Oxygen Binding, Activation, and Reduction to Water by Copper Proteins

Total Page:16

File Type:pdf, Size:1020Kb

Oxygen Binding, Activation, and Reduction to Water by Copper Proteins REVIEWS Oxygen Binding, Activation, and Reduction to Water by Copper Proteins Edward I. Solomon,* Peng Chen, Markus Metz, Sang-Kyu Lee, and Amy E. Palmer Copper active sites play a major role in spectroscopic features indicative of droxylation, and H-atom abstraction biological and abiological dioxygen new geometric and electronic struc- from different substrates, and the re- activation. Oxygen intermediates have tures involved in oxygen activation. ductive cleavage of the OÀO bond in been studied in detail for the proteins The spectroscopic and quantum-me- the formation water. and enzymes involved in reversible O2 chanical study of these intermediates binding (hemocyanin), activation (ty- has defined geometric-and electronic- Keywords: bioinorganic chemistry ¥ rosinase), and four-electron reduction structure/function correlations, and de- copper ¥ electronic structure ¥ metal- to water (multicopper oxidases). These veloped detailed reaction coordinates loenzymes ¥ oxygen activation ¥ reac- oxygen intermediates exhibit unique for the reversible binding of O2 , hy- tion mechanisms 1. Introduction a thioether bond in galactose oxidase. Both functional groups are generated by the post-translational modification of a Copper, along with iron active sites dominate the field of protein residue by the copper center. In the case of amine [1] biological oxygen chemistry and play important roles in oxidase, this involves hydroxylation of a tyrosine by O2 and homogeneous[2] and heterogeneous catalysis.[3, 4] Copper pro- involves a single copper center in a reaction that to date is not teins are involved in reversible dioxygen binding (hemocya- defined, but may involve tyrosine activation by CuII cen- nin),[5] two-electron reduction to peroxide coupled to oxida- ters.[17, 18] tion of substrates (amine, galactose, and catechol oxidases),[6] Dopamine b-hydroxylase (DbH) and peptidylglycine a- activation for hydroxylation (dopamine b-hydroxylase, pepti- hydroxylating monooxygenase (PHM) have noncoupled bi- dylglycine a-hydroxylating monooxygenase, tyrosinase, and nuclear copper sites,[6] where ™coupling∫ refers to magnetic particulate-methane monooxygenase),[6, 7] and the four-elec- interactions between the copper centers. This absence of tron reduction to water coupled to substrate oxidation coupling indicates that the CuII centers of the resting enzyme (laccase, ascorbate oxidase, ceruloplasmin and Fet3p)[7] or active site are at least 7 ä apart with no bridging ligation, proton pumping (cytochrome c oxidase, which also contains which is consistent with the crystallographic study on pepti- heme ± iron centers).[8] The known copper proteins which are dylglycine a-hydroxylating monooxygenase (Figure 1B).[15, 16] involved in dioxygen binding, activation, and reduction are The enzyme has one copper center (referred to as CuM since it given in Scheme 1, which is organized based on active-site has a methionine ligand[19] ) involved in catalysis which is structural type. Key structural features from the Protein thought to proceed through hydrogen-atom abstraction from DataBank (PDB) are given in Figure 1.[9±16] the substrate (the benzylic hydrogen in DbHorthea-carbon Amine oxidase and galactose oxidase catalyze the two- hydrogen in PHM) by an as-yet unobserved hydroperoxide ± II [6] electron reduction of O2 to peroxide at a single copper center, CuM complex. The second electron to form the hydro- [6] which can provide only one electron. As shown in Figure 1A peroxide is derived from CuH (the copper with all histidine this is accomplished with the aid of an additional redox-active ligands). Since the copper centers are not coupled (i.e. there is functional group, a topa-quinone in amine oxidase and a no bridge) the mechanism of transporting the second electron tyrosine ligand covalently linked to a cysteine residue through to CuM is unclear and has been proposed to involve either a new electron-transfer pathway formed by the substrate [16] [*] Prof. Dr. E. I. Solomon, P. Chen, Dr. M. Metz, Dr. S.-K. Lee, bridging the two distant copper centers or by O2 reduction [20] A. E. Palmer to superoxide at CuH and superoxide channeling to CuM . Department of Chemistry The coupled binuclear copper proteins include hemocya- Stanford University nin, tyrosinase, and catechol oxidase.