Initiating Ribosomal Peptide Synthesis with Exotic Building Blocks
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Al Exposure Increases Proline Levels by Different Pathways in An
www.nature.com/scientificreports OPEN Al exposure increases proline levels by diferent pathways in an Al‑sensitive and an Al‑tolerant rye genotype Alexandra de Sousa1,2, Hamada AbdElgawad2,4, Fernanda Fidalgo1, Jorge Teixeira1, Manuela Matos3, Badreldin A. Hamed4, Samy Selim5, Wael N. Hozzein6, Gerrit T. S. Beemster2 & Han Asard2* Aluminium (Al) toxicity limits crop productivity, particularly at low soil pH. Proline (Pro) plays a role in protecting plants against various abiotic stresses. Using the relatively Al‑tolerant cereal rye (Secale cereale L.), we evaluated Pro metabolism in roots and shoots of two genotypes difering in Al tolerance, var. RioDeva (sensitive) and var. Beira (tolerant). Most enzyme activities and metabolites of Pro biosynthesis were analysed. Al induced increases in Pro levels in each genotype, but the mechanisms were diferent and were also diferent between roots and shoots. The Al‑tolerant genotype accumulated highest Pro levels and this stronger increase was ascribed to simultaneous activation of the ornithine (Orn)‑biosynthetic pathway and decrease in Pro oxidation. The Orn pathway was particularly enhanced in roots. Nitrate reductase (NR) activity, N levels, and N/C ratios demonstrate that N‑metabolism is less inhibited in the Al‑tolerant line. The correlation between Pro changes and diferences in Al‑sensitivity between these two genotypes, supports a role for Pro in Al tolerance. Our results suggest that diferential responses in Pro biosynthesis may be linked to N‑availability. Understanding the role of Pro in diferences between genotypes in stress responses, could be valuable in plant selection and breeding for Al resistance. Proline (Pro) is involved in a wide range of plant physiological and developmental processes1. -
Effects of Single Amino Acid Deficiency on Mrna Translation Are Markedly
www.nature.com/scientificreports OPEN Efects of single amino acid defciency on mRNA translation are markedly diferent for methionine Received: 12 December 2016 Accepted: 4 May 2018 versus leucine Published: xx xx xxxx Kevin M. Mazor, Leiming Dong, Yuanhui Mao, Robert V. Swanda, Shu-Bing Qian & Martha H. Stipanuk Although amino acids are known regulators of translation, the unique contributions of specifc amino acids are not well understood. We compared efects of culturing HEK293T cells in medium lacking either leucine, methionine, histidine, or arginine on eIF2 and 4EBP1 phosphorylation and measures of mRNA translation. Methionine starvation caused the most drastic decrease in translation as assessed by polysome formation, ribosome profling, and a measure of protein synthesis (puromycin-labeled polypeptides) but had no signifcant efect on eIF2 phosphorylation, 4EBP1 hyperphosphorylation or 4EBP1 binding to eIF4E. Leucine starvation suppressed polysome formation and was the only tested condition that caused a signifcant decrease in 4EBP1 phosphorylation or increase in 4EBP1 binding to eIF4E, but efects of leucine starvation were not replicated by overexpressing nonphosphorylatable 4EBP1. This suggests the binding of 4EBP1 to eIF4E may not by itself explain the suppression of mRNA translation under conditions of leucine starvation. Ribosome profling suggested that leucine deprivation may primarily inhibit ribosome loading, whereas methionine deprivation may primarily impair start site recognition. These data underscore our lack of a full -
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. -
Relative Reaction Rates of the Amino Acids Cysteine, Methionine, and Histidine with Analogs of the Anti-Cancer Drug Cisplatin Cynthia A
Western Kentucky University TopSCHOLAR® Honors College Capstone Experience/Thesis Honors College at WKU Projects 5-11-2015 Relative Reaction Rates of the Amino Acids Cysteine, Methionine, and Histidine with Analogs of the Anti-Cancer Drug Cisplatin Cynthia A. Tope Western Kentucky University, [email protected] Follow this and additional works at: http://digitalcommons.wku.edu/stu_hon_theses Part of the Medicinal-Pharmaceutical Chemistry Commons Recommended Citation Tope, Cynthia A., "Relative Reaction Rates of the Amino Acids Cysteine, Methionine, and Histidine with Analogs of the Anti-Cancer Drug Cisplatin" (2015). Honors College Capstone Experience/Thesis Projects. Paper 571. http://digitalcommons.wku.edu/stu_hon_theses/571 This Thesis is brought to you for free and open access by TopSCHOLAR®. It has been accepted for inclusion in Honors College Capstone Experience/ Thesis Projects by an authorized administrator of TopSCHOLAR®. For more information, please contact [email protected]. RELATIVE REACTION RATES OF THE AMINO ACIDS CYSTEINE, METHIONINE, AND HISTIDINE WITH ANALOGS OF THE ANTI-CANCER DRUG CISPLATIN A Capstone Experience/Thesis Project Presented in Partial Fulfillment of the Requirements for the Degree Bachelor of Science with Honors College Graduate Distinction at Western Kentucky University By: Cynthia A. Tope ***** Western Kentucky University 2015 CE/T Committee: Approved by: Professor Kevin Williams, Advisor _________________________ Professor Darwin Dahl Advisor Professor Lee Ann Smith Department of Chemistry Copyright: Cynthia A. Tope 2015 ABSTRACT We are studying the reaction of analogs of the anticancer drug cisplatin with amino acids that differ in size and shape. The reaction of cisplatin with proteins likely precedes reaction with DNA in the body, forming a variety of products that may be toxic to the human body. -
