DOCSLIB.ORG

Chapter 5 High-Pressure Stopped-Flow Kinetic Studies of Nnos

Total Page：16

File Type：pdf, Size：1020Kb

Download full-text PDF Read full-text
Chapter 5 High-Pressure Stopped-Flow Kinetic Studies of Nnos Probing the dynamics and conformational landscape of neuronal nitric oxide synthase A thesis submitted to the University of Manchester for the degree of Doctor of Philosophy in the Faculty of Life Sciences 2013 Anna Sobolewska-Stawiarz Contents Contents ...................................................................................................................... 2 List of Figures ............................................................................................................. 6 List of Tables ............................................................................................................ 10 Abstract ..................................................................................................................... 12 Declaration ................................................................................................................ 13 Copyright Statement ................................................................................................ 13 Acknowledgements ................................................................................................... 14 List of Abbreviations ............................................................................................... 15 List of Amino Acids Abbreviations ........................................................................ 17 CHAPTER 1. INTRODUCTION ........................................................................... 18 1.1 Nitric oxide synthase .......................................................................................... 19 1.1.1 Discovery and isoforms ................................................................................. 19 1.1.2 The reaction ................................................................................................... 23 1.1.3 Structure, function and dynamics .................................................................. 27 1.1.3.1 Flavoproteins and flavin cofactors.......................................................... 27 1.1.3.2 Reductase domain ................................................................................... 30 1.1.3.3 Oxygenase domain.................................................................................. 36 1.1.3.4 Function of tetrahydrobiopterin .............................................................. 38 1.1.3.5 Role of calmodulin in control of electron transfer.................................. 43 1.2 Enzymes related to NOS ................................................................................... 47 1.2.1 Cytochrome P450 reductase .......................................................................... 47 1.2.2 Cytochrome P450 .......................................................................................... 49 1.2.3 Flavocytochrome P450 BM3 ......................................................................... 52 1.2.4 Flavocytochrome b2 ...................................................................................... 52 1.2.5 Cellobiose dehydrogenase ............................................................................. 53 1.2.6 Flavohemoglobin ........................................................................................... 54 1.2.7 Methionine synthase reductase ..................................................................... 54 1.2.8 Sulphite reductase .......................................................................................... 57 1.2.9 Novel reductase 1 .......................................................................................... 57 2 1.3 Nitric oxide and the importance of NOS .......................................................... 58 1.3.1 Nitric oxide – cardiovascular physiology concepts ....................................... 59 1.3.2 Nitric oxide and the nervous system ............................................................. 60 1.3.3 Role of NO in the immune system ................................................................ 61 1.3.4 Side effects of uncontrolled nitric oxide production ..................................... 62 1.4 Overview of EPR spectroscopy ......................................................................... 65 1.4.1 Physical origin of the EPR signal .................................................................. 66 1.4.2 PELDOR spectroscopy .................................................................................. 73 1.5 Aims of the project ............................................................................................. 82 CHAPTER 2. MATERIALS AND METHODS .................................................... 85 2.1 Materials ............................................................................................................. 86 2.2 Methods ............................................................................................................... 88 2.2.1 Recombinant DNA technique ........................................................................ 88 2.2.1.1 Site-directed mutagenesis of FL R1400E nNOS .................................... 88 2.2.1.2 DNA transformation of cells .................................................................. 90 2.2.1.2.1 NovaBlue E. coli competent cells ................................................... 90 2.2.1.2.2 BL21(DE3) E. coli competent cells ................................................ 90 2.2.1.3 Preparation of DNA ................................................................................ 90 2.2.1.4 Enzymic DNA modifications ................................................................. 91 2.2.1.4.1 Restriction digestion of pCRNNR ................................................... 91 2.2.1.4.2 Restriction digestion of pCWORI ................................................... 