Nanozymes for Environmental Pollutant Monitoring and Remediation
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Weiterführende Literatur Zum Lehrbuch „Biochemie“ (Kapitel 4 – 50)
Weiterführende Literatur zum Lehrbuch „Biochemie“ (Kapitel 4 – 50) Im Buch ist aus Platzgründen auf die Angabe weiterführender Literatur verzichtet worden. Auskünfte zu den thematischen Schwerpunkten der vier Hauptteile II bis V geben die im Folgenden aufgeführten knapp 1000 einschlägigen Artikel aus wissenschaftlichen Fachzeitschriften. Die Zusammenstellung folgt der Gliederung des Buchs. Jeder Link führt direkt zur Literaturliste des entsprechenden Kapitels, aber es ist stets auch die gesamte Literatur hinterlegt (z.B. für einen kompletten Ausdruck). Die Aufstellung enthält überwiegend Review-Artikel der letzten 4 Jahre, in denen der aktuelle Kenntnisstand zu einem ausgewählten Thema von führenden Wissenschaftlern präsentiert wird. Beim Einführungsteil (Kapitel 1 bis 3) haben wir dagegen bewusst auf Spezialliteratur verzichtet; hier sei auf einschlägige Lehrbücher der Biochemie, Molekularbiologie, Genetik und Zellbiologie, die diesen fundamentalen Aspekten breiten Raum widmen, verwiesen. Falls Sie als Leser interessante Artikel finden, die unsere Literatursammlung ergänzen und bereichern könnten, bitten wir um kurze Mitteilung an den Verlag. Werner Müller-Esterl Ulrich Brandt Oliver Anderka Stefan Kerscher 1 Teil II Struktur und Funktion von Proteinen 4 Proteine – Werkzeuge der Zelle 4.1 Liganden binden an Proteine und verändern deren Konformation Wilson MA, Brunger AT (2000) The 1.0 Å crystal structure of Ca2+-bound calmodulin: an analysis of disorder and implications for functionally relevant plasticity, J Mol Biol 301, 1237-1256 O'Day DH & Myre MA (2004) Calmodulin-binding domains in Alzheimer's disease proteins: extending the calcium hypothesis. Biochemical and Biophysical Research Communications, 320, 1051-1054. 4.2 Enzyme binden Substrate und setzen sie zu Produkten um Showalter AK & Tsai MD (2002) A reexamination of the nucleotide incorporation fidelity of DNA polymerases. -
Part I Principles of Enzyme Catalysis
j1 Part I Principles of Enzyme Catalysis Enzyme Catalysis in Organic Synthesis, Third Edition. Edited by Karlheinz Drauz, Harald Groger,€ and Oliver May. Ó 2012 Wiley-VCH Verlag GmbH & Co. KGaA. Published 2012 by Wiley-VCH Verlag GmbH & Co. KGaA. j3 1 Introduction – Principles and Historical Landmarks of Enzyme Catalysis in Organic Synthesis Harald Gr€oger and Yasuhisa Asano 1.1 General Remarks Enzyme catalysis in organic synthesis – behind this term stands a technology that today is widely recognized as a first choice opportunity in the preparation of a wide range of chemical compounds. Notably, this is true not only for academic syntheses but also for industrial-scale applications [1]. For numerous molecules the synthetic routes based on enzyme catalysis have turned out to be competitive (and often superior!) compared with classic chemicalaswellaschemocatalyticsynthetic approaches. Thus, enzymatic catalysis is increasingly recognized by organic chemists in both academia and industry as an attractive synthetic tool besides the traditional organic disciplines such as classic synthesis, metal catalysis, and organocatalysis [2]. By means of enzymes a broad range of transformations relevant in organic chemistry can be catalyzed, including, for example, redox reactions, carbon–carbon bond forming reactions, and hydrolytic reactions. Nonetheless, for a long time enzyme catalysis was not realized as a first choice option in organic synthesis. Organic chemists did not use enzymes as catalysts for their envisioned syntheses because of observed (or assumed) disadvantages such as narrow substrate range, limited stability of enzymes under organic reaction conditions, low efficiency when using wild-type strains, and diluted substrate and product solutions, thus leading to non-satisfactory volumetric productivities. -
