Al Exposure Increases Proline Levels by Different Pathways in An
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Amino Acid Recognition by Aminoacyl-Trna Synthetases
www.nature.com/scientificreports OPEN The structural basis of the genetic code: amino acid recognition by aminoacyl‑tRNA synthetases Florian Kaiser1,2,4*, Sarah Krautwurst3,4, Sebastian Salentin1, V. Joachim Haupt1,2, Christoph Leberecht3, Sebastian Bittrich3, Dirk Labudde3 & Michael Schroeder1 Storage and directed transfer of information is the key requirement for the development of life. Yet any information stored on our genes is useless without its correct interpretation. The genetic code defnes the rule set to decode this information. Aminoacyl-tRNA synthetases are at the heart of this process. We extensively characterize how these enzymes distinguish all natural amino acids based on the computational analysis of crystallographic structure data. The results of this meta-analysis show that the correct read-out of genetic information is a delicate interplay between the composition of the binding site, non-covalent interactions, error correction mechanisms, and steric efects. One of the most profound open questions in biology is how the genetic code was established. While proteins are encoded by nucleic acid blueprints, decoding this information in turn requires proteins. Te emergence of this self-referencing system poses a chicken-or-egg dilemma and its origin is still heavily debated 1,2. Aminoacyl-tRNA synthetases (aaRSs) implement the correct assignment of amino acids to their codons and are thus inherently connected to the emergence of genetic coding. Tese enzymes link tRNA molecules with their amino acid cargo and are consequently vital for protein biosynthesis. Beside the correct recognition of tRNA features3, highly specifc non-covalent interactions in the binding sites of aaRSs are required to correctly detect the designated amino acid4–7 and to prevent errors in biosynthesis5,8. -
Conformational Properties of Constrained Proline Analogues and Their Application in Nanobiology”
UNIVERSITAT POLITÈCNICA DE CATALUNYA DEPARTAMENT D’ENGINYERIA QUÍMICA “CONFORMATIONAL PROPERTIES OF CONSTRAINED PROLINE ANALOGUES AND THEIR APPLICATION IN NANOBIOLOGY” Alejandra Flores Ortega Supervisors: Dr. Carlos Alemán Llansó and Dr. Jordi Casanovas Salas. th Barcelona, 27 January 2009 “Chance is a word void of sense; nothing can exist without a cause”. François-Marie Arouet, Voltaire “Imagination will often carry us to worlds that never were. But without it, we go nowhere”. Carl Sagan iii ACKNOWLEDGEMENTS I would like to acknowledge to Dr. Carlos Aleman and Dr. Jordi Cassanovas Salas for an interesting research theme, and scientific support. I gratefully acknowledge to Dr. David Zanuy for interesting suggestions and strong discussions, without their support this would be an unfulfilled task. Also I, would like to address my thanks to all my colleagues in my group and department, specially Elaine Armelin for assiting me in many different ways. I thank not only my friends, but also colleagues for helping me to overcome the stressful time, without whom it would have been difficult to cope up. I wish to express my gratefulness to my parents, specially to my mother, María Esther, for all his care, and support. Also I will like to thanks to my friends and specially Jesus, Merches, Laura y Arturo. My PhD thesis have been finished for all this support. I am greatly indepted to Dr. Ruth Nussinov at NCI, Dr. Carlos Cativiela at the University of Zaragoza and Ana I. Jiménez at the “Instituto de Ciencias de Materiales de Aragon” for a collaborative effort. I wish to thank all my colleague in the “Chimie et Biochimie Théoriques, Faculté des Sciences et Techniques” in Nancy France, I will be grateful to have worked with : Pr. -
Low Proline Diet in Type I Hyperprolinaemia