91 2.2.1.5 Agarose gel electrophoresis .................................................................... 92 2.2.2 Isolation of nNOS proteins ............................................................................ 92 2.2.2.1 nNOSred expression and purification ..................................................... 92 2.2.2.2 FL nNOS expression and purification .................................................... 94 2.2.3 Methods of protein analysis ........................................................................... 97 2.2.3.1 Determination of protein concentration .................................................. 97 2.2.3.1.1 nNOSred............................................................................................ 97 2.2.3.1.2 FL nNOS ......................................................................................... 97 2.2.3.2 SDS-PAGE ............................................................................................. 97 2.2.3.3 HPLC identification and quantification of FAD and FMN .................... 98 2.2.3.4 Steady state kinetics ................................................................................ 99 3 2.2.3.4.1 Cytochrome c reduction ................................................................ 100 2.2.3.4.2 NADPH oxidation ......................................................................... 100 2.2.3.4.3 FL nNOS activity - calmodulin dependence ................................. 101 2.2.3.5 Hydrostatic pressure stopped-flow kinetics .......................................... 101 2.2.3.5.1 Flavin reduction ............................................................................. 102 2.2.3.5.2 NADPH oxidation ......................................................................... 103 2.2.3.5.3 NO synthesis ................................................................................. 103 2.2.3.6 Redox potentiometry ............................................................................ 105 2.2.3.7 Electron paramagnetic resonance spectroscopy (EPR) ........................ 106 2.2.3.8 Protein mass spectroscopy .................................................................... 107 CHAPTER 3. CHARACTERISATION OF THE nNOS REDUCTASE DOMAIN ................................................................................................................. 108 3.1 Introduction ...................................................................................................... 109 3.2 Results ............................................................................................................... 111 3.2.1 Overexpression and purification of WT and R1400E nNOSred ................... 111 3.2.2 Steady-state kinetics of cytochrome c reductase activity of WT and R1400E nNOSred ................................................................................................................. 118 3.2.3 EPR redox titration ...................................................................................... 122 3.2.4 EPR Spectroscopic studies .......................................................................... 127 3.2.4.1 CW-EPR studies of nNOSred ................................................................ 127 3.2.4.2 PELDOR studies of nNOSred ................................................................ 133 3.3 Discussion .......................................................................................................... 140 CHAPTER 4. CHARACTERISATION OF FULL LENGTH nNOS ............... 147 4.1 Introduction ...................................................................................................... 148 4.2 Results ..............................................................................................................
Load more

Recommended publications
  • Protein S-Nitrosylation: Methods of Detection and Cellular Regulation
    Protein S-Nitrosylation: Methods of Detection and Cellular Regulation by Michael Tcheupdjian Forrester Department of Biochemistry Duke University Date:_______________________ Approved: ___________________________ Jonathan S. Stamler, MD (Supervisor) ___________________________ Irwin Fridovich, PhD ___________________________ K. V. Rajagopalan, PhD ___________________________ Dennis J. Thiele, PhD ___________________________ Eric J. Toone, PhD Dissertation submitted in partial fulfillment of the requirements for the degree of doctor of philosophy in the Department of Biochemistry in the Graduate School of Duke University 2009 i v ABSTRACT Protein S-Nitrosylation: Methods of Detection and Cellular Regulation by Michael Tcheupdjian Forrester Department of Biochemistry Duke University Date:_______________________ Approved: ___________________________ Jonathan S. Stamler, MD (Supervisor) ___________________________ Irwin Fridovich, PhD ___________________________ K. V. Rajagopalan, PhD ___________________________ Dennis J. Thiele, PhD ___________________________ Eric J. Toone, PhD An abstract of a dissertation submitted in partial fulfillment of the requirements for the degree of doctor of philosophy in the Department of Biochemistry in the Graduate School of Duke University 2009 i v Copyright by Michael T. Forrester 2009 Abstract Protein S-nitrosylation—the post-translational modification of cysteine thiols into S-nitrosothiols—is a principle mechanism of nitric oxide-based signaling. Studies have demonstrated myriad roles for S-nitrosylation in organisms from bacteria to humans, and recent efforts have begun to elucidate how this redox-based modification is regulated during physiological and pathophysiological conditions. This doctoral thesis is focused on the 1) analysis of existing methodologies for the detection of protein S-nitrosylation; 2) development of new methodologies for the detection of protein S-nitrosylation and 3) discovery of novel enzymatic mechanisms by which S-nitrosylation is regulated in vivo.