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. -
Chemical Methods for the Characterization of Proteolysis in Cheese During Ripening Plh Mcsweeney, Pf Fox
Chemical methods for the characterization of proteolysis in cheese during ripening Plh Mcsweeney, Pf Fox To cite this version: Plh Mcsweeney, Pf Fox. Chemical methods for the characterization of proteolysis in cheese during ripening. Le Lait, INRA Editions, 1997, 77 (1), pp.41-76. hal-00929515 HAL Id: hal-00929515 https://hal.archives-ouvertes.fr/hal-00929515 Submitted on 1 Jan 1997 HAL is a multi-disciplinary open access L’archive ouverte pluridisciplinaire HAL, est archive for the deposit and dissemination of sci- destinée au dépôt et à la diffusion de documents entific research documents, whether they are pub- scientifiques de niveau recherche, publiés ou non, lished or not. The documents may come from émanant des établissements d’enseignement et de teaching and research institutions in France or recherche français ou étrangers, des laboratoires abroad, or from public or private research centers. publics ou privés. Lait (1997) 77, 41-76 41 © ElseviernNRA Review Chemical methods for the characterization of proteolysis in cheese during ripening PLH McSweeney, PF Fox Department of Food Chemistry, University College, Cork, Ireland Summary - Proteolysis is the principal and most complex biochemical event which occurs during the maturation of most cheese varieties. Proteolysis has been the subject of much study and a range of analytieal techniques has been developed to assess its extent and nature. Methods for assessing pro- teolysis can he c1assified under two broad headings: non-specifie and specifie techniques, both of which are reviewed. Non-specifie techniques include the quantitation of nitrogen soluble in various extrac- tants or precipitants and the Iiberation of reactive groups. -
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. -
Designing Peptidomimetics
CORE Metadata, citation and similar papers at core.ac.uk Provided by UPCommons. Portal del coneixement obert de la UPC DESIGNING PEPTIDOMIMETICS Juan J. Perez Dept. of Chemical Engineering ETS d’Enginyeria Industrial Av. Diagonal, 647 08028 Barcelona, Spain 1 Abstract The concept of a peptidomimetic was coined about forty years ago. Since then, an enormous effort and interest has been devoted to mimic the properties of peptides with small molecules or pseudopeptides. The present report aims to review different approaches described in the past to succeed in this goal. Basically, there are two different approaches to design peptidomimetics: a medicinal chemistry approach, where parts of the peptide are successively replaced by non-peptide moieties until getting a non-peptide molecule and a biophysical approach, where a hypothesis of the bioactive form of the peptide is sketched and peptidomimetics are designed based on hanging the appropriate chemical moieties on diverse scaffolds. Although both approaches have been used in the past, the former has been more widely used to design peptidomimetics of secretory peptides, whereas the latter is nowadays getting momentum with the recent interest in designing protein-protein interaction inhibitors. The present report summarizes the relevance of the information gathered from structure-activity studies, together with a short review on the strategies used to design new peptide analogs and surrogates. In a following section there is a short discussion on the characterization of the bioactive conformation of a peptide, to continue describing the process of designing conformationally constrained analogs producing first and second generation peptidomimetics. Finally, there is a section devoted to review the use of organic scaffolds to design peptidomimetics based on the information available on the bioactive conformation of the peptide. -
Ratio of Phosphate to Amino Acids
National Institute for Health and Care Excellence Final Neonatal parenteral nutrition [D10] Ratio of phosphate to amino acids NICE guideline NG154 Evidence reviews February 2020 Final These evidence reviews were developed by the National Guideline Alliance which is part of the Royal College of Obstetricians and Gynaecologists FINAL Error! No text of specified style in document. Disclaimer The recommendations in this guideline represent the view of NICE, arrived at after careful consideration of the evidence available. When exercising their judgement, professionals are expected to take this guideline fully into account, alongside the individual needs, preferences and values of their patients or service users. The recommendations in this guideline are not mandatory and the guideline does not override the responsibility of healthcare professionals to make decisions appropriate to the circumstances of the individual patient, in consultation with the patient and/or their carer or guardian. Local commissioners and/or providers have a responsibility to enable the guideline to be applied when individual health professionals and their patients or service users wish to use it. They should do so in the context of local and national priorities for funding and developing services, and in light of their duties to have due regard to the need to eliminate unlawful discrimination, to advance equality of opportunity and to reduce health inequalities. Nothing in this guideline should be interpreted in a way that would be inconsistent with compliance with those duties. NICE guidelines cover health and care in England. Decisions on how they apply in other UK countries are made by ministers in the Welsh Government, Scottish Government, and Northern Ireland Executive. -