[5, 7] The binuclear copper Stanford, CA 94305 (USA) Fax : (1)650-725-0259 centers in these proteins are strongly coupled through a E-mail: [email protected] bridging ligand which provides a direct mechanism for the Angew. Chem. Int. Ed. 2001, 40, 4570 ± 4590 ¹ WILEY-VCH Verlag GmbH, D-69451 Weinheim, 2001 1433-7851/01/4024-4571 $ 17.50+.50/0 4571 REVIEWS E. I. Solomon et al. two-electron reduction of dioxygen. In oxy-hemocyanin (Fig- features. These features are indicative of a novel electronic II ure 1C) this bridge is the dioxygen unit which binds reversibly structure for the side-on peroxo ± Cu2 structure which plays a to deoxy-hemocyanin (2CuI) as peroxide in a side-on bridged key role in reactivity (Section 2).[5] The spectral/structural (m-h2:h2) structure.[14, 21] This is the most stable oxygen features of oxy-hemocyanin and related model complexes intermediate in copper proteins and exhibits unique spectral provide the reference for oxygen intermediates in the other E. I. Solomon P. Chen M. Metz A. Palmer S.-K. Lee Edward I. Solomon grew up in North Miami Beach, FL, received hisPh.D. from Princeton University(with Donald S. McClure), and was a postdoctoral fellow at the H. C. Èrsted Institute (with Carl J. Ballhausen) and then at Caltech (with Harry B. Gray). He was a professor at MIT until 1982. He then moved to Stanford University where he is now the Monroe E. Spaght Professor of Humanities and Sciences. His research is in the fields of physical-inorganic and bioinorganic chemistry with emphasis on the application of a wide variety of spectroscopic methods to elucidate the electronic structures of transition metal complexes and their contributions to physical properties and reactivity. He has presented numerous named lectures including the First Glen Seaborg Lectures at the University of California, Berkeley, and has been an invited professor at the Tokyo Institute of Technology, Japan, University of Paris, Orsay, France, Tata Institute, Bombay, India, Xiamen University, China, and La Plata University, Argentina. He is a Fellow of the American Academy of Arts and Sciences and the American Association for the Advancement of Sciences and has received a range of awards including the Ira Remsen Award from the Maryland Section of the American Chemical Society, the G. W. Wheland Medal from the University of Chicago and the ACS National Award in Inorganic Chemistry for 2001. Peng Chen grew up in Jiangsu, China and received his B.S. from Nanjing University in 1997. After spending a year at University of California at San Diego learning organic synthesis with Prof. Yitzhak Tor, he moved to Stanford University where he isthe Gerhard CasperStanford Graduate Fellow working toward hisPh.D. degree in Prof. Edward I. Solomon×s group. His research focuses on electronic-structure studies of biologically related copper sites involved in oxygen activation by using a combination of spectroscopic methods and theoretical calculations. Markus Metz received his Diploma in Chemistry from the Bayerische Julius-Maximilians-Universit‰t W¸rzburg, Germany, and completed his Ph.D. under the supervision of Prof. Peter Hofmann at he the Ruprecht-Karls-Universit‰t, Heidelberg, on theoretical elucidation of organometallic reaction mechanisms. From 1999 to 2001 he was a DAAD postdoctoral fellow with Professor Edward I. Solomon carrying out theoretical studies on oxygen binding to multinuclear copper proteins. He is a computational chemist at AnorMED Inc. designing metal-based therapeutics. Amy Palmer received her B.A. in biophysical chemistry in 1994 from Dartmouth College where she studied the molecular mechanism of chromium carcinogenicity with Professor Karen E. Wetterhahn. In 1995, she moved to Stanford University and joined the group of Professor Edward I. Solomon. Her research involves spectroscopic and kinetic studies aimed at elucidating the mechanism of substrate oxidation and O2 reduction in multicopper enzymes. She is the Franklin Veatch Memorial Fellow at Stanford. Sang-Kyu Lee, a native of Korea, received hisB.S. degree in biochemistryfrom Lehigh Universityin 1989 and hisPh.D. degree in biochemistry from the University of Minnesota, Minneapolis, in 1998. His Ph.D studies with Prof. John D. Lipscomb focused on the enzyme reaction mechanism of methane monooxygenase and led to the discovery of reactive intermediates P and Q. He continued his pursuit of metalloprotein enzymology in his postdoctoral research with Prof. Edward I. Solomon through detailed spectroscopic characterization of key intermediates in the reduction of dioxygen to water by multicopper oxidases. 4572 Angew. Chem. Int. Ed. 2001, 40, 4570 ± 4590 Copper Proteins REVIEWS Scheme 1. Copper proteins involved in oxygen binding and activation. copper enzymes which perform different reactions, and allow geometric-and electronic-structurecorrelations with function in copper chemistry. While a crystal structure is not yet available for tyrosinase, from its spectral features oxy- tyrosinase has a very similar active site to oxy-hemocyanin, II [22] the side-on peroxo ± Cu2 structure. However, in the case of oxy-tyrosinase, the site catalyzes the electrophilic oxygen- ation of phenol to catechol and the two-electron oxidation