Arch Dis Child: first published as 10.1136/adc.46.245.72 on 1 February 1971. Downloaded from Archives of Disease in Childhood, 1971, 46, 72. Low Proline Diet in Type I Hyperprolinaemia J. T. HARRIES, A. T. PIESOWICZ,* J. W. T. SEAKINS, D. E. M. FRANCIS, and 0. H. WOLFF From The Hospital for Sick Children, and the Institute of Child Health, University of London Harries, J. T., Piesowicz, A. T., Seakins, J. W. T., Francis, D. E. M., and Wolff, 0. H. (1971). Archives of Disease in Childhood, 46, 72. Low proline diet in type I hyperprolinaemia. A diagnosis of Type I hyperprolinaemia was made in a 7-month-old infant who presented with hypocalcaemic convulsions and malabsorp- tion. The plasma levels of proline were grossly raised and the urinary excretion of proline, hydroxyproline, and glycine was increased; neurological development was delayed and there were associated abnormalities of the electroencephalogram, renal tract, and bones. Restriction of dietary proline at the age of 9 months resulted in a prompt fall of plasma levels of proline to normal, and a low proline diet was continued until the age of 27 months when persistence of the biochemical defect was shown. During the period of dietary treatment, growth was satisfactory, mental development improved, and the electroencephalogram, and the renal, skeletal, and intestinal abnormalities disappeared. Proline should be regarded as a 'semi-essential' amino acid in the growing infant. Hyperprolinaemia, appearing in several members balance can be maintained on a proline-free diet copyright. of a family was first described by Scriver, Schafer, (Rose et al., 1955), and therefore the amino acid is and Efron in 1961. -
Dietary and Pharmacological Induction of Serine Synthesis Genes
bioRxiv preprint doi: https://doi.org/10.1101/2020.06.15.151860; this version posted June 15, 2020. The copyright holder for this preprint (which was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under aCC-BY-NC 4.0 International license. Dietary and pharmacological induction of serine synthesis genes Alexei Vazquez1,2,* 1Cancer Research UK Beatson Institute, Glasgow, UK 2Institute of Cancer Sciences, University of Glasgow, Glasgow, UK Email: [email protected] Abstract gene coding for 3-phosphoglycerate dehydrogenase (Phgdh), the first enzyme of serine synthesis, causes There is an increasing interest in the pathway of L-serine neurodevelopmental abnormalities and it is embryonic synthesis and its. Although L-serine and downstream lethal 4 in mice. products can be obtained from the diet, serine deficiency has been documented in neurological disorders, macular The manifestation of serine deficiency in the human degeneration and aging. This evidence calls for strategies population call for strategies to increase the availability of to induce serine synthesis. Here I address this problem serine. Dietary serine supplementation seems the obvious taking advantage of the wealth of data deposited in the strategy 5. However, for a number of reasons, serine gene expression omnibus database. I uncover that low supplementation is not an effective approach in general 5. protein and ketogenic diets increase the expression of Dietary serine is rapidly incorporated into proteins or serine synthesis genes in the liver and the brain relative to broken down to glycine and formate 6. -
Amino Acid Catalyzed Direct Asymmetric Aldol Reactions: a Bioorganic Approach to Catalytic Asymmetric Carbon-Carbon Bond-Forming Reactions
5260 J. Am. Chem. Soc. 2001, 123, 5260-5267 Amino Acid Catalyzed Direct Asymmetric Aldol Reactions: A Bioorganic Approach to Catalytic Asymmetric Carbon-Carbon Bond-Forming Reactions Kandasamy Sakthivel, Wolfgang Notz, Tommy Bui, and Carlos F. Barbas III* Contribution from The Skaggs Institute for Chemical Biology and the Department of Molecular Biology, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, California 92037 ReceiVed January 3, 2001 Abstract: Direct asymmetric catalytic aldol reactions have been successfully performed using aldehydes and unmodified ketones together with commercially available chiral cyclic secondary amines as catalysts. Structure- based catalyst screening identified L-proline and 5,5-dimethyl thiazolidinium-4-carboxylate (DMTC) as the most powerful amino acid catalysts for the reaction of both acyclic and cyclic ketones as aldol donors with aromatic and aliphatic aldehydes to afford the corresponding aldol products with high regio-, diastereo-, and enantioselectivities. Reactions employing hydroxyacetone as an aldol donor provide anti-1,2-diols as the major product with ee values up to >99%. The reactions are assumed to proceed via a metal-free Zimmerman- Traxler-type transition state and involve an enamine intermediate. The observed stereochemistry of the products is in accordance with the proposed transition state. Further supporting evidence is provided by the lack of nonlinear effects. The reactions tolerate a small amount of water (<4 vol %), do not require inert reaction conditions and preformed enolate equivalents, and can be conveniently performed at room temperature in various solvents. In addition, reaction conditions that facilitate catalyst recovery as well as immobilization are described. Finally, mechanistically related addition reactions such as ketone additions to imines (Mannich- type reactions) and to nitro-olefins and R,â-unsaturated diesters (Michael-type reactions) have also been developed. -