Catalytic, Theoretical, and Biological Investigation of an Enzyme Mimic Model
Turkish Journal of Chemistry Turk J Chem (2021) 45: 1270-1278 http://journals.tubitak.gov.tr/chem/ © TÜBİTAK Research Article doi:10.3906/kim-2104-51 Catalytic, theoretical, and biological investigation of an enzyme mimic model Gülcihan GÜLSEREN* Department of Molecular Biology and Genetics, Faculty of Agriculture and Natural Sciences, Konya Food and Agriculture University, Turkey Received: 20.04.2021 Accepted/Published Online: 12.06.2021 Final Version: 27.08.2021 Abstract: Artificial catalyst studies were always stayed at the kinetics investigation level, in this work bioactivity of designed catalyst were shown by the induction of biomineralization of the cells, indicating the possible use of enzyme mimics for biological applications. The development of artificial enzymes is a continuous quest for the development of tailored catalysts with improved activity and stability. Understanding the catalytic mechanism is a replaceable step for catalytic studies and artificial enzyme mimics provide an alternative way for catalysis and a better understanding of catalytic pathways at the same time. Here we designed an artificial catalyst model by decorating peptide nanofibers with a covalently conjugated catalytic triad sequence. Owing to the self-assembling nature of the peptide amphiphiles, multiple action units can be presented on the surface for enhanced catalytic performance. The designed catalyst has shown an enzyme-like kinetics profile with a significant substrate affinity. The cooperative action in between catalytic triad amino acids has shown improved catalytic activity in comparison to only the histidine-containing control group. Histidine is an irreplaceable contributor to catalytic action and this is an additional reason for control group selection. This new method based on the self-assembly of covalently conjugated action units offers a new platform for enzyme investigations and their further applications. -
Enzyme DHRS7
Toward the identification of a function of the “orphan” enzyme DHRS7 Inauguraldissertation zur Erlangung der Würde eines Doktors der Philosophie vorgelegt der Philosophisch-Naturwissenschaftlichen Fakultät der Universität Basel von Selene Araya, aus Lugano, Tessin Basel, 2018 Originaldokument gespeichert auf dem Dokumentenserver der Universität Basel edoc.unibas.ch Genehmigt von der Philosophisch-Naturwissenschaftlichen Fakultät auf Antrag von Prof. Dr. Alex Odermatt (Fakultätsverantwortlicher) und Prof. Dr. Michael Arand (Korreferent) Basel, den 26.6.2018 ________________________ Dekan Prof. Dr. Martin Spiess I. List of Abbreviations 3α/βAdiol 3α/β-Androstanediol (5α-Androstane-3α/β,17β-diol) 3α/βHSD 3α/β-hydroxysteroid dehydrogenase 17β-HSD 17β-Hydroxysteroid Dehydrogenase 17αOHProg 17α-Hydroxyprogesterone 20α/βOHProg 20α/β-Hydroxyprogesterone 17α,20α/βdiOHProg 20α/βdihydroxyprogesterone ADT Androgen deprivation therapy ANOVA Analysis of variance AR Androgen Receptor AKR Aldo-Keto Reductase ATCC American Type Culture Collection CAM Cell Adhesion Molecule CYP Cytochrome P450 CBR1 Carbonyl reductase 1 CRPC Castration resistant prostate cancer Ct-value Cycle threshold-value DHRS7 (B/C) Dehydrogenase/Reductase Short Chain Dehydrogenase Family Member 7 (B/C) DHEA Dehydroepiandrosterone DHP Dehydroprogesterone DHT 5α-Dihydrotestosterone DMEM Dulbecco's Modified Eagle's Medium DMSO Dimethyl Sulfoxide DTT Dithiothreitol E1 Estrone E2 Estradiol ECM Extracellular Membrane EDTA Ethylenediaminetetraacetic acid EMT Epithelial-mesenchymal transition ER Endoplasmic Reticulum ERα/β Estrogen Receptor α/β FBS Fetal Bovine Serum 3 FDR False discovery rate FGF Fibroblast growth factor HEPES 4-(2-Hydroxyethyl)-1-Piperazineethanesulfonic Acid HMDB Human Metabolome Database HPLC High Performance Liquid Chromatography HSD Hydroxysteroid Dehydrogenase IC50 Half-Maximal Inhibitory Concentration LNCaP Lymph node carcinoma of the prostate mRNA Messenger Ribonucleic Acid n.d. -
