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Quantum Chemical Cluster Modeling of Enzymatic Reactions Rong-Zhen
Quantum Chemical Cluster Modeling of Enzymatic Reactions Rong-Zhen Liao 1 Rong-Zhen Liao, Stockholm, 2010 ISBN 978-91-7447-129-8 Printed in Sweden by US-AB, Stockholm 2010 Distributor: Department of Organic Chemistry, Stockholm University 2 3 4 Abstract The Quantum chemical cluster approach has been shown to be quite powerful and efficient in the modeling of enzyme active sites and reaction mechanisms. In this thesis, the reaction mechanisms of several enzymes have been investigated using the hybrid density functional B3LYP. The enzymes studied include four dinuclear zinc enzymes, namely dihydroorotase, N-acyl-homoserine lactone hydrolase, RNase Z, and human renal dipeptidase, two trinuclear zinc enzymes, namely phospholipase C and nuclease P1, two tungstoenzymes, namely formaldehyde ferredoxin oxidoreductase and acetylene hydratase, aspartate α-decarboxylase, and mycolic acid cyclopropane synthase. The potential energy profiles for various mechanistic scenarios have been calculated and analyzed. The role of the metal ions as well as important active site residues has been discussed. In the cluster approach, the effects of the parts of the enzyme that are not explicitly included in the model are taken into account using implicit solvation methods. With aspartate α-decarboxylase as an example, systematic evaluation of the solvation effects with the increase of the model size has been performed. At a model size of 150-200 atoms, the solvation effects almost vanish and the choice of the dielectric constant becomes rather insignificant. For all six zinc-dependent enzymes studied, the di-zinc bridging hydroxide has been shown to be capable of performing nucleophilic attack on the substrate. In addition, one, two, or even all three zinc ions participate in the stabilization of the negative charge in the transition states and intermediates, thereby lowering the barriers. -
Supplemental Methods
Supplemental Methods: Sample Collection Duplicate surface samples were collected from the Amazon River plume aboard the R/V Knorr in June 2010 (4 52.71’N, 51 21.59’W) during a period of high river discharge. The collection site (Station 10, 4° 52.71’N, 51° 21.59’W; S = 21.0; T = 29.6°C), located ~ 500 Km to the north of the Amazon River mouth, was characterized by the presence of coastal diatoms in the top 8 m of the water column. Sampling was conducted between 0700 and 0900 local time by gently impeller pumping (modified Rule 1800 submersible sump pump) surface water through 10 m of tygon tubing (3 cm) to the ship's deck where it then flowed through a 156 µm mesh into 20 L carboys. In the lab, cells were partitioned into two size fractions by sequential filtration (using a Masterflex peristaltic pump) of the pre-filtered seawater through a 2.0 µm pore-size, 142 mm diameter polycarbonate (PCTE) membrane filter (Sterlitech Corporation, Kent, CWA) and a 0.22 µm pore-size, 142 mm diameter Supor membrane filter (Pall, Port Washington, NY). Metagenomic and non-selective metatranscriptomic analyses were conducted on both pore-size filters; poly(A)-selected (eukaryote-dominated) metatranscriptomic analyses were conducted only on the larger pore-size filter (2.0 µm pore-size). All filters were immediately submerged in RNAlater (Applied Biosystems, Austin, TX) in sterile 50 mL conical tubes, incubated at room temperature overnight and then stored at -80oC until extraction. Filtration and stabilization of each sample was completed within 30 min of water collection. -