Proline Oxidase Controls Proline, Glutamate, and Glutamine Cellular Concentrations in a U87 Glioblastoma Cell Line
RESEARCH ARTICLE Proline oxidase controls proline, glutamate, and glutamine cellular concentrations in a U87 glioblastoma cell line Pamela Cappelletti1,2*, Elena Tallarita1, Valentina Rabattoni1, Paola Campomenosi1,2, Silvia Sacchi1,2, Loredano Pollegioni1,2 1 Department of Biotechnology and Life Sciences, University of Insubria, Varese, Italy, 2 The Protein Factory Research Center, Politecnico of Milano and University of Insubria, Milano, Italy a1111111111 * [email protected] a1111111111 a1111111111 a1111111111 a1111111111 Abstract L-Proline is a multifunctional amino acid that plays an essential role in primary metabolism and physiological functions. Proline is oxidized to glutamate in the mitochondria and the FAD-containing enzyme proline oxidase (PO) catalyzes the first step in L-proline degrada- OPEN ACCESS tion pathway. Alterations in proline metabolism have been described in various human dis- Citation: Cappelletti P, Tallarita E, Rabattoni V, eases, such as hyperprolinemia type I, velo-cardio-facial syndrome/Di George syndrome, Campomenosi P, Sacchi S, Pollegioni L (2018) schizophrenia and cancer. In particular, the mutation giving rise to the substitution Leu441- Proline oxidase controls proline, glutamate, and glutamine cellular concentrations in a U87 Pro was identified in patients suffering of schizophrenia and hyperprolinemia type I. Here, glioblastoma cell line. PLoS ONE 13(4): e0196283. we report on the expression of wild-type and L441P variants of human PO in a U87 glioblas- https://doi.org/10.1371/journal.pone.0196283 toma human cell line in an attempt to assess their effect on glutamate metabolism. The sub- Editor: Suzie Chen, Rutgers University, UNITED cellular localization of the flavoenzyme is not altered in the L441P variant, for which specific STATES activity is halved compared to the wild-type PO. -
Proline- and Alanine-Rich N-Terminal Extension of the Basic Bovine P-Crystallin B1 Chains
CORE Metadata, citation and similar papers at core.ac.uk Provided by Elsevier - Publisher Connector Volume 161, number 2 FEBS 0790 September 1983 Proline- and alanine-rich N-terminal extension of the basic bovine P-crystallin B1 chains G.A.M. Berbers, W.A. Hoekman, H. Bloemendal, W.W. de Jong, T. Kleinschmidt* and G. Braunitzer* Laboratorium voor Biochemie, Universiteit van Nijmegen, Geert Grooteplein Noord 21, 6525 EZ Nijmegen, The Netherlands and *Max-Planck-Institut ft’ir Biochemie, Abteilung Proteinchemie, D-8033 Martinsried bei Miinchen, FRG Received 22 June 1983 The amino acid sequence of the N-terminal region of the two basic bovine &crystallin B1 chains has been analyzed. The results reveal that @Bibis derived in vivo from the primary gene product @la by removal of a short N-terminal sequence. It appears that them1 chains have the same domain structure as observed in other /3- and y-crystallin chains. They have, however, a very long N-terminal extension in comparison with other &chains. This extension is mainly composed of a remarkable Pro- and Ala-rich sequence, which suggests an interaction of these structural proteins with the cytoskeleton and/or the plasma membranes of the lens cells. Protein sequence Bovine &crystallin N-terminal extension Proline- and aianine-rich Domain structure 1. INTRODUCTION 33 000 and 31000, respectively, are characteristic for fltikt, [ 111. ,8Fha is a primary gene product, from The crystallins are evolutionary highly conserv- which ,8&b arises by post-translational modifica- ed structural eye lens proteins, which can be divid; tion [lo-121, most probably a proteolytic step ed into 4 classes: (Y-,,&, y- and t-crystallin [ 11. -
Jp Xvii the Japanese Pharmacopoeia