Enzyme Promiscuity Prediction Using Hierarchy-Informed Multi-Label Classification Gian Marco Visani1, Michael C
Bioinformatics doi: 10.1093/bioinformatics/xxxxx Advance Access Publication Date: 22 Jan 2021 Manuscript Category Systems Biology Enzyme promiscuity prediction using hierarchy-informed multi-label classification Gian Marco Visani1, Michael C. Hughes1 and Soha Hassoun1,2,* 1Department of Computer Science, Tufts University, 161 College Ave, Medford, MA, 02155, USA, 2Department of Chemical and Biological Engineering, Tufts University, 4 Colby St, Medford, MA, 02155, USA *To whom correspondence should be addressed. Associate Editor: XXXXXXX Received on XXXXX; revised on XXXXX; accepted on XXXXX Abstract Motivation: As experimental efforts are costly and time consuming, computational characterization of enzyme capabilities is an attractive alternative. We present and evaluate several machine-learning models to predict which of 983 distinct enzymes, as defined via the Enzyme Commission (EC) numbers, are likely to interact with a given query molecule. Our data consists of enzyme-substrate interactions from the BRENDA database. Some interactions are attributed to natural selection and involve the enzyme’s natural substrates. The majority of the interactions however involve non-natural substrates, thus reflecting promiscuous enzymatic activities. Results: We frame this “enzyme promiscuity prediction” problem as a multi-label classification task. We maximally utilize inhibitor and unlabelled data to train prediction models that can take advantage of known hierarchical relationships between enzyme classes. We report that a hierarchical multi-label neural network, EPP-HMCNF, is the best model for solving this problem, outperforming k-nearest neighbours similarity-based and other machine learning models. We show that inhibitor information during training consistently improves predictive power, particularly for EPP-HMCNF. We also show that all promiscuity prediction models perform worse under a realistic data split when compared to a random data split, and when evaluating performance on non-natural substrates compared to natural substrates. -
Biosynthesis of New Alpha-Bisabolol Derivatives Through a Synthetic Biology Approach Arthur Sarrade-Loucheur
Biosynthesis of new alpha-bisabolol derivatives through a synthetic biology approach Arthur Sarrade-Loucheur To cite this version: Arthur Sarrade-Loucheur. Biosynthesis of new alpha-bisabolol derivatives through a synthetic biology approach. Biochemistry, Molecular Biology. INSA de Toulouse, 2020. English. NNT : 2020ISAT0003. tel-02976811 HAL Id: tel-02976811 https://tel.archives-ouvertes.fr/tel-02976811 Submitted on 23 Oct 2020 HAL is a multi-disciplinary open access L’archive ouverte pluridisciplinaire HAL, est archive for the deposit and dissemination of sci- destinée au dépôt et à la diffusion de documents entific research documents, whether they are pub- scientifiques de niveau recherche, publiés ou non, lished or not. The documents may come from émanant des établissements d’enseignement et de teaching and research institutions in France or recherche français ou étrangers, des laboratoires abroad, or from public or private research centers. publics ou privés. THÈSE En vue de l’obtention du DOCTORAT DE L’UNIVERSITÉ DE TOULOUSE Délivré par l'Institut National des Sciences Appliquées de Toulouse Présentée et soutenue par Arthur SARRADE-LOUCHEUR Le 30 juin 2020 Biosynthèse de nouveaux dérivés de l'α-bisabolol par une approche de biologie synthèse Ecole doctorale : SEVAB - Sciences Ecologiques, Vétérinaires, Agronomiques et Bioingenieries Spécialité : Ingénieries microbienne et enzymatique Unité de recherche : TBI - Toulouse Biotechnology Institute, Bio & Chemical Engineering Thèse dirigée par Gilles TRUAN et Magali REMAUD-SIMEON Jury -