Rhodococcus Erythropolis Oleate Hydratase: a New Member in the Oleate Hydratase Family Tree – Biochemical and Structural Studies
Technische Universität München Fakultät für Chemie Werner Siemens-Lehrstuhl für Synthetische Biotechnologie Enzymatic functionalization of bio based fatty acids and algae based triglycerides Jan Lorenzen Vollständiger Abdruck der von der Fakultät für Chemie der Technischen Universität München zur Erlangung des akademischen Grades eines Doktors der Naturwissenschaften (Dr. rer. nat.) genehmigten Dissertation. Vorsitzender Prof. Dr. Tom Nilges Prüfer der Dissertation 1. Prof. Dr. Thomas Brück 2. Prof. Dr. Wolfgang Eisenreich 3. Prof. Dr. Uwe Bornscheuer (schriftliche Beurteilung) Prof. Dr. Thomas Fässler (mündliche Prüfung) Die Dissertation wurde am 26.09.2019 bei der Technischen Universität München eingereicht und durch die Fakultät für Chemie am 19.11.2019 angenommen. Abstracts I Abstracts Chapter I In the first chapter, the optimization of the SCCO2 extraction of microalgae derived biomass in an industrially relevant pilot plant that adheres to ATEX standards was reported for the first time. The SCCO2 extraction procedure of the lipid containing biomass of the microalgae strains Scenedesmus obliquus and Scenedesmus obtusiusculus was optimized with batch sizes of up to 1,3 kg of dried biomass. Under optimal conditions lipid recovery up to 92% w/w of the total lipids fraction could be achieved. Moreover, we addressed the purification of crude microalgae lipid extracts obtained by the SCCO2 extraction procedure. We could identify high amounts of hydrophobic contaminants (e.g. chlorophylls or carotenoids) in the crude lipid extract, which we could effectively remove by the application of the standard mineral adsorber bentonite. The obtained, clean microalgae oil can directly be further processed to lubricants, cosmetics or nutraceutical products. This is the first time that a combined SCCO2 extraction and purification process for algae lipids has been developed that could be integrated into existing industrial processes. -
Production of L-Carnitine by Secondary Metabolism of Bacteria Vicente Bernal, Ángel Sevilla, Manuel Cánovas and José L Iborra*
Microbial Cell Factories BioMed Central Review Open Access Production of L-carnitine by secondary metabolism of bacteria Vicente Bernal, Ángel Sevilla, Manuel Cánovas and José L Iborra* Address: Department of Biochemistry and Molecular Biology B and Immunology, Campus of Espinardo, University of Murcia, E-30100, Spain Email: Vicente Bernal - [email protected]; Ángel Sevilla - [email protected]; Manuel Cánovas - [email protected]; José L Iborra* - [email protected] * Corresponding author Published: 2 October 2007 Received: 19 July 2007 Accepted: 2 October 2007 Microbial Cell Factories 2007, 6:31 doi:10.1186/1475-2859-6-31 This article is available from: http://www.microbialcellfactories.com/content/6/1/31 © 2007 Bernal et al; licensee BioMed Central Ltd. This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/2.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. Abstract The increasing commercial demand for L-carnitine has led to a multiplication of efforts to improve its production with bacteria. The use of different cell environments, such as growing, resting, permeabilized, dried, osmotically stressed, freely suspended and immobilized cells, to maintain enzymes sufficiently active for L-carnitine production is discussed in the text. The different cell states of enterobacteria, such as Escherichia coli and Proteus sp., which can be used to produce L- carnitine from crotonobetaine or D-carnitine as substrate, are analyzed. Moreover, the combined application of both bioprocess and metabolic engineering has allowed a deeper understanding of the main factors controlling the production process, such as energy depletion and the alteration of the acetyl-CoA/CoA ratio which are coupled to the end of the biotransformation. -
