Evaluation of Functioning of Mitochondrial Electron Transport Chain with NADH and FAD Autofluorescence
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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 ......................................................................................... -
Mitochondrial Supercomplex Assembly Promotes Breast and Endometrial Tumorigenesis by Metabolic Alterations and Enhanced Hypoxia Tolerance
ARTICLE https://doi.org/10.1038/s41467-019-12124-6 OPEN Mitochondrial supercomplex assembly promotes breast and endometrial tumorigenesis by metabolic alterations and enhanced hypoxia tolerance Kazuhiro Ikeda1, Kuniko Horie-Inoue1, Takashi Suzuki2, Rutsuko Hobo1,3, Norie Nakasato1,3, Satoru Takeda3,4 & Satoshi Inoue 1,5 1234567890():,; Recent advance in cancer research sheds light on the contribution of mitochondrial respiration in tumorigenesis, as they efficiently produce ATP and oncogenic metabolites that will facilitate cancer cell growth. Here we show that a stabilizing factor for mitochondrial supercomplex assembly, COX7RP/COX7A2L/SCAF1, is abundantly expressed in clinical breast and endometrial cancers. Moreover, COX7RP overexpression associates with prog- nosis of breast cancer patients. We demonstrate that COX7RP overexpression in breast and endometrial cancer cells promotes in vitro and in vivo growth, stabilizes mitochondrial supercomplex assembly even in hypoxic states, and increases hypoxia tolerance. Metabo- lomic analyses reveal that COX7RP overexpression modulates the metabolic profile of cancer cells, particularly the steady-state levels of tricarboxylic acid cycle intermediates. Notably, silencing of each subunit of the 2-oxoglutarate dehydrogenase complex decreases the COX7RP-stimulated cancer cell growth. Our results indicate that COX7RP is a growth- regulatory factor for breast and endometrial cancer cells by regulating metabolic pathways and energy production. 1 Division of Gene Regulation and Signal Transduction, Research Center for Genomic Medicine, Saitama Medical University, 1397-1 Yamane, Hidaka-shi, Saitama 350-1241, Japan. 2 Departments of Pathology and Histotechnology, Tohoku University Graduate School of Medicine, 2-1 Seiryo-machi, Aoba-ku, Sendai 980-8575, Japan. 3 Department of Obstetrics and Gynecology, Saitama Medical Center, Saitama Medical University, 1981, Tsujido, Kamoda, Kawagoe-shi, Saitama 350-8550, Japan. -
Analyzing the Potential Biological Determinants of Autism Spectrum Disorders: from Neuroinflammation to Kynurenines Pathway
Preprints (www.preprints.org) | NOT PEER-REVIEWED | Posted: 19 July 2020 doi:10.20944/preprints202007.0425.v1 Peer-reviewed version available at Brain Sci. 2020, 10, 631; doi:10.3390/brainsci10090631 Review Analyzing the potential biological determinants of Autism Spectrum Disorders: from Neuroinflammation to Kynurenines Pathway Rosa Savino1, Marco Carotenuto2, A. Nunzia Polito1, *, Sofia Di Noia1, Marzia Albenzio6,Alessia Scarinci3, Antonio Ambrosi4, Francesco Sessa5, Nicola Tartaglia4 and Giovanni Messina5 1 Department of Woman and Child, Neuropsychiatry for Child and Adolescent Unit, General Hospital “Riuniti” of Foggia, 71122 Foggia, Italy. [email protected] 2Department of Mental Health, Physical and Preventive Medicine, Clinic of Child and Adolescent Neuropsychiatry, Università degli Studi della Campania "Luigi Vanvitelli", 81100 Caserta, Italy. [email protected] 3Department of Education Sciences, Psychology and Communication, University of Bari, 70121 Bari, Italy. [email protected] 4Department of Medical and Surgical Sciences, University of Foggia, Viale Pinto, 71122, Foggia, Italy. [email protected] 5Department of Clinical and Experimental Medicine, University of Foggia, 71122 Foggia, Italy. [email protected] 6Department of the Sciences of Agriculture, Food and Environment, University of Foggia, Via Napoli, 25, 71100 Foggia, Italy. [email protected] * Correspondence: [email protected], tel: 0881732364. © 2020 by the author(s). Distributed under a Creative Commons CC BY license. Preprints (www.preprints.org) | NOT PEER-REVIEWED | Posted: 19 July 2020 doi:10.20944/preprints202007.0425.v1 Peer-reviewed version available at Brain Sci. 2020, 10, 631; doi:10.3390/brainsci10090631 2 of 32 Abstract: Autism Spectrum Disorder etiopathogenesis is still unclear and no effective preventive and treatment measures have been identified. -