JP XVII THE JAPANESE PHARMACOPOEIA SEVENTEENTH EDITION Official from April 1, 2016 English Version THE MINISTRY OF HEALTH, LABOUR AND WELFARE Notice: This English Version of the Japanese Pharmacopoeia is published for the convenience of users unfamiliar with the Japanese language. When and if any discrepancy arises between the Japanese original and its English translation, the former is authentic. The Ministry of Health, Labour and Welfare Ministerial Notification No. 64 Pursuant to Paragraph 1, Article 41 of the Law on Securing Quality, Efficacy and Safety of Products including Pharmaceuticals and Medical Devices (Law No. 145, 1960), the Japanese Pharmacopoeia (Ministerial Notification No. 65, 2011), which has been established as follows*, shall be applied on April 1, 2016. However, in the case of drugs which are listed in the Pharmacopoeia (hereinafter referred to as ``previ- ous Pharmacopoeia'') [limited to those listed in the Japanese Pharmacopoeia whose standards are changed in accordance with this notification (hereinafter referred to as ``new Pharmacopoeia'')] and have been approved as of April 1, 2016 as prescribed under Paragraph 1, Article 14 of the same law [including drugs the Minister of Health, Labour and Welfare specifies (the Ministry of Health and Welfare Ministerial Notification No. 104, 1994) as of March 31, 2016 as those exempted from marketing approval pursuant to Paragraph 1, Article 14 of the Same Law (hereinafter referred to as ``drugs exempted from approval'')], the Name and Standards established in the previous Pharmacopoeia (limited to part of the Name and Standards for the drugs concerned) may be accepted to conform to the Name and Standards established in the new Pharmacopoeia before and on September 30, 2017. -
The Fate of Arginine and Proline Carbon in Squid Tissuesl
Pacific Science (1982), vol. 36, no. 3 © 1983 by the University of Hawaii Press. All rights reserved The Fate of Arginine and Proline Carbon in Squid Tissuesl T. P. MOMMSEN,2 C. J. FRENCH,2 B. EMMETI,2 and P. W. HOCHACHKA2 ABSTRACT: The metabolism of proline and arginine was investigated in kidney, gill, and heart of the pelagic squid, Symplectoteuthis. The rates of CO2 release from 14C-proline exceeded the rates from 14C-arginine. The metabolic rate of arginine and proline was assessed by monitoring the incorporation of arginine-derived carbon into various intermediates. Arginine was metabolized, through ornithine, to proline as well as to glutamate and various subsequent derivatives (alanine, octopine, aspartate, and carboxylic acids). The same com ponents became labeled using 14C-proline as the starting substrate, but only the gill was capable ofconverting proline to arginine via the urea cycle. In addition, 14C-proline oxidation rates were high enough to exceed those of 14C-glucose in at least three tissues, kidney, heart, and inner mantle muscle. AT LEAST IN PART because ofthe large pool size data for heart, gill, and kidney from the squid, of free amino acids in cephalopod muscles Symplectoteuthis, showing the capacity for ar (e.g., see Hochachka, French, and Meredith ginine conversion to proline. The conversion 1978), interest recently has been focusing ofproline to arginine was measurable only in on their possible roles in energy metabolism. the gill. Although qualitatively similar to re During metabolic studies on the 1979 Alpha sults obtained with other species, these data Helix Cephalopod Expedition, relatively high also show some important, tissue-specific dif rates of CO2 release from arginine and ferences (Mommsen et al. -
Arginine Is Synthesized from Proline, Not Glutamate, in Enterally Fed Human Preterm Neonates
0031-3998/11/6901-0046 Vol. 69, No. 1, 2011 PEDIATRIC RESEARCH Printed in U.S.A. Copyright © 2010 International Pediatric Research Foundation, Inc. Arginine Is Synthesized From Proline, Not Glutamate, in Enterally Fed Human Preterm Neonates CHRIS TOMLINSON, MAHROUKH RAFII, MICHAEL SGRO, RONALD O. BALL, AND PAUL PENCHARZ Department of Paediatrics [C.T., M.S., P.P.], Research Institute [C.T., M.R., P.P.], The Hospital for Sick Children, Toronto, Ontario M5G1X8, Canada; Department of Nutritional Sciences [C.T., M.S., P.P.], University of Toronto, Toronto, Ontario M5S3E2, Canada; Department of Paediatrics [M.S.], St Michael’s Hospital, Toronto, Ontario M5B1W8, Canada; Department of Agricultural, Food and Nutritional Science [R.O.B., P.P.], University of Alberta, Edmonton, Alberta T6G2P5, Canada ABSTRACT: In neonatal mammals, arginine is synthesized in the litis (NEC) (8) and pulmonary hypertension (9). Furthermore, enterocyte, with either proline or glutamate as the dietary precursor. arginine supplementation was shown to reduce the incidence We have shown several times in piglets that proline is the only of all stages of NEC in moderately at risk infants (10) and a precursor to arginine, although in vitro evidence supports glutamate single bolus infusion of i.v. arginine improved oxygenation in in this role. Because of this uncertainty, we performed a multitracer infants with pulmonary hypertension (11). Therefore, because stable isotope study to determine whether proline, glutamate, or both are dietary precursors for arginine in enterally fed human neonates. arginine is clearly important for metabolism in the neonate, it Labeled arginine (M ϩ 2), proline (M ϩ 1), and glutamate (M ϩ 3) is critical to understand the metabolic pathways involved in its were given enterally to 15 stable, growing preterm infants (GA at synthesis. -