Recommended publications
  • Lanosterol 14Α-Demethylase (CYP51)
    463 Lanosterol 14-demethylase (CYP51), NADPH–cytochrome P450 reductase and squalene synthase in spermatogenesis: late spermatids of the rat express proteins needed to synthesize follicular fluid meiosis activating sterol G Majdicˇ, M Parvinen1, A Bellamine2, H J Harwood Jr3, WWKu3, M R Waterman2 and D Rozman4 Veterinary Faculty, Clinic of Reproduction, Cesta v Mestni log 47a, 1000 Ljubljana, Slovenia 1Institute of Biomedicine, Department of Anatomy, University of Turku, Kiinamyllynkatu 10, FIN-20520 Turku, Finland 2Department of Biochemistry, Vanderbilt University School of Medicine, Nashville, Tennessee 37232–0146, USA 3Pfizer Central Research, Department of Metabolic Diseases, Box No. 0438, Eastern Point Road, Groton, Connecticut 06340, USA 4Institute of Biochemistry, Medical Center for Molecular Biology, Medical Faculty University of Ljubljana, Vrazov trg 2, SI-1000 Ljubljana, Slovenia (Requests for offprints should be addressed to D Rozman; Email: [email protected]) (G Majdicˇ is now at Department of Internal Medicine, UT Southwestern Medical Center, Dallas, Texas 75235–8857, USA) Abstract Lanosterol 14-demethylase (CYP51) is a cytochrome detected in step 3–19 spermatids, with large amounts in P450 enzyme involved primarily in cholesterol biosynthe- the cytoplasm/residual bodies of step 19 spermatids, where sis. CYP51 in the presence of NADPH–cytochrome P450 P450 reductase was also observed. Squalene synthase was reductase converts lanosterol to follicular fluid meiosis immunodetected in step 2–15 spermatids of the rat, activating sterol (FF-MAS), an intermediate of cholesterol indicating that squalene synthase and CYP51 proteins are biosynthesis which accumulates in gonads and has an not equally expressed in same stages of spermatogenesis. additional function as oocyte meiosis-activating substance.
    [Show full text]
  • Mrna Vaccine: a Potential Therapeutic Strategy Yang Wang† , Ziqi Zhang† , Jingwen Luo† , Xuejiao Han† , Yuquan Wei and Xiawei Wei*
    Wang et al. Molecular Cancer (2021) 20:33 https://doi.org/10.1186/s12943-021-01311-z REVIEW Open Access mRNA vaccine: a potential therapeutic strategy Yang Wang† , Ziqi Zhang† , Jingwen Luo† , Xuejiao Han† , Yuquan Wei and Xiawei Wei* Abstract mRNA vaccines have tremendous potential to fight against cancer and viral diseases due to superiorities in safety, efficacy and industrial production. In recent decades, we have witnessed the development of different kinds of mRNAs by sequence optimization to overcome the disadvantage of excessive mRNA immunogenicity, instability and inefficiency. Based on the immunological study, mRNA vaccines are coupled with immunologic adjuvant and various delivery strategies. Except for sequence optimization, the assistance of mRNA-delivering strategies is another method to stabilize mRNAs and improve their efficacy. The understanding of increasing the antigen reactiveness gains insight into mRNA-induced innate immunity and adaptive immunity without antibody-dependent enhancement activity. Therefore, to address the problem, scientists further exploited carrier-based mRNA vaccines (lipid-based delivery, polymer-based delivery, peptide-based delivery, virus-like replicon particle and cationic nanoemulsion), naked mRNA vaccines and dendritic cells-based mRNA vaccines. The article will discuss the molecular biology of mRNA vaccines and underlying anti-virus and anti-tumor mechanisms, with an introduction of their immunological phenomena, delivery strategies, their importance on Corona Virus Disease 2019 (COVID-19) and related clinical trials against cancer and viral diseases. Finally, we will discuss the challenge of mRNA vaccines against bacterial and parasitic diseases. Keywords: mRNA vaccine, Self-amplifying RNA, Non-replicating mRNA, Modification, Immunogenicity, Delivery strategy, COVID-19 mRNA vaccine, Clinical trials, Antibody-dependent enhancement, Dendritic cell targeting Introduction scientists are seeking to develop effective cancer vac- A vaccine stimulates the immune response of the body’s cines.