Enzymatic Aminoacylation of Trna with Unnatural Amino Acids
Enzymatic aminoacylation of tRNA with unnatural amino acids Matthew C. T. Hartman, Kristopher Josephson, and Jack W. Szostak* Department of Molecular Biology and Center for Computational and Integrative Biology, Simches Research Center, Massachusetts General Hospital, 185 Cambridge Street, Boston, MA 02114 Edited by Peter G. Schultz, The Scripps Research Institute, La Jolla, CA, and approved January 24, 2006 (received for review October 21, 2005) The biochemical flexibility of the cellular translation apparatus applicable to screening large numbers of unnatural amino acids. offers, in principle, a simple route to the synthesis of drug-like The commonly used ATP-PPi exchange assay, although very modified peptides and novel biopolymers. However, only Ϸ75 sensitive, does not actually measure the formation of the AA- unnatural building blocks are known to be fully compatible with tRNA product (13). A powerful assay developed by Wolfson and enzymatic tRNA acylation and subsequent ribosomal synthesis of Uhlenbeck (14) allows the observation of AA-tRNA synthesis modified peptides. Although the translation system can reject even with unnatural amino acids through the use of tRNA which substrate analogs at several steps along the pathway to peptide is 32P-labeled at the terminal C-p-A phosphodiester linkage (4, synthesis, much of the specificity resides at the level of the 15). Because the assay is based on the separation of AMP and aminoacyl-tRNA synthetase (AARS) enzymes that are responsible esterified AA-AMP by TLC, each amino acid analog must be for charging tRNAs with amino acids. We have developed an AARS tested in a separate assay mixture; moreover, this assay cannot assay based on mass spectrometry that can be used to rapidly generally distinguish between tRNA charged with the desired identify unnatural monomers that can be enzymatically charged unnatural amino acid or with contaminating natural amino acid. -
Design and Synthesis of Novel Prodrugs to Modulate Gaba Receptors in Cancer Hui Zhang
DESIGN AND SYNTHESIS OF NOVEL PRODRUGS TO MODULATE GABA RECEPTORS IN CANCER HUI ZHANG Thesis submitted in partial fulfilment of the requirements of Edinburgh Napier University for the degree of Doctor of Philosophy March 2017 Declaration It is hereby declared that this thesis and the research work upon which it is based were conducted by the author, Hui Zhang. Hui Zhang Abstract of Thesis GABA (gamma-amino butanoic acid) is the main inhibitory neurotransmitter in the mammalian central nervous system. GABA has been found to play an inhibitory role in some cancers, including colon carcinoma, cholangiocarcinoma, and lung adenocarcinoma. Growing evidence shows that GABAB receptors are involved in tumour development. The expression level of GABAB receptors was found to be upregulated in some human tumours, including the pancreas, and cancer cell lines, suggesting that GABAB receptors may be potential targets for cancer therapy and diagnosis. In this research programme, several diverse series of potential anticancer prodrugs of GABA and GABA receptor-targeting agents have been rationally designed and synthesised for selective activation in the tumour microenvironment. In one approach, a series of oligopeptide conjugate prodrugs have been synthesised as protease-activatable substrates for either the extracellular matrix metalloproteinase MMP-9 or the lysosomal endoprotease legumain; each of which are overexpressed in the tumour environment and are effectors of tumour growth and metastasis. Specifically, a novel fluorogenic, oligopeptide FRET substrate prodrug of legumain HZ101 (Rho-Pro-Ala-Asn~GABA-spacer-AQ) has been characterised and shown to have theranostic potential. Proof of principle has been demonstrated using recombinant human legumain for which HZ101 is an efficient substrate and is latently quenched until cleaved. -
L-Methionine
October 24, 2011 Lisa Brines, Ph.D. National List Manager USDA/AMS/NOP, Standards Division 1400 Independence Ave. SW Room 2646-So., Ag Stop 0268 Washington, DC 20250-0268 RE: Petition for inclusion of L-Methionine on the National List at §205.605(b) as a synthetic non-agricultural substance allowed in or on processed infant formula products labeled as “organic” or “made with organic (specified ingredients)” with the annotation “for use only in infant formula based on isolated soy protein.” Dear Dr. Brines, The International Formula Council (IFC) is an association of manufacturers and marketers of formulated nutrition products (e.g., infant formulas and adult nutritionals) whose members are based predominantly in North America. IFC members support the American Academy of Pediatrics’ (AAP) position that breastfeeding is the preferred method of feeding infants. We also agree with the AAP that, for infants who do not receive breast milk, iron-fortified infant formula is the only safe and recommended alternative, IFC members are committed to providing infant formulas of the highest quality for those mothers who cannot or choose not to breastfeed, discontinue breastfeeding prior to one year or choose to supplement. This petition seeks to add L-Methionine to the National List to permit its addition as a nonagricultural ingredient in infant formula based on isolated soy protein. L-Methionine is an essential amino acid for humans of all ages. Amino acids are the building blocks of protein. An essential amino acid is one that must be provided in the foods in our diet since our bodies do not have the capability of producing enough of it for normal metabolism and growth.