Nonproteinogenic Deep Mutational Scanning of Linear and Cyclic Peptides
Nonproteinogenic deep mutational scanning of linear and cyclic peptides Joseph M. Rogersa, Toby Passiouraa, and Hiroaki Sugaa,b,1 aDepartment of Chemistry, Graduate School of Science, The University of Tokyo, Tokyo 113-0033, Japan; and bCore Research for Evolutionary Science and Technology, Japan Science and Technology Agency, Saitama 332-0012, Japan Edited by David Baker, University of Washington, Seattle, WA, and approved September 18, 2018 (received for review June 10, 2018) High-resolution structure–activity analysis of polypeptides re- mutants that can be constructed (18). Moreover, it is possible to quires amino acid structures that are not present in the universal combine parallel peptide synthesis with measures of function genetic code. Examination of peptide and protein interactions (19). However, these approaches cannot construct peptide li- with this resolution has been limited by the need to individually braries with the sequence length and numbers that deep muta- synthesize and test peptides containing nonproteinogenic amino tional scanning can, which, at its core, uses high-fidelity nucleic acids. We describe a method to scan entire peptide sequences with acid-directed synthesis of polypeptides by the ribosome. multiple nonproteinogenic amino acids and, in parallel, determine Ribosomal synthesis (i.e., translation) can be manipulated to the thermodynamics of binding to a partner protein. By coupling include nonproteinogenic amino acids (20). In vitro genetic code genetic code reprogramming to deep mutational scanning, any reprogramming is particularly versatile, allowing for the in- number of amino acids can be exhaustively substituted into pep- corporation of amino acids with diverse chemical structures (21). tides, and single experiments can return all free energy changes of Flexizymes, flexible tRNA-acylation ribozymes, can load almost binding. -
Electrochemical Analysis of Evans Blue by Surfactant Modified Carbon Nanotube Paste Electrode B
Journal of Materials and J. Mater. Environ. Sci., 2019, Volume 10, Issue 9, Page 882-890 Environmental Sciences ISSN : 2028-2508 CODEN : JMESCN http://www.jmaterenvironsci.com Copyright © 2019, University of Mohammed Premier Oujda Morocco Electrochemical Analysis of Evans Blue by Surfactant Modified Carbon Nanotube Paste Electrode 1,2 1* 2 1 B. M. Amrutha , J. G. Manjunatha , S. Aarti Bhatt , N. Hareesha 1 Department of Chemistry, FMKMC College, Madikeri, Constituent College of Mangalore University, Karnataka, India 2 Department of Chemistry, NMAM Institute of Technology, Nitte, Karnataka, India. Received 08 Jul 2019, Abstract Revised 08 Aug 2019, Electrochemical sensor for the specific and sensitive detection of Evans blue (EB) at Accepted 10 Aug 2019 physiological pH in 0.2M phosphate buffer solution (PBS) was developed by the surface modification using Triton X -100 (TX-100) surfactant. The cyclic voltammetry (CV) studies show enhanced peak separation, appreciable sensitivity, selectivity and stability Keywords which allowed this TX-100 surfactant modified carbon nanotube paste electrode (TX- Cyclic Voltammetry, 100MCNTPE) to analyse EB individually and simultaneously along with tartrazine (TZ) in Carbon nanotube, the potential range of 0.2 V to 0.7 V. The electrode morphology was characterised by field TX-100, emission scanning electron microscopy (FESEM). The oxidation potential of EB shifted Evans blue, negatively, and enhanced irreversible oxidation peak current was observed at 0.505V which Tartrazine. served as the analytical response. In the prime condition, the anodic peak current of EB increased linearly, and two linear ranges were observed from 10 µM to 100 µM with the [email protected] limit of detection (LOD) of 5.06 µM and limit of quantification (LOQ) of 16.87 µM.