The Microbiota-Produced N-Formyl Peptide Fmlf Promotes Obesity-Induced Glucose
Page 1 of 230 Diabetes Title: The microbiota-produced N-formyl peptide fMLF promotes obesity-induced glucose intolerance Joshua Wollam1, Matthew Riopel1, Yong-Jiang Xu1,2, Andrew M. F. Johnson1, Jachelle M. Ofrecio1, Wei Ying1, Dalila El Ouarrat1, Luisa S. Chan3, Andrew W. Han3, Nadir A. Mahmood3, Caitlin N. Ryan3, Yun Sok Lee1, Jeramie D. Watrous1,2, Mahendra D. Chordia4, Dongfeng Pan4, Mohit Jain1,2, Jerrold M. Olefsky1 * Affiliations: 1 Division of Endocrinology & Metabolism, Department of Medicine, University of California, San Diego, La Jolla, California, USA. 2 Department of Pharmacology, University of California, San Diego, La Jolla, California, USA. 3 Second Genome, Inc., South San Francisco, California, USA. 4 Department of Radiology and Medical Imaging, University of Virginia, Charlottesville, VA, USA. * Correspondence to: 858-534-2230, [email protected] Word Count: 4749 Figures: 6 Supplemental Figures: 11 Supplemental Tables: 5 1 Diabetes Publish Ahead of Print, published online April 22, 2019 Diabetes Page 2 of 230 ABSTRACT The composition of the gastrointestinal (GI) microbiota and associated metabolites changes dramatically with diet and the development of obesity. Although many correlations have been described, specific mechanistic links between these changes and glucose homeostasis remain to be defined. Here we show that blood and intestinal levels of the microbiota-produced N-formyl peptide, formyl-methionyl-leucyl-phenylalanine (fMLF), are elevated in high fat diet (HFD)- induced obese mice. Genetic or pharmacological inhibition of the N-formyl peptide receptor Fpr1 leads to increased insulin levels and improved glucose tolerance, dependent upon glucagon- like peptide-1 (GLP-1). Obese Fpr1-knockout (Fpr1-KO) mice also display an altered microbiome, exemplifying the dynamic relationship between host metabolism and microbiota. -
UNIVERSITY of EMBU EDWARD NDERITU KARANJA Phd 2020
UNIVERSITY OF EMBU EDWARD NDERITU KARANJA PhD 2020 MICROBIAL COMMUNITY DIVERSITY AND STRUCTURE WITHIN ORGANIC AND CONVENTIONAL FARMING SYSTEMS IN CENTRAL HIGHLANDS OF KENYA EDWARD NDERITU KARANJA (MSc) A THESIS SUBMITTED IN PARTIAL FULFILLMENT FOR THE DEGREE OF DOCTOR OF PHILOSOPHY IN APPLIED MICROBIOLOGY IN THE UNIVERSITY OF EMBU NOVEMBER, 2020 DECLARATION This thesis is my original work and has not been presented for a degree in any other University Signature……………………………. Date………….……….. Edward Nderitu Karanja Department of Biological Science B801/147/2015 This thesis has been submitted for examination with our approval as the University Supervisors Signature……………………………. Date………….………. Prof. Romano Mwirichia Department of Biological science University of Embu (UoEm), Kenya Signature………. …………………………. Date………….…………. Dr. Andreas Fliessbach Department of Soil Science Research Institute of Organic Agriculture - FIBL, Switzerland i DEDICATION I dedicated to my family; my wife Anne Kelly Kambura, my children; Shawn Karanja, Melissa Wangithi, Joseph Munyuithia, Shayne Koome and Ann Wanjiku, my parents; Mr. Samuel Karanja and Mrs. Agnes Wangithi, my siblings, Ruth Wairimu, Juliet Muthoni, Alex Ngochi, James Karuma and Nelly Njoki. I appreciate the support you have accorded me during my studies. Your inspiration and backing in this journey made it easier to manage all challenges encountered. ii ACKNOWLEDGEMENT I express gratitude toward