Structure of the Intact 14-Subunit Human Cytochrome C Oxidase
www.nature.com/cr www.cell-research.com ARTICLE Structure of the intact 14-subunit human cytochrome c oxidase Shuai Zong 1, Meng Wu1, Jinke Gu1, Tianya Liu1, Runyu Guo1 and Maojun Yang1,2 Respiration is one of the most basic features of living organisms, and the electron transport chain complexes are probably the most complicated protein system in mitochondria. Complex-IV is the terminal enzyme of the electron transport chain, existing either as randomly scattered complexes or as a component of supercomplexes. NDUFA4 was previously assumed as a subunit of complex-I, but recent biochemical data suggested it may be a subunit of complex-IV. However, no structural evidence supporting this notion was available till now. Here we obtained the 3.3 Å resolution structure of complex-IV derived from the human supercomplex I1III2IV1 and assigned the NDUFA4 subunit into complex-IV. Intriguingly, NDUFA4 lies exactly at the dimeric interface observed in previously reported crystal structures of complex-IV homodimer which would preclude complex- IV dimerization. Combining previous structural and biochemical data shown by us and other groups, we propose that the intact complex-IV is a monomer containing 14 subunits. Cell Research (2018) 28:1026–1034; https://doi.org/10.1038/s41422-018-0071-1 INTRODUCTION states under physiological conditions, either being assembled into Mitochondria are critical to many cellular activities. Respiration is supercomplexes or freely scattered on mitochondrial inner the central function of mitochondria, and is exquisitely regulated membrane.36 NDUFA4 was originally considered as a subunit of in multiple ways in response to varying cell conditions.1–3 The Complex-I37 but was proposed to belong to Complex-IV recently.38 assembly of respiratory chain complexes, Complex I–IV (CI, NADH: However, the precise location of NDUFA4 in CIV remains unknown, ubiquinone oxidoreductase; CII, succinate:ubiquinone oxidoreduc- and thus this notion still lacks structural support. -
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. -
Thiol Switches in Mitochondria: Operation and Physiological Relevance
Biol. Chem. 2015; aop Review Jan Riemer * , Markus Schwarzl ä nder * , Marcus Conrad * and Johannes M. Herrmann * Thiol switches in mitochondria: operation and physiological relevance Abstract : Mitochondria are a major source of reactive Introduction – mitochondria oxygen species (ROS) in the cell, particularly of super- oxide and hydrogen peroxide. A number of dedicated contain two distinct redox networks enzymes regulate the conversion and consumption of superoxide and hydrogen peroxide in the intermem- Mitochondria are essential organelles of eukaryotic cells. brane space and the matrix of mitochondria. Neverthe- They produce not only the bulk of cellular energy in the less, hydrogen peroxide can also interact with many other form of ATP, but they also generate numerous important mitochondrial enzymes, particularly those with reactive metabolites and cofactors, and they serve as critical sign- cysteine residues, modulating their reactivity in accord- aling stations that, for example, integrate cellular signals ance with changes in redox conditions. In this review we to initiate apoptosis. In turn, mitochondria also commu- will describe the general redox systems in mitochondria nicate their metabolic and fitness state to the remainder of animals, fungi and plants and discuss potential target of the cell to trigger cellular adaptation processes. proteins that were proposed to contain regulatory thiol Mitochondria contain two distinct aqueous sub- switches. compartments, the intermembrane space (IMS) and the matrix. Both subcompartments differ strongly with Keywords: glutathione; hydrogen peroxide; mitochon- respect to their biological activity, their protein composi- dria; NADPH; reactive oxygen species; redox regulation; tion ( Herrmann and Riemer, 2010 ) as well as their redox ROS; signaling; thiol switch. properties. -
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. -
Mitochondrial Probe Methyltriphenylphosphonium (TPMP) Inhibits the Krebs Cycle Enzyme 2- Oxoglutarate Dehydrogenase