Mechanistic Studies of Biomimetic Reactions by Synthetic Enzyme Mimics by William Michael Hart-Cooper a Dissertation Submitted I
Mechanistic Studies of Biomimetic Reactions by Synthetic Enzyme Mimics By William Michael Hart-Cooper A dissertation submitted in partial satisfaction of the requirements for the degree of Doctor of Philosophy in Chemistry in the Graduate Division of the University of California, Berkeley Committee in charge: Professor Kenneth N. Raymond, Co-chair Professor Robert G. Bergman, Co-chair Professor Alexander Katz Summer 2015 Abstract Mechanistic Studies of Biomimetic Reactions by Synthetic Enzyme Mimics By William Michael Hart-Cooper Doctor of Philosophy in Chemistry University of California, Berkeley Professor Kenneth N. Raymond, Co-chair Professor Robert G. Bergman, Co-chair Chapter 1. A brief introduction to common synthetic host structures and justification for the work described herein is provided. Chapter 2. The development of 1 and related hosts as a new class terpene synthase mimics that catalyze intramolecular Prins cyclizations. The property of water exclusion is observed. Host 1 is also shown to compensate for the gem-disubstituent effect. Chapter 3. The development of new terephthalamide hosts enabled an investigation of the effect of host structure on the enantio- and diastereoselectivity of these reactions, as well as a simple kinetic analysis. Rate accelerations and turnover numbers are notably high. Chapter 4. The mechanism of proton transfer in an archetypal enzyme mimic is studied using amide hydrogen deuterium exchange (HDX) kinetics. Collectively, these data shed light on the role of acid, base and water-mediated proton transfer in a synthetic active site with relevance to proton-mediated catalysis. Moreover, the emergent mechanism of solvent-occupied proton transfer raises the prospect of designable hosts with properties that are unique to the integration of their parts Chapter 5. -
Proton Affinity Studies of Nickel N2S2 Complexes and Control of Aggregation
JBIC Journal of Biological Inorganic Chemistry https://doi.org/10.1007/s00775-019-01671-4 ORIGINAL PAPER Proton afnity studies of nickel N2S2 complexes and control of aggregation Nicholas A. Arnet1 · Nattamai Bhuvanesh1 · Marcetta Y. Darensbourg1 Received: 1 April 2019 / Accepted: 22 May 2019 © Society for Biological Inorganic Chemistry (SBIC) 2019 Abstract The thiolate ligands of [NiFe]-H2ase enzymes have been implicated as proton-binding sites for the reduction/oxidation of + H /H2. This study examines the ligand efect on reactivity of NiN2S2 complexes with an array of acids in methanol solu- tion. UV–Vis absorption spectroscopy is utilized to observe the transformation from the monomeric species to a trimetallic complex that is formed after proton-induced ligand dissociation. Nickel complexes with a fexible (propyl and ethyl) N to N linker were found to readily form the trimetallic complex with acids as weak as ammonium (pKa = 10.9 in methanol). A more constrained nickel complex with a diazacycloheptane N to N linker required stronger acids such as 2,2-dichloroacetic + acid (pKa = 6.38 in methanol) to form the trimetallic complex and featured the formation of an NiN 2S2H complex with acetic acid (pK a = 9.63 in methanol). The most strained ligand, which featured a diazacyclohexane backbone, readily disso- ciated from the nickel center upon mixture with acids with pKa ≤ 9.63 and showed no evidence of a trimetallic species with any acid. This research highlights the dramatic diferences in reactivity with proton sources that can be imparted by minor alterations to ligand geometry and strain. Graphical abstract Electronic supplementary material The online version of this article (https ://doi.org/10.1007/s0077 5-019-01671 -4) contains supplementary material, which is available to authorized users. -
