To see the other types of publications on this topic, follow the link: Enzymes - Catalysis.
Journal articles on the topic 'Enzymes - Catalysis'
Create a spot-on reference in APA, MLA, Chicago, Harvard, and other styles
Consult the top 50 journal articles for your research on the topic 'Enzymes - Catalysis.'
Next to every source in the list of references, there is an 'Add to bibliography' button. Press on it, and we will generate automatically the bibliographic reference to the chosen work in the citation style you need: APA, MLA, Harvard, Chicago, Vancouver, etc.
You can also download the full text of the academic publication as pdf and read online its abstract whenever available in the metadata.
Browse journal articles on a wide variety of disciplines and organise your bibliography correctly.
1
Carballares, Diego, Roberto Morellon-Sterling, and Roberto Fernandez-Lafuente. "Design of Artificial Enzymes Bearing Several Active Centers: New Trends, Opportunities and Problems." International Journal of Molecular Sciences 23, no. 10 (May 10, 2022): 5304. http://dx.doi.org/10.3390/ijms23105304.
Full textAbstract:
Harnessing enzymes which possess several catalytic activities is a topic where intense research has been carried out, mainly coupled with the development of cascade reactions. This review tries to cover the different possibilities to reach this goal: enzymes with promiscuous activities, fusion enzymes, enzymes + metal catalysts (including metal nanoparticles or site-directed attached organometallic catalyst), enzymes bearing non-canonical amino acids + metal catalysts, design of enzymes bearing a second biological but artificial active center (plurizymes) by coupling enzyme modelling and directed mutagenesis and plurizymes that have been site directed modified in both or in just one active center with an irreversible inhibitor attached to an organometallic catalyst. Some examples of cascade reactions catalyzed by the enzymes bearing several catalytic activities are also described. Finally, some foreseen problems of the use of these multi-activity enzymes are described (mainly related to the balance of the catalytic activities, necessary in many instances, or the different operational stabilities of the different catalytic activities). The design of new multi-activity enzymes (e.g., plurizymes or modified plurizymes) seems to be a topic with unarguable interest, as this may link biological and non-biological activities to establish new combo-catalysis routes.
2
Chen, Jianfeng, Xing Gong, Jianyu Li, Yingkun Li, Jiguo Ma, Chengkang Hou, Guoqing Zhao, Weicheng Yuan, and Baoguo Zhao. "Carbonyl catalysis enables a biomimetic asymmetric Mannich reaction." Science 360, no. 6396 (June 28, 2018): 1438–42. http://dx.doi.org/10.1126/science.aat4210.
Full textAbstract:
Chiral amines are widely used as catalysts in asymmetric synthesis to activate carbonyl groups for α-functionalization. Carbonyl catalysis reverses that strategy by using a carbonyl group to activate a primary amine. Inspired by biological carbonyl catalysis, which is exemplified by reactions of pyridoxal-dependent enzymes, we developed an N-quaternized pyridoxal catalyst for the asymmetric Mannich reaction of glycinate with aryl N-diphenylphosphinyl imines. The catalyst exhibits high activity and stereoselectivity, likely enabled by enzyme-like cooperative bifunctional activation of the substrates. Our work demonstrates the catalytic utility of the pyridoxal moiety in asymmetric catalysis.
3
Bearne, Stephen L. "Asymmetry in catalysis: ‘unidirectional’ amino acid racemases." Biochemist 43, no. 1 (January 22, 2021): 28–34. http://dx.doi.org/10.1042/bio_2020_101.
Full textAbstract:
d-Amino acids play widespread structural, functional and regulatory roles in organisms. These d-amino acids often arise through the stereoinversion of the more plentiful l-amino acids catalysed by amino acid racemases and epimerases. Such enzymes are of interest since many are recognized targets for the development of drugs or may be employed industrially in biotransformation reactions. Despite their enzyme–substrate complexes being diastereomers, some racemases and epimerases exhibit a kinetic pseudo-symmetry, binding their enantiomeric or epimeric substrate pairs with roughly equal affinities and catalyzing their stereoinversion with similar turnover numbers. In other cases, this kinetic pseudo-symmetry is absent or may be ‘broken’ by substitution of a catalytic Cys by Ser at the active site of cofactor-independent racemases and epimerases, or by altering the Brønsted base of the catalytic dyad that facilitates deprotonation of the Cys residue. Moreover, a natural Thr-containing l-Asp/Glu racemase was discovered that catalyses ‘unidirectional’ substrate turnover, unlike the typical bidirectional racemases and epimerases. These observations suggest that bidirectional Cys–Cys racemases may be re-engineered into ‘unidirectional’ racemases through substitution of the thiol by a hydroxyl group. Catalysis by such ‘unidirectional’ racemase precursors could then be optimized further by site-directed mutagenesis and directed evolution to furnish useful enzymes for biotechnological applications.
4
Page, Michael I. "Past times: The efficiency of enzyme catalysis." Biochemist 25, no. 4 (August 1, 2003): 52–53. http://dx.doi.org/10.1042/bio02504052.
Full textAbstract:
Understanding enzyme catalysis on a molecular and energetic basis has fascinated scientists for more than half a century. In addition to their obvious physiological involvement, the incredible efficiency of enzymes continues to intrigue us. In the absence of enzymes, many reactions of biological interest, e.g. the hydrolysis of proteins, carbohydrates and DNA, have half-lives of hundreds to millions of years. After a substrate is bound at an enzyme's active site, its halflife is usually milliseconds. The low concentration of enzymes in cells, which is often at or below the micromolar level, means that a rapid turnover is necessary to produce a significant rate of reaction and many reactions occur at near the diffusion controlled limit. The high catalytic efficiency of enzymes has not been emulated by artificial systems and therefore many have wondered if they could even be understood by ordinary chemistry.
5
Bhide, Yogesh S., Jitendra Y. Nehete, and Rajendra S. Bhambar. "Extraction, Characterization and Therapeutic Evaluation of Seeds of Phaseolus vulgaris L. for Inhibition of Carbohydrate Uptake." INTERNATIONAL JOURNAL OF DRUG DELIVERY TECHNOLOGY 13, no. 01 (March 25, 2023): 105–11. http://dx.doi.org/10.25258/ijddt.13.1.16.
Full textAbstract:
Phaseolamin-rich beans, also known as -amylase inhibitor 1 (AI) bean. AI has shown promise in treating diabetes and obesity in human studies. Since enzymes speed up chemical reactions, thus they are needed for most biological processes. Humans have used catalysts for centuries. Chemical catalysis was a heavy, often-used method. The method lacks sensitivity, and catalysis requires high temperature and pressure. Enzymes may function under more benign settings than chemical catalysts. Enzymes speed up chemical processes more than chemical catalysts due to their specifi city. Enzymes are used in practically every industry today. Enzymes have always been crucial. Enzymes have also been used to treat digestive diseases, coagulate milk for cheese, and process starch for drinks. Amylase is becoming increasingly popular because it may break down starch in multiple ways. Amylase reactions then cover amylases and other enzymatic reactions covered in this article as a catalyst. Amylases, a kind of hydrolase enzyme, are widely used. These enzymes randomly disrupt the glycosidic connections within starch molecules, releasing dextrin and oligosaccharides. Amylase is the most versatile type of amylase. Enzymes are replacing traditional chemical catalysts as consumers become more ecologically conscious
6
Ye, Rong, Tyler J. Hurlburt, Kairat Sabyrov, Selim Alayoglu, and Gabor A. Somorjai. "Molecular catalysis science: Perspective on unifying the fields of catalysis." Proceedings of the National Academy of Sciences 113, no. 19 (April 25, 2016): 5159–66. http://dx.doi.org/10.1073/pnas.1601766113.