RESEARCH ARTICLE Mitochondrial Probe Methyltriphenylphosphonium (TPMP) Inhibits the Krebs Cycle Enzyme 2- Oxoglutarate Dehydrogenase Moustafa Elkalaf1,4, Petr Tůma2,4, Martin Weiszenstein3,4, Jan Polák3,4, Jan Trnka1,2,4* 1 Laboratory for Metabolism and Bioenergetics, Third Faculty of Medicine, Charles University, Prague, Czech Republic, 2 Department of Biochemistry, Cell and Molecular Biology, Third Faculty of Medicine, a11111 Charles University, Prague, Czech Republic, 3 Department of Sport Medicine, Third Faculty of Medicine, Charles University, Prague, Czech Republic, 4 Centre for Research on Diabetes, Metabolism and Nutrition, Third Faculty of Medicine, Charles University, Prague, Czech Republic * [email protected] OPEN ACCESS Abstract ů Citation: Elkalaf M, T ma P, Weiszenstein M, Polák Methyltriphenylphosphonium (TPMP) salts have been widely used to measure the mito- J, Trnka J (2016) Mitochondrial Probe + Methyltriphenylphosphonium (TPMP) Inhibits the chondrial membrane potential and the triphenylphosphonium (TPP ) moiety has been Krebs Cycle Enzyme 2-Oxoglutarate attached to many bioactive compounds including antioxidants to target them into mitochon- Dehydrogenase. PLoS ONE 11(8): e0161413. dria thanks to their high affinity to accumulate in the mitochondrial matrix. The adverse doi:10.1371/journal.pone.0161413 effects of these compounds on cellular metabolism have been insufficiently studied and are Editor: Janine Santos, National Institute of still poorly understood. Micromolar concentrations of TPMP cause a progressive -
Safety Assessment of Ubiquinone Ingredients As Used in Cosmetics
Safety Assessment of Ubiquinone Ingredients as Used in Cosmetics Status: Draft Tentative Report for Panel Review Release Date: August 20, 2021 Panel Meeting Date: September 13-14, 2021 The Expert Panel for Cosmetic Ingredient Safety members are: Chair, Wilma F. Bergfeld, M.D., F.A.C.P.; Donald V. Belsito, M.D.; David E. Cohen, M.D.; Curtis D. Klaassen, Ph.D.; Daniel C. Liebler, Ph.D.; Lisa A. Peterson, Ph.D.; Ronald C. Shank, Ph.D.; Thomas J. Slaga, Ph.D.; and Paul W. Snyder, D.V.M., Ph.D. Previous Panel member involved in this assessment: James G. Marks, Jr., M.D. The Cosmetic Ingredient Review (CIR) Executive Director is Bart Heldreth, Ph.D. This safety assessment was prepared by Preethi S. Raj, M.Sc., Senior Scientific Analyst/Writer, CIR. © Cosmetic Ingredient Review 1620 L Street, NW, Suite 1200 ♢ Washington, DC 20036-4702 ♢ ph 202.331.0651 ♢ fax 202.331.0088 ♢ [email protected] Distributed for Comment Only -- Do Not Cite or Quote Commitment & Credibility since 1976 Memorandum To: Expert Panel for Cosmetic Ingredient Safety Members and Liaisons From: Preethi S. Raj, M.Sc. Senior Scientific AnWriter CIR Date: August 20, 2021 Subject: Safety Assessment of Ubiquinone Ingredients as Used in Cosmetics Enclosed is the Draft Tentative Report of the Safety Assessment of Ubiquinone Ingredients as Used in Cosmetics (identified as ubiqui092021rep in the pdf). This is the second time the Panel is seeing a safety assessment of these 4 cosmetic ingredients. At the September 2020 meeting, the Panel issued an Insufficient Data Announcement (IDA), and the following data needs were identified: • Method of manufacture for Hydroxydecyl Ubiquinone and Ubiquinol • Concentration of use data for Hydroxydecyl Ubiquinone and Ubiquinol A memo stating no reported concentrations of use for Ubiquinol was received (ubiqui092021data). -
Ubiquinol Is Superior to Ubiquinone to Enhance Coenzyme Q10 Status in Older Men
Food & Function Ubiquinol is superior to ubiquinone to enhance Coenzyme Q10 status in older men Journal: Food & Function Manuscript ID FO-ART-05-2018-000971.R1 Article Type: Paper Date Submitted by the Author: 08-Sep-2018 Complete List of Authors: Zhang, Ying; Northeast Forestry University, Key Laboratory of Forest Plant Ecology, Ministry of Education Liu, Jin; Systems Engineering Research Institute Chen, Xiaoqiang; Northeast Forestry University, Chen, C-Y.Oliver; Tufts University Page 1 of 12 PleaseFood do not & Functionadjust margins Food & Function ARTICLE Ubiquinol is superior to ubiquinone to enhance Coenzyme Q10 status in older men Received 00th January 20xx, a,b b,c a,b b Accepted 00th January 20xx Ying Zhang , Jin Liu , Xiao-qiang Chen and C-Y. Oliver Chen * DOI: 10.1039/x0xx00000x Abstract Coenzyme Q10 (CoQ10) exerts its functions in the body through the ability of its benzoquinone head group to www.rsc.org/ accept and donate electrons. The primary functions are to