provides critical information for understanding the reaction kinetics of C5-epi, which may result in improved methods for the chemoenzymatic synthesis of bioengineered heparin.