Enzyme Promiscuity of Carbohydrate Active Enzymes and Their Applications in Biocatalysis Pallister E, Gray CJ and Flitsch SL
Enzyme Promiscuity of Carbohydrate Active Enzymes and their applications in Biocatalysis Pallister E, Gray CJ and Flitsch SL School of Chemistry & Manchester Institute of Biotechnology, The University of Manchester, 131 Princess Street, Manchester M1 7DN, UK Corresponding Author: Sabine Flitsch ([email protected]) Abstract The application of biocatalysis for the synthesis of glycans and glycoconjugates is a well-established and successful strategy, both for small and large scale synthesis. Compared to chemical synthesis, is has the advantage of high selectivity, but biocatalysis had been largely limited to natural glycans both in terms of reactivity and substrates. This review describes recent advances in exploiting enzyme promiscuity to expand the range of substrates and reactions that carbohydrate active enzymes (CAZymes) can catalyse. The main focus is on formation and hydrolysis of glycosidic linkages, including sugar kinases, reactions that are central to glycobiotechnology. In addition, biocatalysts that generate sugar analogues and modify carbohydrates, such as oxidases, transaminases and acylases are reviewed. As carbohydrate active enzymes become more accessible and protein engineering strategies become faster, the application of biocatalysis in the generation of a wide range of glycoconjugates, beyond natural structures is expected to expand. Introduction Carbohydrate active enzymes (CAZymes) are responsible for the biosynthesis and metabolism of all sugars and in Nature they often have to be highly selective in a biochemically complex environment. However, as observed with other enzymes1,2, CAZymes do display ‘promiscuity’, a term that describes the capability of catalysing non-physiological secondary reactions. With the advent of high-throughput screening approaches, many examples of enzyme promiscuity have been identified and discussed in the context of evolution. -
Investigation of Nitrous Oxide
INVESTIGATION OF NITROUS OXIDE BIOSYNTHESIS BY A BACTERIAL NITRIC OXIDE REDUCTASE (NOR) AND AN ENGINEERED NOR MIMIC USING STABLE ISOTOPE RATIO MASS SPECTROMETRY By Clarisse Marie Finders A THESIS Submitted to Michigan State University in partial fulfillment of the requirements for the degree of Biochemistry and Molecular Biology—Master of Science 2018 ABSTRACT INVESTIGATION OF NITROUS OXIDE BIOSYNTHESIS BY A BACTERIAL NITRIC OXIDE REDUCTASE (NOR) AND AN ENGINEERED NOR MIMIC USING STABLE ISOTOPE RATIO MASS SPECTROMETRY By Clarisse Marie Finders While carbon dioxide (CO2) is the most prevalent greenhouse gas, nitrous oxide (N2O) is far more potent, with a global warming potential ~265 times greater than that of carbon dioxide over 1 a 100-year period. Additionally, N2O is capable of destroying ozone, making it doubly concerning as a greenhouse gas. Approximately half of the N2O produced yearly is from anthropogenic sources. The largest contributor to anthropogenic N2O is the over-fertilization of agricultural soils, which fuels a host of microbial nitrogen cycling processes that produce N2O. One of these processes is denitrification, and N2O is known to be an obligate intermediate in this process. In denitrification, N2O is synthesized by an enzyme known as nitric oxide reductase (NOR). A thorough understanding of the enzymatic mechanisms by which N2O is produced is essential to mitigating anthropogenic N2O emissions. To this end, this thesis contains the examination of N2O produced by a bacterial cytochrome c NOR (cNOR) from Paracoccus dentrificans and a cNOR mimic, I107EFeBMb, using stable isotope ratio mass spectrometry (IRMS). The first chapter provides the reader with an introduction to the nitrogen cycle, the known NORs, and the basics of isotope theory. -