    [Show full text]
  • KEGG Orthology-Based Annotation of the Predicted
    Dunlap et al. BMC Genomics 2013, 14:509 http://www.biomedcentral.com/1471-2164/14/509 DATABASE Open Access KEGG orthology-based annotation of the predicted proteome of Acropora digitifera: ZoophyteBase - an open access and searchable database of a coral genome Walter C Dunlap1,2, Antonio Starcevic4, Damir Baranasic4, Janko Diminic4, Jurica Zucko4, Ranko Gacesa4, Madeleine JH van Oppen1, Daslav Hranueli4, John Cullum5 and Paul F Long2,3* Abstract Background: Contemporary coral reef research has firmly established that a genomic approach is urgently needed to better understand the effects of anthropogenic environmental stress and global climate change on coral holobiont interactions. Here we present KEGG orthology-based annotation of the complete genome sequence of the scleractinian coral Acropora digitifera and provide the first comprehensive view of the genome of a reef-building coral by applying advanced bioinformatics. Description: Sequences from the KEGG database of protein function were used to construct hidden Markov models. These models were used to search the predicted proteome of A. digitifera to establish complete genomic annotation. The annotated dataset is published in ZoophyteBase, an open access format with different options for searching the data. A particularly useful feature is the ability to use a Google-like search engine that links query words to protein attributes. We present features of the annotation that underpin the molecular structure of key processes of coral physiology that include (1) regulatory proteins of
    [Show full text]
  • Biochemical and Cellular Studies of Vertebrate Globins
    Biochemical and Cellular Studies of Vertebrate Globins By Shun Wilford Tse Thesis submitted for the degree of Doctor of Philosophy School of Biological Sciences University of East Anglia September 2015 © 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 no quotations from the thesis, nor any information derived there-from may be published without the author's prior, written consent. Abstract Human cytoglobin is a small heme-containing protein in the globin superfamily with a wide range of tissue and organ distribution. Although several cellular functions have been proposed for cytoglobin, the exact physiological function is still not fully defined. Recently, cytoglobin has been implicated to have a regulatory role in cancer cells to control cell proliferation and migration depending on cellular oxygen level. In order to gain a better understanding of a structure-to-function relationship of cytoglobin as a heme-protein and to evaluate its possible physiological function(s) in cancer cells, a combination of techniques, including protein engineering and advanced spectroscopies, was deployed. In this study, recombinant human cytoglobin purified from E.coli was purified as a monomeric protein, but displayed a dimeric property in solution. An intra-molecular disulphide bond is formed within the protein which has a redox potential at ca -280 mV. Advanced spectroscopic studies confirmed a low-spin bis-histidyl heme in cytoglobin in both ferric and ferrous state regardless of the state of the disulphide bond. Furthermore, nitrite reductase activitiy in globins was investigated in detail using myoglobin as a model to explore the biochemical basis of the distal histidine residue in determining activity.
    [Show full text]
  • Nitric Oxide Dioxygenase: an Enzymic Function for Flavohemoglobin
    Proc. Natl. Acad. Sci. USA Vol. 95, pp. 10378–10383, September 1998 Biochemistry Nitric oxide dioxygenase: An enzymic function for flavohemoglobin PAUL R. GARDNER*, ANNE M. GARDNER,LORI A. MARTIN, AND ANDREW L. SALZMAN Division of Critical Care Medicine, Children’s Hospital Medical Center, and Department of Pediatrics, University of Cincinnati, 3333 Burnet Avenue, Cincinnati, OH 45229 Communicated by Irwin Fridovich, Duke University Medical Center, Durham, NC, July 7, 1998 (received for review June 9, 1998) ABSTRACT Nitric oxide (NO•) is a toxin, and various life Moreover, this aerobic cyanide-sensitive NO• consumption forms appear to have evolved strategies for its detoxification. activity appeared to constitute part of an adaptive defense NO•-resistant mutants of Escherichia coli were isolated that against NO• toxicity. Thus, we supposed that E. coli mutants rapidly consumed NO•.AnNO•-converting activity was re- containing elevated activity might be selected for resistance to • constituted in extracts that required NADPH, FAD, and O2, 2 NO -mediated killing, and furthermore, that they could be was cyanide-sensitive, and produced NO3 . This nitric oxide used to facilitate the biochemical and genetic characterization dioxygenase (NOD) contained 19 of 20 N-terminal amino of the NO• scavenging activity. acids identical to those of the E. coli flavohemoglobin. Fur- Here, we describe the isolation and characterization of an thermore, NOD activity was produced by the flavohemoglobin O2-dependent and cyanide-sensitive nitric oxide dioxygenase gene and was inducible by NO•. FlavohemoglobinyNOD- (NOD) from NO•-resistant E. coli, which is a flavohemoglo- deficient mutants were also sensitive to growth inhibition by bin. The identification of NOD with flavohemoglobin is sig- gaseous NO•.