Full textAbstract:
Colloidal chemistry is used to control the size, shape, morphology, and composition of metal nanoparticles. Model catalysts as such are applied to catalytic transformations in the three types of catalysts: heterogeneous, homogeneous, and enzymatic. Real-time dynamics of oxidation state, coordination, and bonding of nanoparticle catalysts are put under the microscope using surface techniques such as sum-frequency generation vibrational spectroscopy and ambient pressure X-ray photoelectron spectroscopy under catalytically relevant conditions. It was demonstrated that catalytic behavior and trends are strongly tied to oxidation state, the coordination number and crystallographic orientation of metal sites, and bonding and orientation of surface adsorbates. It was also found that catalytic performance can be tuned by carefully designing and fabricating catalysts from the bottom up. Homogeneous and heterogeneous catalysts, and likely enzymes, behave similarly at the molecular level. Unifying the fields of catalysis is the key to achieving the goal of 100% selectivity in catalysis.
7
Ratautas, Dalius, and Marius Dagys. "Nanocatalysts Containing Direct Electron Transfer-Capable Oxidoreductases: Recent Advances and Applications." Catalysts 10, no. 1 (December 19, 2019): 9. http://dx.doi.org/10.3390/catal10010009.
Full textAbstract:
Direct electron transfer (DET)-capable oxidoreductases are enzymes that have the ability to transfer/receive electrons directly to/from solid surfaces or nanomaterials, bypassing the need for an additional electron mediator. More than 100 enzymes are known to be capable of working in DET conditions; however, to this day, DET-capable enzymes have been mainly used in designing biofuel cells and biosensors. The rapid advance in (semi) conductive nanomaterial development provided new possibilities to create enzyme-nanoparticle catalysts utilizing properties of DET-capable enzymes and demonstrating catalytic processes never observed before. Briefly, such nanocatalysts combine several cathodic and anodic catalysis performing oxidoreductases into a single nanoparticle surface. Hereby, to the best of our knowledge, we present the first review concerning such nanocatalytic systems involving DET-capable oxidoreductases. We outlook the contemporary applications of DET-capable enzymes, present a principle of operation of nanocatalysts based on DET-capable oxidoreductases, provide a review of state-of-the-art (nano) catalytic systems that have been demonstrated using DET-capable oxidoreductases, and highlight common strategies and challenges that are usually associated with those type catalytic systems. Finally, we end this paper with the concluding discussion, where we present future perspectives and possible research directions.
8
Ball, Philip. "Catalysis: facing the future." National Science Review 2, no. 2 (April 24, 2015): 202–4. http://dx.doi.org/10.1093/nsr/nwv022.
Full textAbstract:
Abstract Most of the chemical reactions used to produce the molecules and materials that our societies need—for example, in the petrochemical and pharmaceutical industries, the synthesis of plastics and other materials, and the production of foods and drinks—make use of catalysts. These speed up the rate at which atoms and molecules rearrange themselves into new forms, and provide a degree of control over the shape and form of those rearrangements. Catalysts let us drive a chemical reaction in a selected direction, in preference to others that could occur. In this way they turn chemistry from crude cookery into a rational and precise form of molecular engineering. And always we can draw inspiration, and sometimes borrow tricks, from the delicate and precise catalytic processes that occur in nature, where enzymes carry out processes in aqueous solution and at mild temperatures and pressures that often we struggle to achieve with far more extreme conditions—such as the fixation of atmospheric nitrogen into useful forms. It is often claimed that this particular catalytic process—the Haber–Bosch process for converting nitrogen into ammonia, discovered just over a century ago—has, by making possible the synthesis of artificial fertilizers, had a greater effect on humankind than any other single chemical innovation. It is what allows us to feed the world. Yet while nature performs this reaction using soluble molecules (enzymes) as catalysts, the Haber–Bosch process uses powdered iron (plus some additives). The reactions between nitrogen and hydrogen take place on the surface of iron particles: this is so-called heterogeneous catalysis, involving surface chemistry, rather than the homogeneous catalysis of enzyme reactions, in which the catalysts are soluble molecules. Both homogeneous and heterogeneous catalysis are essential to the chemical industries. National Science Review spoke with two of the foremost practitioners of the latter field—Nobel laureate Gerhard Ertl of the Fritz Haber Institute in Berlin, Germany, and Avelino Corma of the Institute of Chemical Technology (ITQ) at the Polytechnic University of Valencia, Spain—about the current status of research in catalysis and prospects for the future.
9
S. Borkar, Sucharitha, Mithali Shetty, Aravind Pai, K. S. Chandrashekar, H. N. Aswatha Ram, Kiran Kumar Kolathur, Venkatesh Kamath B., and Kanav Khera. "TREASURE WRAPPED IN AN ENIGMA: CHEMISTRY AND INDUSTRIAL RELEVANCE OF ENZYMES FROM RARE ACTINOMYCETES." RASAYAN Journal of Chemistry 15, no. 04 (2022): 2493–501. http://dx.doi.org/10.31788/rjc.2022.1546997.
Full textAbstract:
Microbial enzymes are known for their versatile catalytic property. With the advent of enzyme engineering, stringent environmental rules restraining the use of toxic chemicals, and need for the sustainable resource, there is a mounting demand for the utilization of these enzymes. Classified under Gram-positive filamentous bacteria, actinomycetes are ubiquitous and are one of the major sources of enzymes, antibiotics, and various such bioactive molecules. Rare actinomycetes are a less explored genera of actinomycetes. However, they are also a potential source of a diverse spectrum of enzymes that are principal of commercial importance. Enzymes produced by rare actinomycetes have a wide array of applications ranging from bioremediation techniques to the estimation of serum cholesterol levels. This untapped resource is industrially as well as biotechnologically valuable. Oxidative enzymes and esterases are two very important classes of enzymes produced by rare actinomycetes. The fundamental principles of catalysis applied by the organic catalysts are also relevant to the enzymes. This review highlights how this unexploited resource could be effectively exploited for various commercial applications and gives an overview of the industrial and biochemical applications of oxidative enzymes and esterases produced by rare actinomycetes. Protein engineering and modern biotechnology have been capable of manipulating the enzyme design making it a more stable and efficient asset to the industries
10
Smith, Nathan, and Mark A. Wilson. "Understanding Cysteine Chemistry Using Conventional and Serial X-ray Protein Crystallography." Crystals 12, no. 11 (November 19, 2022): 1671. http://dx.doi.org/10.3390/cryst12111671.
Full textAbstract:
Proteins that use cysteine residues for catalysis or regulation are widely distributed and intensively studied, with many biomedically important examples. Enzymes where cysteine is a catalytic nucleophile typically generate covalent catalytic intermediates whose structures are important for understanding mechanism and for designing targeted inhibitors. The formation of catalytic intermediates can change enzyme conformational dynamics, sometimes activating protein motions that are important for catalytic turnover. However, these transiently populated intermediate species have been challenging to structurally characterize using traditional crystallographic approaches. This review describes the use and promise of new time-resolved serial crystallographic methods to study cysteine-dependent enzymes, with a focus on the main (Mpro) and papain-like (PLpro) cysteine proteases of SARS-CoV-2, as well as on other examples. We review features of cysteine chemistry that are relevant for the design and execution of time-resolved serial crystallography experiments. In addition, we discuss emerging X-ray techniques, such as time-resolved sulfur X-ray spectroscopy, that may be able to detect changes in sulfur charge states and covalency during catalysis or regulatory modification. In summary, cysteine-dependent enzymes have features that make them especially attractive targets for new time-resolved serial crystallography approaches, which can reveal both changes to enzyme structures and dynamics during catalysis in crystalline samples.