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by Submitted in partial satisfaction of the requirements for degree of in in the GRADUATE DIVISION of the UNIVERSITY OF CALIFORNIA, SAN FRANCISCO Approved: ______________________________________________________________________________ Chair ______________________________________________________________________________ ______________________________________________________________________________ ______________________________________________________________________________ ______________________________________________________________________________ Committee Members Copyright 2019 by Adolfo Cuesta ii Acknowledgements For me, completing a doctoral dissertation was a huge undertaking that was only possible with the support of many people along the way. First, I would like to thank my PhD advisor, Jack Taunton. He always gave me the space to pursue my own ideas and interests, while providing thoughtful guidance. Nearly every aspect of this project required a technique that was completely new to me. He trusted that I was up to the challenge, supported me throughout, helped me find outside resources when necessary. I remain impressed with his voracious appetite for the literature, and ability to recall some of the most subtle, yet most important details in a paper. Most of all, I am thankful that Jack has always been so generous with his time, both in person, and remotely. I’ve enjoyed our many conversations and hope that they will continue. I’d also like to thank my thesis committee, Kevan Shokat and David Agard for their valuable support, insight, and encouragement throughout this project. My lab mates in the Taunton lab made this such a pleasant experience, even on the days when things weren’t working well. I worked very closely with Tangpo Yang on the mass spectrometry aspects of this project. Xiaobo Wan taught me almost everything I know about protein crystallography. Thank you as well to Geoff Smith, Jordan Carelli, Pat Sharp, Yazmin Carassco, Keely Oltion, Nicole Wenzell, Haoyuan Wang, Steve Sethofer, and Shyam Krishnan, Shawn Ouyang and Qian Zhao. -
Published Version
This is an open access article published under a Creative Commons Non-Commercial No Derivative Works (CC-BY-NC-ND) Attribution License, which permits copying and redistribution of the article, and creation of adaptations, all for non-commercial purposes. Research Article Cite This: ACS Catal. 2018, 8, 11648−11656 pubs.acs.org/acscatalysis Side-Chain Pruning Has Limited Impact on Substrate Preference in a Promiscuous Enzyme Maximilian J. L. J. Fürst,† Elvira Romero,† J. Rubeń Gomeź Castellanos,‡ Marco W. Fraaije,*,† and Andrea Mattevi*,‡ † Molecular Enzymology Group, University of Groningen, Nijenborgh 4, 9747AG, Groningen, The Netherlands ‡ Department of Biology and Biotechnology, University of Pavia, Via Ferrata 1, 27100, Pavia, Italy *S Supporting Information ABSTRACT: Detoxifying enzymes such as flavin-containing monoox- ygenases deal with a huge array of highly diverse xenobiotics and toxic compounds. In addition to being of high physiological relevance, these drug-metabolizing enzymes are useful catalysts for synthetic chemistry. Despite the wealth of studies, the molecular basis of their relaxed substrate selectivity remains an open question. Here, we addressed this issue by applying a cumulative alanine mutagenesis approach to cyclohexanone monooxygenase from Thermocrispum municipale,aflavin-dependent Baeyer−Villiger monooxygenase which we chose as a model system because of its pronounced thermostability and substrate promiscuity. Simultaneous removal of up to eight noncatalytic active-site side chains including four phenylalanines had no effect on protein folding, thermo- stability, and cofactor loading. We observed a linear decrease in activity, rather than a selectivity switch, and attributed this to a less efficient catalytic environment in the enlarged active-site space. Time-resolved kinetic studies confirmed this interpretation.