    [Show full text]
  • Current Advances of Nitric Oxide in Cancer and Anticancer Therapeutics
    Review Current Advances of Nitric Oxide in Cancer and Anticancer Therapeutics Joel Mintz 1,†, Anastasia Vedenko 2,†, Omar Rosete 3 , Khushi Shah 4, Gabriella Goldstein 5 , Joshua M. Hare 2,6,7 , Ranjith Ramasamy 3,6,* and Himanshu Arora 2,3,6,* 1 Dr. Kiran C. Patel College of Allopathic Medicine, Nova Southeastern University, Davie, FL 33328, USA; [email protected] 2 John P Hussman Institute for Human Genomics, Miller School of Medicine, University of Miami, Miami, FL 33136, USA; [email protected] (A.V.); [email protected] (J.M.H.) 3 Department of Urology, Miller School of Medicine, University of Miami, Miami, FL 33136, USA; [email protected] 4 College of Arts and Sciences, University of Miami, Miami, FL 33146, USA; [email protected] 5 College of Health Professions and Sciences, University of Central Florida, Orlando, FL 32816, USA; [email protected] 6 The Interdisciplinary Stem Cell Institute, Miller School of Medicine, University of Miami, Miami, FL 33136, USA 7 Department of Medicine, Cardiology Division, Miller School of Medicine, University of Miami, Miami, FL 33136, USA * Correspondence: [email protected] (R.R.); [email protected] (H.A.) † These authors contributed equally to this work. Abstract: Nitric oxide (NO) is a short-lived, ubiquitous signaling molecule that affects numerous critical functions in the body. There are markedly conflicting findings in the literature regarding the bimodal effects of NO in carcinogenesis and tumor progression, which has important consequences for treatment. Several preclinical and clinical studies have suggested that both pro- and antitumori- Citation: Mintz, J.; Vedenko, A.; genic effects of NO depend on multiple aspects, including, but not limited to, tissue of generation, the Rosete, O.; Shah, K.; Goldstein, G.; level of production, the oxidative/reductive (redox) environment in which this radical is generated, Hare, J.M; Ramasamy, R.; Arora, H.
    [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]
  • The Role of Nitrite and Nitric Oxide Under Low Oxygen Conditions in Plants Gupta, Kapuganti Jagadis; Mur, Luis A
    Aberystwyth University The role of nitrite and nitric oxide under low oxygen conditions in plants Gupta, Kapuganti Jagadis; Mur, Luis A. J.; Wany, Aakanksha; Kumari, Aprajita; Fernie, Alisdair R.; Ratcliffe, R. George Published in: New Phytologist DOI: 10.1111/nph.15969 Publication date: 2019 Citation for published version (APA): Gupta, K. J., Mur, L. A. J., Wany, A., Kumari, A., Fernie, A. R., & Ratcliffe, R. G. (2019). The role of nitrite and nitric oxide under low oxygen conditions in plants. New Phytologist. https://doi.org/10.1111/nph.15969 General rights Copyright and moral rights for the publications made accessible in the Aberystwyth Research Portal (the Institutional Repository) are retained by the authors and/or other copyright owners and it is a condition of accessing publications that users recognise and abide by the legal requirements associated with these rights. • Users may download and print one copy of any publication from the Aberystwyth Research Portal for the purpose of private study or research. • You may not further distribute the material or use it for any profit-making activity or commercial gain • You may freely distribute the URL identifying the publication in the Aberystwyth Research Portal Take down policy If you believe that this document breaches copyright please contact us providing details, and we will remove access to the work immediately and investigate your claim. tel: +44 1970 62 2400 email: [email protected] Download date: 23. Sep. 2021 DR JAGADIS GUPTA KAPUGANTI (Orcid ID : 0000-0002-7090-5097) DR LUIS ALEJANDRO MUR (Orcid ID : 0000-0002-0961-9817) DR ALISDAIR FERNIE (Orcid ID : 0000-0001-9000-335X) Article type : Research Review The role of nitrite and nitric oxide under low oxygen conditions in plants Kapuganti Jagadis Gupta1*, Luis A.J.