11
Breijyeh, Zeinab, and Rafik Karaman. "Enzyme Models—From Catalysis to Prodrugs." Molecules 26, no. 11 (May 28, 2021): 3248. http://dx.doi.org/10.3390/molecules26113248.
Full textAbstract:
Enzymes are highly specific biological catalysts that accelerate the rate of chemical reactions within the cell. Our knowledge of how enzymes work remains incomplete. Computational methodologies such as molecular mechanics (MM) and quantum mechanical (QM) methods play an important role in elucidating the detailed mechanisms of enzymatic reactions where experimental research measurements are not possible. Theories invoked by a variety of scientists indicate that enzymes work as structural scaffolds that serve to bring together and orient the reactants so that the reaction can proceed with minimum energy. Enzyme models can be utilized for mimicking enzyme catalysis and the development of novel prodrugs. Prodrugs are used to enhance the pharmacokinetics of drugs; classical prodrug approaches focus on alternating the physicochemical properties, while chemical modern approaches are based on the knowledge gained from the chemistry of enzyme models and correlations between experimental and calculated rate values of intramolecular processes (enzyme models). A large number of prodrugs have been designed and developed to improve the effectiveness and pharmacokinetics of commonly used drugs, such as anti-Parkinson (dopamine), antiviral (acyclovir), antimalarial (atovaquone), anticancer (azanucleosides), antifibrinolytic (tranexamic acid), antihyperlipidemia (statins), vasoconstrictors (phenylephrine), antihypertension (atenolol), antibacterial agents (amoxicillin, cephalexin, and cefuroxime axetil), paracetamol, and guaifenesin. This article describes the works done on enzyme models and the computational methods used to understand enzyme catalysis and to help in the development of efficient prodrugs.
12
Köhler, Valentin, and Nicholas J. Turner. "Artificial concurrent catalytic processes involving enzymes." Chemical Communications 51, no. 3 (2015): 450–64. http://dx.doi.org/10.1039/c4cc07277d.
Full text
13
Qu, Rui, Hongyi Suo, Yanan Gu, Yunxuan Weng, and Yusheng Qin. "Sidechain Metallopolymers with Precisely Controlled Structures: Synthesis and Application in Catalysis." Polymers 14, no. 6 (March 11, 2022): 1128. http://dx.doi.org/10.3390/polym14061128.
Full textAbstract:
Inspired by the cooperative multi-metallic activation in metalloenzyme catalysis, artificial enzymes as multi-metallic catalysts have been developed for improved kinetics and higher selectivity. Previous models about multi-metallic catalysts, such as cross-linked polymer-supported catalysts, failed to precisely control the number and location of their active sites, leading to low activity and selectivity. In recent years, metallopolymers with metals in the sidechain, also named as sidechain metallopolymers (SMPs), have attracted much attention because of their combination of the catalytic, magnetic, and electronic properties of metals with desirable mechanical and processing properties of polymeric backbones. Living and controlled polymerization techniques provide access to SMPs with precisely controlled structures, for example, controlled degree of polymerization (DP) and molecular weight dispersity (Đ), which may have excellent performance as multi-metallic catalysts in a variety of catalytic reactions. This review will cover the recent advances about SMPs, especially on their synthesis and application in catalysis. These tailor-made SMPs with metallic catalytic centers can precisely control the number and location of their active sites, exhibiting high catalytic efficiency.
14
Fang, Yi, Aihua Zhang, Shaohua Li, Michael Sproviero, and Ming-Qun Xu. "Enzyme Immobilization for Solid-Phase Catalysis." Catalysts 9, no. 9 (August 29, 2019): 732. http://dx.doi.org/10.3390/catal9090732.
Full textAbstract:
The covalent immobilization of an enzyme to a solid support can broaden its applicability in various workflows. Immobilized enzymes facilitate catalyst re-use, adaptability to automation or high-throughput applications and removal of the enzyme without heat inactivation or reaction purification. In this report, we demonstrate a step-by-step procedure to carry out the bio-orthogonal immobilization of DNA modifying enzymes employing the self-labelling activity of the SNAP-tag to covalently conjugate the enzyme of interest to the solid support. We also demonstrate how modifying the surface functionality of the support can improve the activity of the immobilized enzyme. Finally, the utility of immobilized DNA-modifying enzymes is depicted through sequential processing of genomic DNA libraries for Illumina next-generation sequencing (NGS), resulting in improved read coverage across AT-rich sequences.
15
Cottone, Grazia, Sergio Giuffrida, Stefano Bettati, Stefano Bruno, Barbara Campanini, Marialaura Marchetti, Stefania Abbruzzetti, et al. "More than a Confinement: “Soft” and “Hard” Enzyme Entrapment Modulates Biological Catalyst Function." Catalysts 9, no. 12 (December 4, 2019): 1024. http://dx.doi.org/10.3390/catal9121024.
Full textAbstract:
Catalysis makes chemical and biochemical reactions kinetically accessible. From a technological point of view, organic, inorganic, and biochemical catalysis is relevant for several applications, from industrial synthesis to biomedical, material, and food sciences. A heterogeneous catalyst, i.e., a catalyst confined in a different phase with respect to the reagents’ phase, requires either its physical confinement in an immobilization matrix or its physical adsorption on a surface. In this review, we will focus on the immobilization of biological catalysts, i.e., enzymes, by comparing hard and soft immobilization matrices and their effect on the modulation of the catalysts’ function. Indeed, unlike smaller molecules, the catalytic activity of protein catalysts depends on their structure, conformation, local environment, and dynamics, properties that can be strongly affected by the immobilization matrices, which, therefore, not only provide physical confinement, but also modulate catalysis.
16
Yuan, Zeqin, Jun Liao, Hao Jiang, Peng Cao, and Yang Li. "Aldehyde catalysis – from simple aldehydes to artificial enzymes." RSC Advances 10, no. 58 (2020): 35433–48. http://dx.doi.org/10.1039/d0ra06651f.
Full text
17
Li, Cheng-Hsuan, Rui Huang, Jessa Marie Makabenta, Suzannah Schmidt-Malan, Robin Patel, and Vincent M. Rotello. "In situ Generation of Antibiotics using Bioorthogonal “Nanofactories”." Microbiology Insights 14 (January 2021): 117863612199712. http://dx.doi.org/10.1177/1178636121997121.
Full textAbstract:
Prodrug strategies use chemical modifications to improve the pharmacokinetic properties and therefore therapeutic effects of parent drugs. Traditional prodrug approaches use endogenous enzymes for activation. Bioorthogonal catalysis uses processes that endogenous enzymes cannot access, providing a complementary strategy for prodrug uncaging. Site-selective activation of prodrugs to drugs (uncaging) using synthetic catalysts is a promising strategy for localized drug activation. We discuss here recent studies that incorporate metal catalysts into polymers and nanoparticle scaffolds to provide biocompatible “enzyme-like” catalysts that can penetrate bacterial biofilms and activate prodrug antibiotics in situ, affording a new strategy to treat bacterial biofilm infections with the potential for reduced off-target effects.
18
Švarc, Anera, Dino Skendrović, and Ana Vrsalović Presečki. "Biocatalysis for the Production of Pharmaceutical Intermediates." Kemija u industriji 68, no. 9-10 (2019): 469–76. http://dx.doi.org/10.15255/kui.2019.037.