    [Show full text]
  • Characterization of Methylene Diphenyl Diisocyanate Protein Conjugates
    Portland State University PDXScholar Dissertations and Theses Dissertations and Theses Spring 6-5-2014 Characterization of Methylene Diphenyl Diisocyanate Protein Conjugates Morgen Mhike Portland State University Follow this and additional works at: https://pdxscholar.library.pdx.edu/open_access_etds Part of the Allergy and Immunology Commons, and the Chemistry Commons Let us know how access to this document benefits ou.y Recommended Citation Mhike, Morgen, "Characterization of Methylene Diphenyl Diisocyanate Protein Conjugates" (2014). Dissertations and Theses. Paper 1844. https://doi.org/10.15760/etd.1843 This Dissertation is brought to you for free and open access. It has been accepted for inclusion in Dissertations and Theses by an authorized administrator of PDXScholar. Please contact us if we can make this document more accessible: [email protected]. Characterization of Methylene Diphenyl Diisocyanate Protein Conjugates by Morgen Mhike A dissertation submitted in partial fulfillment of the requirements for the degree of Doctor of Philosophy in Chemistry Dissertation Committee: Reuben H. Simoyi, Chair Paul D. Siegel Itai Chipinda Niles Lehman Shankar B. Rananavare Robert Strongin E. Kofi Agorsah Portland State University 2014 © 2014 Morgen Mhike ABSTRACT Diisocyanates (dNCO) such as methylene diphenyl diisocyanate (MDI) are used primarily as cross-linking agents in the production of polyurethane products such as paints, elastomers, coatings and adhesives, and are the most frequently reported cause of chemically induced immunologic sensitization and occupational asthma (OA). Immune mediated hypersensitivity reactions to dNCOs include allergic rhinitis, asthma, hypersensitivity pneumonitis and allergic contact dermatitis. There is currently no simple diagnosis for the identification of dNCO asthma due to the variability of symptoms and uncertainty regarding the underlying mechanisms.
    [Show full text]
  • Cytochrome Oxidase (A3) Heme and Copper Observed by Low- Temperature Fourier Transform Infrared Spectroscopy Ofthe CO Complex (Photolysis/Mitoehondria/Beef Heart) J
    Proc. Natl Acad. Sci. USA Vol. 78, No. 1, pp. 234-237, January 1981 Biochemistry Cytochrome oxidase (a3) heme and copper observed by low- temperature Fourier transform infrared spectroscopy ofthe CO complex (photolysis/mitoehondria/beef heart) J. 0. ALBEN, P. P. MOH, F. G. FIAMINGO, AND R. A. ALTSCHULD Department ofPhysiological Chemistry, The Ohio State University, Columbus, Ohio 43210 Communicated by Hans Frauenfelder, October 10, 1980 ABSTRACT Carbon monoxide bound to iron or copper in sub- chondria is bound reversibly to the a3 copper would appear to strate-reduced mitochondrial cytochrome c oxidase (ferrocyto- explain these results. Here, we extend the observations to lower chrome c:oxygen oxidoreductase, EC 1.9.3.1) from beefheart has beenused toexplore the structural interaction ofthea3 heme-copper temperatures, illustrate the structural differences between pocket at.15 K and 80 K in the dark and in the presence ofvisible heme and copper CO complexes in cytochrome a3, and show light. The vibrational absorptions of CO measured by a Fourier how this may be related to the functional contributions ofthese transform infrared interferometer occur in the dark at 1963 cm-' metal centers. with small absorptions near 1952 cm-', and aredue toa3 heme-CO complexes. These disappear in strong visible light and are re- placed by a major absorption at 2062 cm' and a minor one at 2043 MATERIALS AND METHODS cm' due to CU-CO. Relaxation in the dark is rapid and quantita- tive at 210 K, but becomes negligible below 140 K. The multiple Mitochondria, prepared from fresh beef heart by use of Nagarse absorptions indicate structural heterogeneity of.cytochrome oxi- (8), were kindly donated by G.