    [Show full text]
  • Curriculum Vitae
    Curriculum Vitae JONATHAN S. STAMLER Dr Stamler is an internationally acclaimed physician scientist known for the discovery of protein S- nitrosylation, a global post-translational modification of proteins that is widely involved in both physiology and disease, and for a track record of innovation and entrepreneurship as a founder of institutes, biotechnology companies, medical societies, innovation platforms and impact investment funds. He has co-authored over 300 original manuscripts and 125 patents/patent applications. His work has been covered in numerous lay publications, including the front page and science sections of the New York Times, as well as Time Magazine and The Economist, in books on the history of science and luck, and in works on outlier innovators. Current Address: Office: Case Western Reserve University Home: 19401 South Park Boulevard 2103 Cornell Road, WRB 4129 Shaker Heights, OH 44122 Cleveland, Ohio 44106-7294 cell: (919) 971-0328 phone: (216) 368-5724 fax: (216) 368-2968 e-mail: [email protected] e-mail: [email protected] Birthdate: June 23, 1959 (Wallingford, England) Citizenship: United States Education: 1981 B.A. Brandeis University, Boston, MA 1985 M.D. Mount Sinai School of Medicine, New York, NY Postdoctoral Training: Internship and Residency 1985-1986 Internship, Medicine, Brigham and Women's Hospital, Harvard Medical School. Boston, MA 1986-1987 Resident, Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA 1987-1988 Resident, Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA Fellowships 1985-1989 Clinical Fellow in Medicine, Harvard Medical School, Boston, MA 1988-1989 Clinical Fellow in Medicine (Pulmonary Medicine), Brigham and Women's Hospital 1989-1993 Research Fellow in Medicine, Harvard Medical School 1989-1993 Clinical/Research Fellow in Medicine (Cardiovascular Medicine), Brigham and Women's Hospital, Boston, MA and West Roxbury V.A.
    [Show full text]
  • Regulation of Hepatic Stellate Cell Phenotype and Cytoglobin Expression by Extracellular Matrix Proteins
    Regulation of hepatic stellate cell phenotype and cytoglobin expression by extracellular matrix proteins By Louise Catherine Stone A thesis submitted to The University of Birmingham for the degree of DOCTOR OF PHILOSOPHY School of Biosciences The University of Birmingham October 2014 University of Birmingham Research Archive e-theses repository This unpublished thesis/dissertation is copyright of the author and/or third parties. The intellectual property rights of the author or third parties in respect of this work are as defined by The Copyright Designs and Patents Act 1988 or as modified by any successor legislation. Any use made of information contained in this thesis/dissertation must be in accordance with that legislation and must be properly acknowledged. Further distribution or reproduction in any format is prohibited without the permission of the copyright holder. Abstract All chronic liver diseases can induce fibrosis and lead to liver cirrhosis. Within liver disease, hepatic stellate cells (HSC) are accepted as the major effectors of fibrogenesis and changes in the extracellular matrix (ECM). Cytoglobin (CYGB), a hexacoordinated globin, is upregulated in liver disease, and expression has been reported to be specific to HSCs in the liver, though this is disputed. Data presented in Chapter 3 of this thesis confirm upregulation of Cygb in murine models of liver disease and diseased human liver tissue. Chapter 4 shows how ECM can effect HSC morphology, behaviour and phenotype with collagen I, an important component of the hepatic scar conferring an activated HSC phenotype, and laminin, a basal protein in a normal liver, inducing a more quiescent phenotype in HSC cell lines HSC-T6 and LX-2.
    [Show full text]
  • Design and Fine-Tuning Redox Potentials of Metalloproteins Involved in Electron Transfer in Bioenergetics
    1 Design and Fine-tuning Redox Potentials of Metalloproteins Involved in Electron Transfer in Bioenergetics Parisa Hosseinzadeh and Yi Lu Abstract: 1. Introduction A significant portion of biological processes are involved with providing vital energy sources such as ATP, and controlling the flow of energy through living systems. These bioenergetics processes, the most important of which are photosynthesis and respiration, require electron transfer (ET) between different redox partners. Metalloproteins are one of the most widely used ET centers in biology. They can be classified into three major classes: cupredoxins, which include type 1 copper (T1Cu) proteins and CuA centers [1- 10], cytochromes [10-17], and iron-sulfur (FeS) proteins [10,18-24]. Each class of ET proteins transfer electrons between different redox partners which possess different reduction potentials (E°) (Figure 1). Therefore, the ET centers need to adjust their E° in a way that matches those of their redox partners. No single class of protein can cover the entire range of physiological E°, which is between ~ -1V, at which protons are reduced to H2, and 1V, at which water is oxidized to O2. Cupredoxins usually function at the high end of the E°, while FeS proteins are mostly involved in ET reactions possessing relatively low E° [10]. The E°’s of FeS proteins overlap significantly with those of cytochromes that often have intermediate E° among the three classes of ET proteins. Figure 1. Reduction potential range of metal centers in electron transfer metalloprotein. Adapted from ref. [10] 2 In this review, we first describe the importance of tuning E° of ET centers, including the metalloproteins described above.