Full textAbstract:
The application of enzymes in chemical synthesis, due to the recent advances, has a strong impact in multiple industries, especially the pharmaceutical industry. Namely, the use of enzymes shows remarkable advantages over classical chemical catalysis and therefore it is considered a ‘green’ solution. By using novel techniques, it is possible to tailor the enzymes to adapt them for a given process. Today, several pharmaceutical companies are successfully producing valuable precursors for the production of active pharmaceutical ingredients using enzymes, some of them being statin precursors. Statins are hypolipidemics, drugs used for the prevention of cardiovascular diseases and lowering cholesterol concentration in blood. Due to challenges in the chemical synthesis of statin intermediates, the production of statin intermediates using enzyme-catalysed reactions shows some notable advantages. Therefore, research and development laboratories, combined with reaction engineering techniques, have shifted their focus towards applying biochemical catalysis for the production of statin intermediates.
19
Lewis, David F. V. "Structural Models for Cytochrome P450�Mediated Catalysis." Scientific World JOURNAL 3 (2003): 536–45. http://dx.doi.org/10.1100/tsw.2003.41.
Full textAbstract:
This review focuses on the structural models for cytochrome P450 that are improving our knowledge and understanding of the P450 catalytic cycle, and the way in which substrates bind to the enzyme leading to catalytic conversion and subsequent formation of mono-oxygenated metabolites. Various stages in the P450 reaction cycle have now been investigated using X-ray crystallography and electronic structure calculations, whereas homology modelling of mammalian P450s is currently revealing important aspects of pharmaceutical and other xenobiotic metabolism mediated by P450 involvement. These features are explored in the current review on P450-based catalysis, which emphasises the importance of structural modelling to our understanding of this enzyme's function. In addition, the results of various QSAR analyses on series of chemicals, which are metabolised via P450 enzymes, are presented such that the importance of electronic and other structural factors in explaining variations in rates of metabolism can be appreciated.
20
Melanori, B. A. "Covalent Catalysis by Enzymes." Bioelectrochemistry and Bioenergetics 15, no. 1 (February 1986): 142. http://dx.doi.org/10.1016/0302-4598(86)80018-6.
Full text
21
Náray-Szabó, Gábor. "Electrostatic catalysis in enzymes." Journal of Molecular Catalysis 47, no. 2-3 (September 1988): 281–87. http://dx.doi.org/10.1016/0304-5102(88)85052-1.
Full text
22
Moreira, Cátia, Ana Rita Calixto, John P. Richard, and Shina Caroline Lynn Kamerlin. "The role of ligand-gated conformational changes in enzyme catalysis." Biochemical Society Transactions 47, no. 5 (October 28, 2019): 1449–60. http://dx.doi.org/10.1042/bst20190298.
Full textAbstract:
Abstract Structural and biochemical studies on diverse enzymes have highlighted the importance of ligand-gated conformational changes in enzyme catalysis, where the intrinsic binding energy of the common phosphoryl group of their substrates is used to drive energetically unfavorable conformational changes in catalytic loops, from inactive open to catalytically competent closed conformations. However, computational studies have historically been unable to capture the activating role of these conformational changes. Here, we discuss recent experimental and computational studies, which can remarkably pinpoint the role of ligand-gated conformational changes in enzyme catalysis, even when not modeling the loop dynamics explicitly. Finally, through our joint analyses of these data, we demonstrate how the synergy between theory and experiment is crucial for furthering our understanding of enzyme catalysis.
23
AN, Jae Hyung, Gha Young LEE, Jin-Won JUNG, Weontae LEE, and Yu Sam KIM. "Identification of residues essential for a two-step reaction by malonyl-CoA synthetase from Rhizobium trifolii." Biochemical Journal 344, no. 1 (November 8, 1999): 159–66. http://dx.doi.org/10.1042/bj3440159.
Full textAbstract:
Malonyl-CoA synthetase (MCS) catalyses the formation of malonyl-CoA in a two-step reaction consisting of the adenylation of malonate with ATP followed by malonyl transfer from malonyl-AMP to CoA. In order to identify amino acid residues essential for each step of the enzyme, catalysis based on chemical modification and database analysis, Arg-168, Lys-170, and His-206 were selected for site-directed mutagenesis. Glutathione-S-transferase-fused enzyme (GST-MCS) was constructed and mutagenized to make R168G, K170M, R168G/K170M and H206L mutants, respectively. The MCS activity of soluble form GST-MCS was the same as that of wild-type MCS. Circular dichroism spectra for the four mutant enzymes were nearly identical to that for the GST-MCS, indicating that Arg-168, Lys-170 and His-206 are not important for conformation but presumably for substrate binding and/or catalysis. HPLC analysis of products revealed that the intermediate malonyl-AMP is not accumulated during MCS catalysis and that none of the mutant enzymes accumulated it either.
24
Tran, Luyen Van. "ID2018 Radioisotope Enzymes And Cancer Study." Biomedical Research and Therapy 4, S (September 5, 2017): 51. http://dx.doi.org/10.15419/bmrat.v4is.261.
Full textAbstract:
Cancer is a pathological symptom, when abnormal cells appear in certain human tissues or organs. These cells can reproduce beyond the control of normal biological protection mechanism. Because they multiply themselves rapidly, the metabolic process is accelerated, which causes an extreme need for energy, substrate material and catalyzing enzyme. Bases on these needs, we can control the metabolic process by: • Stopping the supply of energy. • Stopping the supply of substrate materials to build up the cell’s structure. • Stopping the catalysis process by breaking out the enzyme’s structure and/or deactivating the catalytic function of existing enzymes. • Destroying the tumor cells by extraneous agents such as radiations and chemicals. All of these methods have been studied for a long time, with a lot of resources to be spent. Although we obtained some positive result, it is nowhere closed to satisfactory. There are many reasons for this situation but the main issue is the lack of information of the processes taking place in human’s cells and body. In this paper, we, however, would like to propose a method to break the structure and/or to deactivate the catalytic function of the enzyme by nuclear decay process.
25
Shteinman, Albert A. "Metallocavitins as Advanced Enzyme Mimics and Promising Chemical Catalysts." Catalysts 13, no. 2 (February 15, 2023): 415. http://dx.doi.org/10.3390/catal13020415.
Full textAbstract:
The supramolecular approach is becoming increasingly dominant in biomimetics and chemical catalysis due to the expansion of the enzyme active center idea, which now includes binding cavities (hydrophobic pockets), channels and canals for transporting substrates and products. For a long time, the mimetic strategy was mainly focused on the first coordination sphere of the metal ion. Understanding that a highly organized cavity-like enzymatic pocket plays a key role in the sophisticated functionality of enzymes and that the activity and selectivity of natural metalloenzymes are due to the effects of the second coordination sphere, created by the protein framework, opens up new perspectives in biomimetic chemistry and catalysis. There are two main goals of mimicking enzymatic catalysis: (1) scientific curiosity to gain insight into the mysterious nature of enzymes, and (2) practical tasks of mankind: to learn from nature and adopt from its many years of evolutionary experience. Understanding the chemistry within the enzyme nanocavity (confinement effect) requires the use of relatively simple model systems. The performance of the transition metal catalyst increases due to its retention in molecular nanocontainers (cavitins). Given the greater potential of chemical synthesis, it is hoped that these promising bioinspired catalysts will achieve catalytic efficiency and selectivity comparable to and even superior to the creations of nature. Now it is obvious that the cavity structure of molecular nanocontainers and the real possibility of modifying their cavities provide unlimited possibilities for simulating the active centers of metalloenzymes. This review will focus on how chemical reactivity is controlled in a well-defined cavitin nanospace. The author also intends to discuss advanced metal–cavitin catalysts related to the study of the main stages of artificial photosynthesis, including energy transfer and storage, water oxidation and proton reduction, as well as highlight the current challenges of activating small molecules, such as H2O, CO2, N2, O2, H2, and CH4.
26
Léonard, Nadia G., Rakia Dhaoui, Teera Chantarojsiri, and Jenny Y. Yang. "Electric Fields in Catalysis: From Enzymes to Molecular Catalysts." ACS Catalysis 11, no. 17 (August 18, 2021): 10923–32. http://dx.doi.org/10.1021/acscatal.1c02084.