Almighty God for his mercies from the beginning of this long and thought-provoking journey. This was conducted in the framework of long-term systems comparison program, with financial support from Biovision Foundation, Coop Sustainability Fund, Liechtenstein Development Service (LED) and the Swiss Agency for Development and Cooperation (SDC). I acknowledge icipe core funding for the kind contribution provided by UK-Aid from UK Government, Swedish International Development Cooperation Agency, Swiss Agency for Development and Cooperation, Federal Democratic Republic of Ethiopia and the Kenyan Government. -
(12) Patent Application Publication (10) Pub. No.: US 2015/0037860 A1 B0tes Et Al
US 2015 0037860A1 (19) United States (12) Patent Application Publication (10) Pub. No.: US 2015/0037860 A1 B0tes et al. (43) Pub. Date: Feb. 5, 2015 (54) METHODS FOR BOSYNTHESIS OF Publication Classification ISOPRENE (51) Int. C. (71) Applicant: INVISTA North America S.ár.l., CI2P 5/00 (2006.01) Wilmington, DE (US) CI2N 15/70 (2006.01) (52) U.S. C. (72) Inventors: Adriana Leonora Botes, Rosedale East CPC ................. CI2P5/007 (2013.01); C12N 15/70 (GB); Alex Van Eck Conradie, (2013.01) Eaglescliffe (GB) USPC ................... 435/167; 435/252.33: 435/252.3: 435/252.32; 435/252.34; 435/252.31; (21) Appl. No.: 14/452,201 435/254.3; 435/254.21: 435/254.23; 435/254.2: 435/254.11: 435/254.22 (22) Filed: Aug. 5, 2014 (57) ABSTRACT This document describes biochemical pathways for produc ing isoprene by forming two vinyl groups in a central precur Related U.S. Application Data sor produced from isobutyryl-CoA, 3-methyl-2-oxopen (60) Provisional application No. 61/862,401, filed on Aug. tanoate, or 4-methyl-2-oxopentanoate as well as recombinant 5, 2013. hosts for producing isoprene. Patent Application Publication Feb. 5, 2015 Sheet 1 of 19 US 2015/0037860 A1 FIGURE 1. O O CoA Acetyl-CoA --sca {YN 1 -sc.AO Acetoacetyl-CoA EC 2.3.1.9 Acetyl-CoA Acetyl-CoA t HO -->Cs.O OH Q CoA 3-Hydroxy 3-methylglutaryl-CoA gy 2.H a. CoA Co a 2NAD(P)* Jyu HO OH (R)-mevalonate t ATP c N N e d ADP O HO o–F–o OH (R)-5-phosphomevalonate t ATP c N s na No ADP JyuO HO O-P-O-P-OH OH OH (R)-5-Diphosphomevalonate t ATP c a g ADP PP CO2 N-1 -- P-O-P-OH HEos3.32 -- . -
Fermentation of Acetylene by an Obligate Anaerobe, Pelobacter Acetylenicus Sp
Archives of Arch Microbiol (1985) 142: 295- 301 Microbiology Springer-Verlag 1985 Fermentation of acetylene by an obligate anaerobe, Pelobacter acetylenicus sp. nov. * Bernhard Schink Fakult/it ffir Biologie, Universit/it Konstanz, Postfach 5560, D-7750 Konstanz, Federal Republic of Germany Abstract. Four strains of strictly anaerobic Gram-negative tion reactions (Schink 1985a). No significant anaerobic rod-shaped non-sporeforming bacteria were enriched and degradation could be observed with ethylene (ethene), the isolated from marine and freshwater sediments with acety- most simple unsaturated hydrocarbon (Schink 1985 a, b). lene (ethine) as sole source of carbon and energy. Acetylene, It was reported recently that also acetylene can be metab- acetoin, ethanolamine, choline, 1,2-propanediol, and glyc- olized in the absence of molecular oxygen (Watanabe and erol were the only substrates utilized for growth, the latter de Guzman 1980). Enrichment cultures with acetylene as two only in the presence of small amounts of acetate. Sub- sole carbon source were obtained in mineral media with strates were fermented by disproportionation to acetate and sulfate as electron acceptor, and acetate could be identified ethanol or the respective higher acids and alcohols. No as an intermediary metabolite (Culbertson et al. 1981). How- cytochromes were detectable; the guanine plus cytosine ever, these enrichment cultures were difficult to maintain, content of the DNA was 57.1 _+ 0.2 tool%. Alcohol dehy- and the acetylene-degrading bacteria could not be identified drogenase, aldehyde dehydrogenase, phosphate acetyl- (C. W. Culbertson and R. S. Oremland, Abstr. 3rd Int. transferase, and acetate kinase were found in high activities Syrup. -