    [Show full text]
  • 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.
    [Show full text]
  • Noelia Díaz Blanco
    Effects of environmental factors on the gonadal transcriptome of European sea bass (Dicentrarchus labrax), juvenile growth and sex ratios Noelia Díaz Blanco Ph.D. thesis 2014 Submitted in partial fulfillment of the requirements for the Ph.D. degree from the Universitat Pompeu Fabra (UPF). This work has been carried out at the Group of Biology of Reproduction (GBR), at the Department of Renewable Marine Resources of the Institute of Marine Sciences (ICM-CSIC). Thesis supervisor: Dr. Francesc Piferrer Professor d’Investigació Institut de Ciències del Mar (ICM-CSIC) i ii A mis padres A Xavi iii iv Acknowledgements This thesis has been made possible by the support of many people who in one way or another, many times unknowingly, gave me the strength to overcome this "long and winding road". First of all, I would like to thank my supervisor, Dr. Francesc Piferrer, for his patience, guidance and wise advice throughout all this Ph.D. experience. But above all, for the trust he placed on me almost seven years ago when he offered me the opportunity to be part of his team. Thanks also for teaching me how to question always everything, for sharing with me your enthusiasm for science and for giving me the opportunity of learning from you by participating in many projects, collaborations and scientific meetings. I am also thankful to my colleagues (former and present Group of Biology of Reproduction members) for your support and encouragement throughout this journey. To the “exGBRs”, thanks for helping me with my first steps into this world. Working as an undergrad with you Dr.
    [Show full text]
  • Project List 2020
    Nottingham BBSRC DTP Project List 2020 For interview candidates Contents Introduction ............................................................................................................................................ 2 Ageing...................................................................................................................................................... 3 Animal Health .......................................................................................................................................... 5 Animal Welfare ........................................................................................................................................ 7 Bioenergy ................................................................................................................................................ 7 Chemical Biology ..................................................................................................................................... 8 Crop Science .......................................................................................................................................... 10 Diet and Health ..................................................................................................................................... 11 Immunology .......................................................................................................................................... 12 Industrial Biotechnology .......................................................................................................................
    [Show full text]
  • Relating Metatranscriptomic Profiles to the Micropollutant
    1 Relating Metatranscriptomic Profiles to the 2 Micropollutant Biotransformation Potential of 3 Complex Microbial Communities 4 5 Supporting Information 6 7 Stefan Achermann,1,2 Cresten B. Mansfeldt,1 Marcel Müller,1,3 David R. Johnson,1 Kathrin 8 Fenner*,1,2,4 9 1Eawag, Swiss Federal Institute of Aquatic Science and Technology, 8600 Dübendorf, 10 Switzerland. 2Institute of Biogeochemistry and Pollutant Dynamics, ETH Zürich, 8092 11 Zürich, Switzerland. 3Institute of Atmospheric and Climate Science, ETH Zürich, 8092 12 Zürich, Switzerland. 4Department of Chemistry, University of Zürich, 8057 Zürich, 13 Switzerland. 14 *Corresponding author (email: [email protected] ) 15 S.A and C.B.M contributed equally to this work. 16 17 18 19 20 21 This supporting information (SI) is organized in 4 sections (S1-S4) with a total of 10 pages and 22 comprises 7 figures (Figure S1-S7) and 4 tables (Table S1-S4). 23 24 25 S1 26 S1 Data normalization 27 28 29 30 Figure S1. Relative fractions of gene transcripts originating from eukaryotes and bacteria. 31 32 33 Table S1. Relative standard deviation (RSD) for commonly used reference genes across all 34 samples (n=12). EC number mean fraction bacteria (%) RSD (%) RSD bacteria (%) RSD eukaryotes (%) 2.7.7.6 (RNAP) 80 16 6 nda 5.99.1.2 (DNA topoisomerase) 90 11 9 nda 5.99.1.3 (DNA gyrase) 92 16 10 nda 1.2.1.12 (GAPDH) 37 39 6 32 35 and indicates not determined. 36 37 38 39 S2 40 S2 Nitrile hydration 41 42 43 44 Figure S2: Pearson correlation coefficients r for rate constants of bromoxynil and acetamiprid with 45 gene transcripts of ECs describing nucleophilic reactions of water with nitriles.