Full text
27
Sher, Hassan, Hazrat Ali, Muhammad H. Rashid, Fariha Iftikhar, Saif-ur-Rehman, Muhammad S. Nawaz, and Waheed S. Khan. "Enzyme Immobilization on Metal-Organic Framework (MOF): Effects on Thermostability and Function." Protein & Peptide Letters 26, no. 9 (September 16, 2019): 636–47. http://dx.doi.org/10.2174/0929866526666190430120046.
Full textAbstract:
MOFs are porous materials with adjustable porosity ensuing a tenable surface area and stability. MOFs consist of metal containing joint where organic ligands are linked with coordination bonding rendering a unique architecture favouring the diverse applications in attachment of enzymes, Chemical catalysis, Gases storage and separation, biomedicals. In the past few years immobilization of soluble enzymes on/in MOF has been the topic of interest for scientists working in diverse field. The activity of enzyme, reusability, storage, chemical and thermal stability, affinity with substrate can be greatly improved by immobilizing of enzyme on MOFs. Along with improvement in enzymes properties, the high loading of enzyme is also observed while using MOFs as immobilization support. In this review a detail study of immobilization on/in Metalorganic Frameworks (MOFs) have been described. Furthermore, strategies for the enzyme immobilization on MOFs and resulting in improved catalytic performance of immobilized enzymes have been reported.
28
ABBADI, Amine, Monika BRUMMEL, Burkhardt S. SCHüTT, Mary B. SLABAUGH, Ricardo SCHUCH, and Friedrich SPENER. "Reaction mechanism of recombinant 3-oxoacyl-(acyl-carrier-protein) synthase III from Cuphea wrightii embryo, a fatty acid synthase type II condensing enzyme." Biochemical Journal 345, no. 1 (December 17, 1999): 153–60. http://dx.doi.org/10.1042/bj3450153.
Full textAbstract:
A unique feature of fatty acid synthase (FAS) type II of higher plants and bacteria is 3-oxoacyl-[acyl-carrier-protein (ACP)] synthase III (KAS III), which catalyses the committing condensing reaction. Working with KAS IIIs from Cuphea seeds we obtained kinetic evidence that KAS III catalysis follows a Ping-Pong mechanism and that these enzymes have substrate-binding sites for acetyl-CoA and malonyl-ACP. It was the aim of the present study to identify these binding sites and to elucidate the catalytic mechanism of recombinant Cuphea wrightii KAS III, which we expressed in Escherichia coli. We engineered mutants, which allowed us to dissect the condensing reaction into three stages, i.e. formation of acyl-enzyme, decarboxylation of malonyl-ACP, and final Claisen condensation. Incubation of recombinant enzyme with [1-14C]acetyl-CoA-labelled Cys111, and the replacement of this residue by Ala and Ser resulted in loss of overall condensing activity. The Cys111Ser mutant, however, still was able to bind acetyl-CoA and to catalyse subsequent binding and decarboxylation of malonyl-ACP to acetyl-ACP. We replaced His261 with Ala and Arg and found that the former lost activity, whereas the latter retained overall condensing activity, which indicated a general-base action of His261. Double mutants Cys111Ser/His261Ala and Cys111Ser/His261Arg were not able to catalyse overall condensation, but the double mutant containing Arg induced decarboxylation of [2-14C]malonyl-ACP, a reaction indicating the role of His261 in general-acid catalysis. Finally, alanine scanning revealed the involvement of Arg150 and Arg306 in KAS III catalysis. The results offer for the first time a detailed mechanism for a condensing reaction catalysed by a FAS type II condensing enzyme.
29
Raven, Emma L., Latesh Lad, Katherine H. Sharp, Martin Mewies, and Peter C. E. Moody. "Defining substrate specificity and catalytic mechanism in ascorbate peroxidase." Biochemical Society Symposia 71 (March 1, 2004): 27–38. http://dx.doi.org/10.1042/bss0710027.
Full textAbstract:
Haem peroxidases catalyse the H2O2-dependent oxidation of a variety of, usually organic, substrates. Mechanistically, these enzymes are very well characterized: they share a common catalytic cycle that involves formation of a two-electron oxidized intermediate (Compound I) followed by reduction of Compound I by substrate. The substrate specificity is more diverse, however. Most peroxidases oxidize small organic substrates, but there are prominent exceptions to this and the structural features that control substrate specificity remain poorly defined. APX (ascorbate peroxidase) catalyses the H2O2-dependent oxidation of l-ascorbate and has properties that place it at the interface between the class I (e.g. cytochrome c peroxidase) and classical class III (e.g. horseradish peroxidase) peroxidase enzymes. We present a unified analysis of the catalytic and substrate-binding properties of APX, including the crystal structure of the APX-ascorbate complex. Our results provide new rationalization of the unusual functional features of the related cytochrome c peroxidase enzyme, which has been a benchmark for peroxidase-mediated catalysis for more than 20 years.
30
Takeuchi, Nobuto, and Kunihiko Kaneko. "The origin of the central dogma through conflicting multilevel selection." Proceedings of the Royal Society B: Biological Sciences 286, no. 1912 (October 2, 2019): 20191359. http://dx.doi.org/10.1098/rspb.2019.1359.
Full textAbstract:
The central dogma of molecular biology rests on two kinds of asymmetry between genomes and enzymes: informatic asymmetry, where information flows from genomes to enzymes but not from enzymes to genomes; and catalytic asymmetry, where enzymes provide chemical catalysis but genomes do not. How did these asymmetries originate? Here, we show that these asymmetries can spontaneously arise from conflict between selection at the molecular level and selection at the cellular level. We developed a model consisting of a population of protocells, each containing a population of replicating catalytic molecules. The molecules are assumed to face a trade-off between serving as catalysts and serving as templates. This trade-off causes conflicting multilevel selection: serving as catalysts is favoured by selection between protocells, whereas serving as templates is favoured by selection between molecules within protocells. This conflict induces informatic and catalytic symmetry breaking, whereby the molecules differentiate into genomes and enzymes, establishing the central dogma. We show mathematically that the symmetry breaking is caused by a positive feedback between Fisher’s reproductive values and the relative impact of selection at different levels. This feedback induces a division of labour between genomes and enzymes, provided variation at the molecular level is sufficiently large relative to variation at the cellular level, a condition that is expected to hinder the evolution of altruism. Taken together, our results suggest that the central dogma is a logical consequence of conflicting multilevel selection.
31
Ciulli, A., and C. Abell. "Biophysical tools to monitor enzyme–ligand interactions of enzymes involved in vitamin biosynthesis." Biochemical Society Transactions 33, no. 4 (August 1, 2005): 767–71. http://dx.doi.org/10.1042/bst0330767.
Full textAbstract:
Knowledge of biomolecular interactions is of importance to our understanding of biological processes such as enzyme catalysis and inhibition. Biophysical techniques enable sensitive detection and accurate characterization of binding and are therefore powerful tools in enzymology and rational drug design. The applications of NMR spectroscopy and isothermal titration calorimetry to study enzyme–ligand interactions will be discussed. Recent work on ketopantoate reductase, which catalyses an important step on the biosynthetic pathway to vitamin B5, is used to illustrate the potential of this approach.
32
Hay, Sam, Christopher Pudney, Parvinder Hothi, Linus O. Johannissen, Laura Masgrau, Jiayun Pang, David Leys, Michael J. Sutcliffe, and Nigel S. Scrutton. "Atomistic insight into the origin of the temperature-dependence of kinetic isotope effects and H-tunnelling in enzyme systems is revealed through combined experimental studies and biomolecular simulation." Biochemical Society Transactions 36, no. 1 (January 22, 2008): 16–21. http://dx.doi.org/10.1042/bst0360016.