relay electrons for the ATP production in the electron transport chain and to act as an important lipophilic antioxidant. Ubiquinone, the oxidized form of CoQ10, is commonly formulated in commercial supplements, and it must be reduced to ubiquinol to exert CoQ10’s functions after consumption. Thus, we aimed to examine whether as compared to ubiquinone, ubiquinol would be more effective to enhance CoQ10 status in older men. We conducted a double-blind, randomized, crossover trial with two 2-week intervention phases and a 2-week washout between crossover. Ten eligible older men were randomized to consume with one of the main meals either ubiquinol or ubiquinone supplement at the dose of 200 mg/d. -
Structural Basis of Inter-Domain Electron Transfer in Ncb5or, a Redox Enzyme Implicated in Diabetes and Lipid Metabolism
STRUCTURAL BASIS OF INTER-DOMAIN ELECTRON TRANSFER IN NCB5OR, A REDOX ENZYME IMPLICATED IN DIABETES AND LIPID METABOLISM By Bin Deng Submitted to the graduate degree program in Rehabilitation Science and the Graduate Faculty of the University of Kansas in partial fulfillment of the requirements for the degree of Doctor of Philosophy Hao Zhu, Ph.D. (co-chair, advisor) Irina Smirnova, Ph.D. (co-chair) David Benson, Ph.D. (co-advisor) WenFang Wang, Ph.D. Aron Fenton, Ph.D. Date defended: August 17, 2011 The Dissertation Committee for Bin Deng certifies that this is the approved version of the following dissertation STRUCTURAL BASIS OF INTER-DOMAIN ELECTRON TRANSFER IN NCB5OR, A REDOX ENZYME IMPLICATED IN DIABETES AND LIPID METABOLISM Hao Zhu, Ph.D. (co-chair, advisor) Irina Smirnova, Ph.D. (co-chair) Date approved: August 22, 2011 ii ABSTRACT NADH cytochrome b5 oxidoreductase (Ncb5or) is a multi-domain redox enzyme found in all animal tissues and associated with the endoplasmic reticulum (ER). Ncb5or contains (from N-terminus to C terminus) a novel N-terminal region, the b5 domain (Ncb5or-b5), the CS domain, and the b5R domain (Ncb5or-b5R). Ncb5or-b5, the heme binding domain, is homologous to microsomal cytochrome b5 (Cyb5A) and belongs to cytochrome b5 superfamily. Ncb5or-b5R, the FAD (flavin adenine dinucleotide) binding domain, is homologous to cytochrome b5 reductase (Cyb5R3) and belongs to ferredoxin NADP+ reductase superfamily. Both superfamilies are of great biological significance whose members have important functions. The CS domain can be assigned into the heat shock protein 20 (HSP20, or p23) family, whose members are known to mediate protein-protein interactions. -
Prognostic Implications and Molecular Associations of NADH Dehydrogenase Subunit 4 (ND4) Mutations in Acute Myeloid Leukemia
Leukemia (2012) 26, 289–295 & 2012 Macmillan Publishers Limited All rights reserved 0887-6924/12 www.nature.com/leu ORIGINAL ARTICLE Prognostic implications and molecular associations of NADH dehydrogenase subunit 4 (ND4) mutations in acute myeloid leukemia F Damm1, T Bunke1, F Thol1, B Markus1, K Wagner1,GGo¨hring2, B Schlegelberger2, G Heil1,3, CWM Reuter1,KPu¨llmann1, RF Schlenk4,KDo¨hner4, M Heuser1, J Krauter1,HDo¨hner4, A Ganser1 and MA Morgan1 1Department of Hematology, Hemostasis, Oncology, and Stem Cell Transplantation, Hannover Medical School, Hannover, Germany; 2Institute of Cell and Molecular Pathology, Hannover Medical School, Hannover, Germany; 3Department of Internal Medicine V, Klinikum Lu¨denscheid, Lu¨denscheid, Germany and 4Department of Internal Medicine III, University Hospital of Ulm, Ulm, Germany To study the prevalence and prognostic importance of muta- novel somatic mutations affecting other genes, such as IDH1/ tions in NADH dehydrogenase subunit 4 (ND4), a mitochondrial IDH2 or DNMT3A, suggesting that multiple genetic aberrations encoded transmembrane component of the electron transport contribute to leukemic clone evolution and expansion.4–6 Using chain respiratory Complex I, 452 AML patients were examined for ND4 mutations by direct sequencing. The prognostic impact the same approach, mutations in the mitochondrial NADH of ND4 mutations was evaluated in the context of other clinical dehydrogenase subunit 4 (ND4) were described in 3 out of prognostic markers and genetic risk factors. In all, 29 of 452 93 AML patients.6 patients (6.4%) had either somatic (n ¼ 12) or germline (n ¼ 17) Mitochondria contribute to several key components of ND4 mutations predicted to affect translation.