    [Show full text]
  • Bacterial Oxygen Production in the Dark
    HYPOTHESIS AND THEORY ARTICLE published: 07 August 2012 doi: 10.3389/fmicb.2012.00273 Bacterial oxygen production in the dark Katharina F. Ettwig*, Daan R. Speth, Joachim Reimann, Ming L. Wu, Mike S. M. Jetten and JanT. Keltjens Department of Microbiology, Institute for Water and Wetland Research, Radboud University Nijmegen, Nijmegen, Netherlands Edited by: Nitric oxide (NO) and nitrous oxide (N2O) are among nature’s most powerful electron Boran Kartal, Radboud University, acceptors. In recent years it became clear that microorganisms can take advantage of Netherlands the oxidizing power of these compounds to degrade aliphatic and aromatic hydrocar- Reviewed by: bons. For two unrelated bacterial species, the “NC10” phylum bacterium “Candidatus Natalia Ivanova, Lawrence Berkeley National Laboratory, USA Methylomirabilis oxyfera” and the γ-proteobacterial strain HdN1 it has been suggested Carl James Yeoman, Montana State that under anoxic conditions with nitrate and/or nitrite, monooxygenases are used for University, USA methane and hexadecane oxidation, respectively. No degradation was observed with *Correspondence: nitrous oxide only. Similarly, “aerobic” pathways for hydrocarbon degradation are employed − Katharina F.Ettwig, Department of by (per)chlorate-reducing bacteria, which are known to produce oxygen from chlorite (ClO ). Microbiology, Institute for Water and 2 Wetland Research, Radboud In the anaerobic methanotroph M. oxyfera, which lacks identifiable enzymes for nitrogen University Nijmegen, formation, substrate activation in the presence of nitrite was directly associated with both Heyendaalseweg 135, 6525 AJ oxygen and nitrogen formation. These findings strongly argue for the role of NO, or an Nijmegen, Netherlands. e-mail: [email protected] oxygen species derived from it, in the activation reaction of methane.
    [Show full text]
  • Bacterial Degradation of Isoprene in the Terrestrial Environment Myriam
    Bacterial Degradation of Isoprene in the Terrestrial Environment Myriam El Khawand A thesis submitted to the University of East Anglia in fulfillment of the requirements for the degree of Doctor of Philosophy School of Environmental Sciences November 2014 ©This copy of the thesis has been supplied on condition that anyone who consults it is understood to recognise that its copyright rests with the author and that use of any information derive there from must be in accordance with current UK Copyright Law. In addition, any quotation or extract must include full attribution. Abstract Isoprene is a climate active gas emitted from natural and anthropogenic sources in quantities equivalent to the global methane flux to the atmosphere. 90 % of the emitted isoprene is produced enzymatically in the chloroplast of terrestrial plants from dimethylallyl pyrophosphate via the methylerythritol pathway. The main role of isoprene emission by plants is to reduce the damage caused by heat stress through stabilizing cellular membranes. Isoprene emission from microbes, animals, and humans has also been reported, albeit less understood than isoprene emission from plants. Despite large emissions, isoprene is present at low concentrations in the atmosphere due to its rapid reactions with other atmospheric components, such as hydroxyl radicals. Isoprene can extend the lifetime of potent greenhouse gases, influence the tropospheric concentrations of ozone, and induce the formation of secondary organic aerosols. While substantial knowledge exists about isoprene production and atmospheric chemistry, our knowledge of isoprene sinks is limited. Soils consume isoprene at a high rate and contain numerous isoprene-utilizing bacteria. However, Rhodococcus sp. AD45 is the only terrestrial isoprene-degrading bacterium characterized in any detail.