Full textAbstract:
The physical basis of the catalytic power of enzymes remains contentious despite sustained and intensive research efforts. Knowledge of enzyme catalysis is predominantly descriptive, gained from traditional protein crystallography and solution studies. Our goal is to understand catalysis by developing a complete and quantitative picture of catalytic processes, incorporating dynamic aspects and the role of quantum tunnelling. Embracing ideas that we have spearheaded from our work on quantum mechanical tunnelling effects linked to protein dynamics for H-transfer reactions, we review our recent progress in mapping macroscopic kinetic descriptors to an atomistic understanding of dynamics linked to biological H-tunnelling reactions.
33
MORI, Toshifumi. "Are Conformational Dynamics of Enzymes Important for Enzyme Catalysis?" Seibutsu Butsuri 59, no. 5 (2019): 271–72. http://dx.doi.org/10.2142/biophys.59.271.
Full text
34
Dong, ZeYuan, JunYan Zhu, Quan Luo, and JunQiu Liu. "Understanding enzyme catalysis by means of supramolecular artificial enzymes." Science China Chemistry 56, no. 8 (April 22, 2013): 1067–74. http://dx.doi.org/10.1007/s11426-013-4871-3.
Full text
35
Jain, Mahendra Kumar, Bao-Zhu Yu, Michael H. Gelb, and Otto G. Berg. "Assay of phospholipases A2and their inhibitors by kinetic analysis in the scooting mode." Mediators of Inflammation 1, no. 2 (1992): 85–100. http://dx.doi.org/10.1155/s0962935192000164.
Full textAbstract:
Several cellular processes are regulated by interfacial catalysis on biomembrane surfaces. Phospholipases A2(PLA2) are interesting not only as prototypes for interfacial catalysis, but also because they mobilize precursors for the biosynthesis of eicosanoids and platelet activating factor, and these agents ultimately control a wide range of secretory and inflammatory processes. Since PLA2carry out their catalytic function at membrane surfaces, the kinetics of these enzymes depends on what the enzyme ‘sees’ at the interface, and thus the observed rate is profoundly influenced by the organization and dynamics of the lipidwater interface (‘quality of the interface’). In this review we elaborate the advantages of monitoring interfacial catalysis in the scooting mode, that is, under the conditions where the enzyme remains bound to vesicles for several thousand catalytic turnover cycles. Such a highly processive catalytic turnover in the scooting mode is useful for a rigorous and quantitative characterization of the kinetics of interfacial catalysis. This analysis is now extended to provide insights into designing strategy for PLA2assays and screens for their inhibitors.
36
Cao, Yufei, Xiaoyang Li, Jiarong Xiong, Licheng Wang, Li-Tang Yan, and Jun Ge. "Investigating the origin of high efficiency in confined multienzyme catalysis." Nanoscale 11, no. 45 (2019): 22108–17. http://dx.doi.org/10.1039/c9nr07381g.
Full text
37
Faggiano, Antonio, Maria Ricciardi, and Antonio Proto. "Catalytic Routes to Produce Polyphenolic Esters (PEs) from Biomass Feedstocks." Catalysts 12, no. 4 (April 18, 2022): 447. http://dx.doi.org/10.3390/catal12040447.
Full textAbstract:
Polyphenolic esters (PEs) are valuable chemical compounds that display a wide spectrum of activities (e.g., anti-oxidative effects). As a result, their production through catalytic routes is an attractive field of research. The present review aims to discuss recent studies from the literature regarding the catalytic production of PEs from biomass feedstocks, namely, naturally occurred polyphenolic compounds. Several synthetic approaches are reported in the literature, mainly bio-catalysis and to a lesser extent acid catalysis. Immobilized lipases (e.g., Novozym 435) are the preferred enzymes thanks to their high reactivity, selectivity and reusability. Acid catalysis is principally investigated for the esterification of polyphenolic acids with fatty alcohols and/or glycerol, using both homogeneous (p-toluensulfonic acid, sulfonic acid and ionic liquids) and heterogeneous (strongly acidic cation exchange resins) catalysts. Based on the reviewed publications, we propose some suggestions to improve the synthesis of PEs with the aim of increasing the greenness of the overall production process. In fact, much more attention should be paid to the use of new and efficient acid catalysts and their reuse for multiple reaction cycles.
38
Fyfe, Cameron D., Noelia Bernardo-García, Laura Fradale, Stéphane Grimaldi, Alain Guillot, Clémence Brewee, Leonard M. G. Chavas, Pierre Legrand, Alhosna Benjdia, and Olivier Berteau. "Crystallographic snapshots of a B12-dependent radical SAM methyltransferase." Nature 602, no. 7896 (February 2, 2022): 336–42. http://dx.doi.org/10.1038/s41586-021-04355-9.
Full textAbstract:
AbstractBy catalysing the microbial formation of methane, methyl-coenzyme M reductase has a central role in the global levels of this greenhouse gas1,2. The activity of methyl-coenzyme M reductase is profoundly affected by several unique post-translational modifications3–6, such as a unique C-methylation reaction catalysed by methanogenesis marker protein 10 (Mmp10), a radical S-adenosyl-l-methionine (SAM) enzyme7,8. Here we report the spectroscopic investigation and atomic resolution structure of Mmp10 from Methanosarcina acetivorans, a unique B12 (cobalamin)-dependent radical SAM enzyme9. The structure of Mmp10 reveals a unique enzyme architecture with four metallic centres and critical structural features involved in the control of catalysis. In addition, the structure of the enzyme–substrate complex offers a glimpse into a B12-dependent radical SAM enzyme in a precatalytic state. By combining electron paramagnetic resonance spectroscopy, structural biology and biochemistry, our study illuminates the mechanism by which the emerging superfamily of B12-dependent radical SAM enzymes catalyse chemically challenging alkylation reactions and identifies distinctive active site rearrangements to provide a structural rationale for the dual use of the SAM cofactor for radical and nucleophilic chemistry.
39
Scott, William G. "Biophysical and biochemical investigations of RNA catalysis in the hammerhead ribozyme." Quarterly Reviews of Biophysics 32, no. 3 (August 1999): 241–84. http://dx.doi.org/10.1017/s003358350000353x.
Full textAbstract:
1. How do ribozymes work? 2412. The hammerhead RNA as a prototype ribozyme 2422.1 RNA enzymes 2422.2 Satellite self-cleaving RNAs 2422.3 Hammerhead RNAs and hammerhead ribozymes 2443. The chemical mechanism of hammerhead RNA self-cleavage 2463.1 Phosphodiester isomerization via an SN2(P) reaction 2473.2 The canonical role of divalent metal ions in the hammerhead ribozyme reaction 2513.3 The hammerhead ribozyme does not actually require metal ions for catalysis 2543.4 Hammerhead RNA enzyme kinetics 2574. Sequence requirements for hammerhead RNA self-cleavage 2604.1 The conserved core, mutagenesis and functional group modifications 2604.2 Ground-state vs. transition-state effects 2615. The three-dimensional structure of the hammerhead ribozyme 2625.1 Enzyme–inhibitor complexes 2625.2 Enzyme–substrate complex in the initial state 2645.3 Hammerhead ribozyme self-cleavage in the crystal 2645.4 The requirement for a conformational change 2655.5 Capture of conformational intermediates using crystallographic freeze-trapping 2665.6 The structure of a hammerhead ribozyme ‘early’ conformational intermediate 2675.7 The structure of a hammerhead ribozyme ‘later’ conformational intermediate 2685.8 Is the conformational change pH dependent? 2695.9 Isolating the structure of the cleavage product 2715.10 Evidence for and against additional large-scale conformation changes 2745.11 NMR spectroscopic studies of the hammerhead ribozyme 2786. Concluding remarks 2807. Acknowledgements 2818. References 2811. How do ribozymes work? 241The discovery that RNA can be an enzyme (Guerrier-Takada et al. 1983; Zaug & Cech, 1986) has created the fundamental question of how RNA enzymes work. Before this discovery, it was generally assumed that proteins were the only biopolymers that had sufficient complexity and chemical heterogeneity to catalyze biochemical reactions. Clearly, RNA can adopt sufficiently complex tertiary structures that make catalysis possible. How does the three- dimensional structure of an RNA endow it with catalytic activity? What structural and functional principles are unique to RNA enzymes (or ribozymes), and what principles are so fundamental that they are shared with protein enzymes?