    [Show full text]
  • Characterisation, Classification and Conformational Variability Of
    Characterisation, Classification and Conformational Variability of Organic Enzyme Cofactors Julia D. Fischer European Bioinformatics Institute Clare Hall College University of Cambridge A thesis submitted for the degree of Doctor of Philosophy 11 April 2011 This dissertation is the result of my own work and includes nothing which is the outcome of work done in collaboration except where specifically indicated in the text. This dissertation does not exceed the word limit of 60,000 words. Acknowledgements I would like to thank all the members of the Thornton research group for their constant interest in my work, their continuous willingness to answer my academic questions, and for their company during my time at the EBI. This includes Saumya Kumar, Sergio Martinez Cuesta, Matthias Ziehm, Dr. Daniela Wieser, Dr. Xun Li, Dr. Irene Pa- patheodorou, Dr. Pedro Ballester, Dr. Abdullah Kahraman, Dr. Rafael Najmanovich, Dr. Tjaart de Beer, Dr. Syed Asad Rahman, Dr. Nicholas Furnham, Dr. Roman Laskowski and Dr. Gemma Holli- day. Special thanks to Asad for allowing me to use early development versions of his SMSD software and for help and advice with the KEGG API installation, to Roman for knowing where to find all kinds of data, to Dani for help with R scripts, to Nick for letting me use his E.C. tree program, to Tjaart for python advice and especially to Gemma for her constant advice and feedback on my work in all aspects, in particular the chemistry side. Most importantly, I would like to thank Prof. Janet Thornton for giving me the chance to work on this project, for all the time she spent in meetings with me and reading my work, for sharing her seemingly limitless knowledge and enthusiasm about the fascinating world of enzymes, and for being such an experienced and motivational advisor.
    [Show full text]
  • Functional Challenges for Technology Fraser Armstrong1, Kylie A
    J Biol Inorg Chem (2007) 12 (Suppl 1):S53–S98 DOI 10.1007/s00775-007-0256-4 2. METALLOPROTEINS DNA; the properties of two of these enzymes (hABH1 and hABH5) are described. KEYNOTE LECTURES KL10 KL08 Towards the Mechanism of N2 Reduction by Nitrogenase Electrocatalytic hydrogen cycling by hydrogenases in the Brian M. Hoffman, Northwestern University, Evanston, IL, USA. Contact e-mail: [email protected] presence of O2: functional challenges for technology Fraser Armstrong1, Kylie A. Vincent1, James A. Cracknell1, 1 1 2 A major obstacle to understanding the reduction of N2 to NH3 by Annemarie Wait , Gabrielle Goldet , Baebel Friedrich , Oliver nitrogenase has been the impossibility of synchronizing electron Lenz2, Marcus Ludwig3, 1University of Oxford, Department of 2 delivery to the MoFe protein so that intermediates along the N2 Chemistry, Oxford, United Kingdom; Institut für reduction pathway can be accumulated for characterization. Biologie/Mikrobiologie, Humboldt-Universität zu Berlin, Germany; 3 Recently, however, in a collaboration with the groups of Dennis Institut für Biologie/Mikrobiologie,, Humboldt-Universität zu Dean and Lance Seefeldt, a number of intermediates have been Berlin, Germany. trapped by freeze-quenching, and ENDOR spectroscopy has proven Contact e-mail: [email protected] to be the method of choice for characterizing substrate-derived species bound to FeMo-co of trapped enzymatic intermediates. This Hydrogenases are usually inactivated under oxidizing conditions presentation will describe current understanding of the structure of [1]. Yet many aerobic microbes obtain energy using [NiFe]- trapped intermediates and of the mechanistic sequence of hydrogen hydrogenases that can oxidize traces of H in air [2,3].
    [Show full text]