ATP-Dependent Substrate Reduction at an [Fe8s9] Double-Cubane Cluster
ATP-dependent substrate reduction at an [Fe8S9] double-cubane cluster Jae-Hun Jeounga and Holger Dobbeka,1 aInstitut für Biologie, Strukturbiologie/Biochemie, Humboldt-Universität zu Berlin, D-10099 Berlin, Germany Edited by Amy C. Rosenzweig, Northwestern University, Evanston, IL, and approved February 2, 2018 (received for review November 23, 2017) Chemically demanding reductive conversions in biology, such as the We have characterized the two components of a widespread reduction of dinitrogen to ammonia or the Birch-type reduction of system of the third type and find that the electron-accepting – aromatic compounds, depend on Fe/S-cluster containing ATPases. component features a double-cubane [Fe8S9]-cluster. This [Fe8S9]- These reductions are typically catalyzed by two-component systems, cluster, so far unknown to biology, catalyzes reductive reactions in which an Fe/S-cluster–containing ATPase energizes an electron to otherwise associated only with the complex iron–sulfur clusters reduce a metal site on the acceptor protein that drives the reductive of nitrogenases. Our results reveal several parallels between the reaction. Here, we show a two-component system featuring a double-cubane cluster-containing enzymes and nitrogenases μ double-cubane [Fe8S9]-cluster [{Fe4S4(SCys)3}2( 2-S)]. The double- and suggest that an unexplored biochemical reactivity space cubane–cluster-containing enzyme is capable of reducing small mol- may be hidden among the diverse ATP-dependent two-component − ecules, such as acetylene (C2H2), azide (N3 ), and hydrazine (N2H4). enzymes. We thus present a class of metalloenzymes akin in fold, metal clus- ters, and reactivity to nitrogenases. Results Distribution of Double-Cubane Cluster Protein-Like Proteins. -
Substratstereochemie Und Untersuchungen Zum Mechanismus Der 4-Hydroxybutyryl-Coa-Dehydratase Aus Clostridium Aminobutyricum
Substratstereochemie und Untersuchungen zum Mechanismus der 4-Hydroxybutyryl-CoA-Dehydratase aus Clostridium aminobutyricum Dissertation zur Erlangung des Doktorgrades der Naturwissenschaften (Dr. rer. nat.) dem Fachbereich Biologie der Philipps-Universität Marburg vorgelegt von Peter Friedrich aus Marburg/Lahn Marburg/Lahn 2008 Die Untersuchungen zur vorliegenden Arbeit wurden von November 2003 bis November 2008 am Fachbereich Biologie der Philipps-Universität Marburg unter der Leitung von Herrn Prof. Dr. W. Buckel durchgeführt. Vom Fachbereich Biologie der Philipps-Universität Marburg als Dissertation am angenommen. Erstgutachter: Prof. Dr. W. Buckel Zweitgutachter: Prof. Dr. R. Thauer Tag der mündlichen Prüfung: 18.12.2008 für meine Familie für Christine Die Ergebnisse dieser Dissertation sind in folgenden Publikationen veröffentlicht: Friedrich P, Darley DJ, Golding BT, Buckel W (2008) The complete stereochemistry of the enzymatic dehydration of 4-hydroxybutyryl coenzyme A to crotonyl coenzyme A. Angew. Chem. Int. Ed. Engl. 47:3254-3257. Der stereochemische Verlauf der enzymatischen Wassereliminierung von 4-Hydroxybutyryl-Coenzym A zu Crotonyl- Coenzym A. Angew. Chem. 120:3298-3301 Martins BM, Messerschmidt A, Friedrich P, Zhang J, Buckel W (2007) 4-Hydroxybutyryl- CoA dehydratase. In: Messerschmidt A (ed) Handbook of Metalloproteins Online Edition. John Wiley & Sons Ltd., Sussex, UK. Publisched online Dez 2007 weitere Veröffentlichungen: Scott R, Näser U, Friedrich P, Selmer T, Buckel W, Golding BT (2004) Stereochemistry of hydrogen -