40
Davidi, Dan, Elad Noor, Wolfram Liebermeister, Arren Bar-Even, Avi Flamholz, Katja Tummler, Uri Barenholz, Miki Goldenfeld, Tomer Shlomi, and Ron Milo. "Global characterization of in vivo enzyme catalytic rates and their correspondence to in vitrokcatmeasurements." Proceedings of the National Academy of Sciences 113, no. 12 (March 7, 2016): 3401–6. http://dx.doi.org/10.1073/pnas.1514240113.
Full textAbstract:
Turnover numbers, also known askcatvalues, are fundamental properties of enzymes. However,kcatdata are scarce and measured in vitro, thus may not faithfully represent the in vivo situation. A basic question that awaits elucidation is: how representative arekcatvalues for the maximal catalytic rates of enzymes in vivo? Here, we harness omics data to calculatekmaxvivo, the observed maximal catalytic rate of an enzyme inside cells. Comparison withkcatvalues fromEscherichia coli, yields a correlation ofr2= 0.62 in log scale (p<10−10), with a root mean square difference of 0.54 (3.5-fold in linear scale), indicating that in vivo and in vitro maximal rates generally concur. By accounting for the degree of saturation of enzymes and the backward flux dictated by thermodynamics, we further refine the correspondence betweenkmaxvivoandkcatvalues. The approach we present here characterizes the quantitative relationship between enzymatic catalysis in vitro and in vivo and offers a high-throughput method for extracting enzyme kinetic constants from omics data.
41
Kadiri, Alarcón-Correa, Ruppert, Günther, Bill, Rothenstein, and Fischer. "Genetically Modified M13 Bacteriophage Nanonets for Enzyme Catalysis and Recovery." Catalysts 9, no. 9 (August 27, 2019): 723. http://dx.doi.org/10.3390/catal9090723.
Full textAbstract:
Enzyme-based biocatalysis exhibits multiple advantages over inorganic catalysts, including the biocompatibility and the unchallenged specificity of enzymes towards their substrate. The recovery and repeated use of enzymes is essential for any realistic application in biotechnology, but is not easily achieved with current strategies. For this purpose, enzymes are often immobilized on inorganic scaffolds, which could entail a reduction of the enzymes’ activity. Here, we show that immobilization to a nano-scaled biological scaffold, a nanonetwork of end-to-end cross-linked M13 bacteriophages, ensures high enzymatic activity and at the same time allows for the simple recovery of the enzymes. The bacteriophages have been genetically engineered to express AviTags at their ends, which permit biotinylation and their specific end-to-end self-assembly while allowing space on the major coat protein for enzyme coupling. We demonstrate that the phages form nanonetwork structures and that these so-called nanonets remain highly active even after re-using the nanonets multiple times in a flow-through reactor.
42
Shomar, Helena, and Gregory Bokinsky. "Towards a Synthetic Biology Toolset for Metallocluster Enzymes in Biosynthetic Pathways: What We Know and What We Need." Molecules 26, no. 22 (November 17, 2021): 6930. http://dx.doi.org/10.3390/molecules26226930.
Full textAbstract:
Microbes are routinely engineered to synthesize high-value chemicals from renewable materials through synthetic biology and metabolic engineering. Microbial biosynthesis often relies on expression of heterologous biosynthetic pathways, i.e., enzymes transplanted from foreign organisms. Metallocluster enzymes are one of the most ubiquitous family of enzymes involved in natural product biosynthesis and are of great biotechnological importance. However, the functional expression of recombinant metallocluster enzymes in live cells is often challenging and represents a major bottleneck. The activity of metallocluster enzymes requires essential supporting pathways, involved in protein maturation, electron supply, and/or enzyme stability. Proper function of these supporting pathways involves specific protein–protein interactions that remain poorly characterized and are often overlooked by traditional synthetic biology approaches. Consequently, engineering approaches that focus on enzymatic expression and carbon flux alone often overlook the particular needs of metallocluster enzymes. This review highlights the biotechnological relevance of metallocluster enzymes and discusses novel synthetic biology strategies to advance their industrial application, with a particular focus on iron-sulfur cluster enzymes. Strategies to enable functional heterologous expression and enhance recombinant metallocluster enzyme activity in industrial hosts include: (1) optimizing specific maturation pathways; (2) improving catalytic stability; and (3) enhancing electron transfer. In addition, we suggest future directions for developing microbial cell factories that rely on metallocluster enzyme catalysis.
43
Yan, Junjun, Peng Chen, Yan Zeng, Yan Men, Shicheng Mu, Yueming Zhu, Yefu Chen, and Yuanxia Sun. "The Characterization and Modification of a Novel Bifunctional and Robust Alginate Lyase Derived from Marinimicrobium sp. H1." Marine Drugs 17, no. 10 (September 23, 2019): 545. http://dx.doi.org/10.3390/md17100545.
Full textAbstract:
Alginase lyase is an important enzyme for the preparation of alginate oligosaccharides (AOS), that possess special biological activities and is widely used in various fields, such as medicine, food, and chemical industry. In this study, a novel bifunctional alginate lyase (AlgH) belonging to the PL7 family was screened and characterized. The AlgH exhibited the highest activity at 45 °C and pH 10.0, and was an alkaline enzyme that was stable at pH 6.0–10.0. The enzyme showed no significant dependence on metal ions, and exhibited unchanged activity at high concentration of NaCl. To determine the function of non-catalytic domains in the multi-domain enzyme, the recombinant AlgH-I containing only the catalysis domain and AlgH-II containing the catalysis domain and the carbohydrate binding module (CBM) domain were constructed and characterized. The results showed that the activity and thermostability of the reconstructed enzymes were significantly improved by deletion of the F5/8 type C domain. On the other hand, the substrate specificity and the mode of action of the reconstructed enzymes showed no change. Alginate could be completely degraded by the full-length and modified enzymes, and the main end-products were alginate disaccharide, trisaccharide, and tetrasaccharide. Due to the thermo and pH-stability, salt-tolerance, and bifunctionality, the modified alginate lyase was a robust enzyme which could be applied in industrial production of AOS.
44
Oliveira-Ribeiro, Livia Maria, Lucas Meili, Georgia Nayane Silva-Belo-Gois, Renata Maria Rosas-Garcia-Almeida, and José Leandro da Silva-Duarte. "Immobilization of lipase in biochar obtained from Manihot esculenta Crantz." Revista ION 32, no. 2 (November 19, 2019): 7–13. http://dx.doi.org/10.18273/revion.v32n2-2019001.