    [Show full text]
  • Integrative Structure Modeling: Overview and Assessment
    BI88CH06_Kalisman ARjats.cls May 17, 2019 13:46 Annual Review of Biochemistry Integrative Structure Modeling: Overview and Assessment Merav Braitbard,1 Dina Schneidman-Duhovny,1,2 and Nir Kalisman1 1Department of Biological Chemistry, Institute of Life Sciences, The Hebrew University of Jerusalem, Jerusalem 9190401, Israel; email: [email protected] 2School of Computer Science and Engineering, The Hebrew University of Jerusalem, Jerusalem 9190401, Israel; email: [email protected] Annu. Rev. Biochem. 2019. 88:113–35 Keywords First published as a Review in Advance on integrative modeling, macromolecular assemblies, protein structure, March 4, 2019 cross-linking, mass spectrometry, cryo–electron microscopy, cryo-EM The Annual Review of Biochemistry is online at biochem.annualreviews.org Abstract https://doi.org/10.1146/annurev-biochem-013118- Integrative structure modeling computationally combines data from multi- Access provided by Howard University on 11/09/19. For personal use only. 111429 ple sources of information with the aim of obtaining structural insights that Annu. Rev. Biochem. 2019.88:113-135. Downloaded from www.annualreviews.org Copyright © 2019 by Annual Reviews. are not revealed by any single approach alone. In the first part of this re- All rights reserved view, we survey the commonly used sources of structural information and the computational aspects of model building. Throughout the past decade, integrative modeling was applied to various biological systems, with a focus on large protein complexes. Recent progress in the field of cryo–electron mi- croscopy (cryo-EM) has resolved many of these complexes to near-atomic resolution. In the second part of this review, we compare a range of pub- lished integrative models with their higher-resolution counterparts with the aim of critically assessing their accuracy.
    [Show full text]
  • 17F8-Estradiol Hydroxylation Catalyzed by Human Cytochrome P450 Lbl (Catechol Estrogen/Indole Carbinol/Dioxin/Breast Cancer/Uterine Cancer) CARRIE L
    Proc. Natl. Acad. Sci. USA Vol. 93, pp. 9776-9781, September 1996 Medical Sciences 17f8-Estradiol hydroxylation catalyzed by human cytochrome P450 lBl (catechol estrogen/indole carbinol/dioxin/breast cancer/uterine cancer) CARRIE L. HAYES*, DAVID C. SPINKt, BARBARA C. SPINKt, JOAN Q. CAOt, NIGEL J. WALKER*, AND THOMAS R. SUTTER*t *Department of Environmental Health Sciences, Johns Hopkins University, School of Hygiene and Public Health, Baltimore, MD 21205-2179; and tWadsworth Center, New York State Department of Health, Albany, NY 12201-0509 Communicated by Paul Talalay, Johns Hopkins University, Baltimore, MD, June 11, 1996 (received for review April 24, 1996) ABSTRACT The 4-hydroxy metabolite of 178-estradiol of 4-hydroxyestradiol (4-OHE2), and lack of activity of 2-hy- (E2) has been implicated in the carcinogenicity of this hor- droxyestradiol (2-OHE2), (17-19), implicate the 4-hydroxy- mone. Previous studies showed that aryl hydrocarbon- lated metabolites in estrogen-induced carcinogenesis. Perti- receptor agonists induced a cytochrome P450 that catalyzed nent to elucidating the contribution of 4-OHE2 to the devel- the 4-hydroxylation of E2. This activity was associated with opment of human cancer is the identification of the enzyme(s) human P450 lBi. To determine the relationship of the human that produce this metabolite. P450 lBl gene product and E2 4-hydroxylation, the protein Previous studies demonstrated that treatment of MCF-7 was expressed in Saccharomyces cerevisiae. Microsomes from breast cancer cells with 2,3,7,8-tetrachlorodibenzo-p-dioxin the transformed yeast catalyzed the 4- and 2-hydroxylation of (TCDD), an environmental pollutant and potent agonist of the E2 with Km values of 0.71 and 0.78 ,uM and turnover numbers aryl hydrocarbon (Ah)-receptor, resulted in greater than 10- of 1.39 and 0.27 nmol product min'l nmol P450-1, respec- fold increases in the rates of E2 4- and 2-hydroxylation (20).
    [Show full text]