Supplementary Table S1. the Key Enzymes for Autotrophic Growth in C
Electronic Supplementary Material (ESI) for Metallomics. This journal is © The Royal Society of Chemistry 2015 Supplementary Table S1. The key enzymes for autotrophic growth in C. metallidurans Name Rmet-number Spec. Predicted Mass, (kDa) Determined Mass, (kDa) Activity HOS Rmet_1522 to Rmet_1525 28.7 65.2, 25.4, 23.4, 52.8 = 166.8 62.4±1.8, 26.4±1.3, 24.0±0.6, 54.1±2.5, =235±20a HOP Rmet_1297, Rmet_1298, 67.0 69.0 + 38.6 = 108 148±24a CAX Rmet_1500, Rmet_1501 2.82 8 * (13.6 + 52.5) = 529 475±36a PRK Rmet_1512 0.994 8 * 32.4 = 259 256±11a aMean value of masses determined by S300 size exclusion chromatography and sucrose gradient centrifugation. HOS, NAD-reducing soluble hydrogenase; HOP, membrane-bound hydrogenase; CAX, ribulose-bis-phosphate carboxylase/oxygenase; PRK, phosphoribulokinase. Specific activity in U/mg protein. Supplementary Table S2. Genes expressed differently in AE104 compared to CH34 wild typea Operon Region Name Gene Q D Description UP Op1321r Rmet_4594 zntA 1.72 2.88 Q1LEH0 Heavy metal translocating P -type ATPase Op1322f Rmet_4595 czcI2 2.03 2.92 Q1LEG9 Putative uncharacterized protein Op1322f Rmet_4596 czcC2 23.34 5.36 Q1LEG8 Outer membrane efflux protein Op1322f Rmet_4597 czcB2' 15.36 9.68 Q1LEG7 Secretion protein HlyD Op0075f Rmet_0260 - 2.31 2.48 Q1LRT0 Putative transmembrane protein Op0075f Rmet_0261 coxB 2.08 2.49 Q1LRS9 Cytochrome c oxidase subunit 2 Adjacent to CMGI-7 Op0335f Rmet_1171 tnpA 7.03 21.74 Q9F8S6 Transposase (Transposase, IS4 family) CMGI-2 Op0362r Rmet_1251 tnp 4.08 0.61 Q1LNY9 Putative uncharacterized -
6.2 Oleate Hydratase
Study Towards Carotenoid 1,2-Hydratase and Oleate Hydratase as Novel Biocatalysts Aida HISENI Study Towards Carotenoid 1,2-Hydratase and Oleate Hydratase as Novel Biocatalysts PROEFSCHRIFT ter verkrijging van de graad van doctor aan de Technische universiteit Delft, op gezag van de Rector Magnificus prof. ir. K.C.A.M Luyben, voorzitter van het College voor promoties, in het openbaar te verdedigen op dinsdag 22 april 2014 om 10:00 uur door Aida HISENI Diplom-Biologin, Heinrich-Heine-Universität Düsseldorf geboren te Doboj, Bosnië en Hercegovina. Dit proefschrift is goedgekeurd door de promotor: Prof. dr. I.W.C.E Arends Samenstelling promotiecommissie: Rector Magnificus voorzitter Prof. dr. I.W.C.E. Arends Technische Universiteit Delft, promotor Prof. dr. U. Hanefeld Technische Universiteit Delft Prof. dr. J.H. de Winde Universiteit Leiden Prof. dr. G. Muijzer Universiteit van Amsterdam Prof. dr. R. Wever Universiteit van Amsterdam Dr. L.G. Otten Technische Universiteit Delft Dr. P. Dominguez De Maria Sustainable Momentum Prof. dr. S. de Vries Technische Universiteit Delft, reservelid This project is financially supported by The Netherlands Ministry of Economic Affairs and the B-Basic partner organizations (http://www.b-basic.nl) through B-Basic, a public- private NWO-ACTS programme [Advanced Chemical Technologies for Sustainability (ACTS)]. ISBN Copyright © 2014 by Aida HISENI All rights reserved. No part of this publication may be reproduced or distributed in any form or by any means, or stored in a database or retrieval system, without any prior permission of the copyright owner. To my father Ismet Nukičić Table of Contents 1 General introduction .................................................................................................