Full textAbstract:
The immobilized enzymes are catalysts of great industrial interest, as it unites the advantages of heterogeneous catalysis with the high selectivity and mild operation conditions of the enzymes. Biochar is a porous carbonaceous material, which have characteristic that it makes a strong candidate to incorporate enzymes in its structure. Another relevant fact is the possibility of changes and adaptations by synthesis condition in the biochar structure due to the application needs. In this context, the objective of this work was the study of immobilization of lipase (type II, code l3126, Sigma Aldrich) in a biochar produced by pyrolysis (600oC) from an agricultural residue called cassava stump. It was evaluated different enzymatic concentrations (0.1, 0.25 and 0.5 g/L) in order to determine the affinity between the enzyme and biochar. The obtained results showed that the enzyme studied could be easily immobilized in the biochar, obtaining as immobilization yield 61.2% when using the highest concentration of enzyme.
45
Fried, Stephen D., Sayan Bagchi, and Steven G. Boxer. "Extreme electric fields power catalysis in the active site of ketosteroid isomerase." Science 346, no. 6216 (December 18, 2014): 1510–14. http://dx.doi.org/10.1126/science.1259802.
Full textAbstract:
Enzymes use protein architecture to impose specific electrostatic fields onto their bound substrates, but the magnitude and catalytic effect of these electric fields have proven difficult to quantify with standard experimental approaches. Using vibrational Stark effect spectroscopy, we found that the active site of the enzyme ketosteroid isomerase (KSI) exerts an extremely large electric field onto the C=O chemical bond that undergoes a charge rearrangement in KSI’s rate-determining step. Moreover, we found that the magnitude of the electric field exerted by the active site strongly correlates with the enzyme’s catalytic rate enhancement, enabling us to quantify the fraction of the catalytic effect that is electrostatic in origin. The measurements described here may help explain the role of electrostatics in many other enzymes and biomolecular systems.
46
Fujihashi, Masahiro, Toyokazu Ishida, Shingo Kuroda, Kazuya Mito, Lakshmi Kotra, Emil Pai, and Kunio Miki. "Substrate distortion in the catalysis of orotidine monophosphate decarboxylase." Acta Crystallographica Section A Foundations and Advances 70, a1 (August 5, 2014): C447. http://dx.doi.org/10.1107/s2053273314095527.
Full textAbstract:
One way for enzymes to affect reactions they catalyze is through transition state stabilization. Another factor to be considered is the contribution of substrate distortion, although it has been thoroughly described for only a few enzymes. We have a longstanding interest in the reaction mechanism of orotidine monophosphate decarboxylase (ODCase) and determined various crystal structures bound with distorted substrates at around 1.5 Å resolution. The enzyme is known as one of the most proficient enzymes, which accelerates the decarboxylation of orotidine 5'-monophosphate (OMP) to form uridine 5'-monophosphate (UMP) by 17 orders of magnitude. One argument against the contribution of substrate distortion to the ODCase reaction is the weak affinity of UMP. The distortions observed so far all appear at the C6-substituent of the pyrimidine ring, which corresponds to the carboxylate of OMP. Since the carboxylate is removed by the reaction, the product UMP should bind more tightly to ODCase than OMP, if the distortion of C6-substituent contributes to the catalysis. In order to investigate this inconsistency, we determined the crystal structure of ODCase with UMP at atomic resolution (1.03 Å). The structure showed an unfavorable interaction between UMP and the catalytic residue K72, an interaction considered to be absent in the OMP complex. Surface plasmon resonance analysis indicated that UMP binds stronger to the K72A mutant than to the wild-type enzyme by 5 orders of magnitude. These analyses invalidate the argument against a contribution of substrate distortion to ODCase catalysis. Finally, we estimated how much the distortion contributes to the catalysis using computational simulation methods. The results indicated that 10-15% decrease of the ΔΔG‡ value is contributed by substrate distortion.
47
Kurumbail, R. "Cyclooxygenase enzymes: catalysis and inhibition." Current Opinion in Structural Biology 11, no. 6 (December 1, 2001): 752–60. http://dx.doi.org/10.1016/s0959-440x(01)00277-9.
Full text
48
Ngo, Ho-Phuong-Thuy, Nuno M. F. S. A. Cerqueira, Jin-Kwang Kim, Myoung-Ki Hong, Pedro Alexandrino Fernandes, Maria João Ramos, and Lin-Woo Kang. "PLP undergoes conformational changes during the course of an enzymatic reaction." Acta Crystallographica Section D Biological Crystallography 70, no. 2 (January 31, 2014): 596–606. http://dx.doi.org/10.1107/s1399004713031283.
Full textAbstract:
Numerous enzymes, such as the pyridoxal 5′-phosphate (PLP)-dependent enzymes, require cofactors for their activities. Using X-ray crystallography, structural snapshots of the L-serine dehydratase catalytic reaction of a bacterial PLP-dependent enzyme were determined. In the structures, the dihedral angle between the pyridine ring and the Schiff-base linkage of PLP varied from 18° to 52°. It is proposed that the organic cofactor PLP directly catalyzes reactions by active conformational changes, and the novel catalytic mechanism involving the PLP cofactor was confirmed by high-level quantum-mechanical calculations. The conformational change was essential for nucleophilic attack of the substrate on PLP, for concerted proton transfer from the substrate to the protein and for directing carbanion formation of the substrate. Over the whole catalytic cycle, the organic cofactor catalyzes a series of reactions, like the enzyme. The conformational change of the PLP cofactor in catalysis serves as a starting point for identifying the previously unknown catalytic roles of organic cofactors.
49
Zartner, Luisa, Viviana Maffeis, Cora-Ann Schoenenberger, Ionel Adrian Dinu, and Cornelia G. Palivan. "Membrane protein channels equipped with a cleavable linker for inducing catalysis inside nanocompartments." Journal of Materials Chemistry B 9, no. 43 (2021): 9012–22. http://dx.doi.org/10.1039/d1tb01463c.
Full text
50
Bernhardt, Paul V. "Enzyme Electrochemistry — Biocatalysis on an Electrode." Australian Journal of Chemistry 59, no. 4 (2006): 233. http://dx.doi.org/10.1071/ch05340.
Full textAbstract:
Oxidoreductase enzymes catalyze single- or multi-electron reduction/oxidation reactions of small molecule inorganic or organic substrates, and they are integral to a wide variety of biological processes including respiration, energy production, biosynthesis, metabolism, and detoxification. All redox enzymes require a natural redox partner such as an electron-transfer protein (e.g. cytochrome, ferredoxin, flavoprotein) or a small molecule cosubstrate (e.g. NAD(P)H, dioxygen) to sustain catalysis, in effect to balance the substrate/product redox half-reaction. In principle, the natural electron-transfer partner may be replaced by an electrochemical working electrode. One of the great strengths of this approach is that the rate of catalysis (equivalent to the observed electrochemical current) may be probed as a function of applied potential through linear sweep and cyclic voltammetry, and insight to the overall catalytic mechanism may be gained by a systematic electrochemical study coupled with theoretical analysis. In this review, the various approaches to enzyme electrochemistry will be discussed, including direct and indirect (mediated) experiments, and a brief coverage of the theory relevant to these techniques will be presented. The importance of immobilizing enzymes on the electrode surface will be presented and the variety of ways that this may be done will be reviewed. The importance of chemical modification of the electrode surface in ensuring an environment conducive to a stable and active enzyme capable of functioning natively will be illustrated. Fundamental research into electrochemically driven enzyme catalysis has led to some remarkable practical applications. The glucose oxidase enzyme electrode is a spectacularly successful application of enzyme electrochemistry. Biosensors based on this technology are used worldwide by sufferers of diabetes to provide rapid and accurate analysis of blood glucose concentrations. Other applications of enzyme electrochemistry are in the sensing of macromolecular complexation events such as antigen–antibody binding and DNA hybridization. The review will include a selection of enzymes that have been successfully investigated by electrochemistry and, where appropriate, discuss their development towards practical biotechnological applications.