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A Few Experimental Suggestions Using Minerals to Obtain Peptides with a High Concentration of L-Amino Acids and Protein Amino Acids
S S symmetry Hypothesis A Few Experimental Suggestions Using Minerals to Obtain Peptides with a High Concentration of L-Amino Acids and Protein Amino Acids Dimas A. M. Zaia 1,* and Cássia Thaïs B. V. Zaia 2 1 Laboratório de Química Prebiótica-LQP, Departamento de Química, Universidade Estadual de Londrina, CEP 86 057-970 Londrina, Brazil 2 Laboratório de Fisiologia Neuroendocrina e Metabolismo–LaFiNeM, Departamento de Ciências Fisiológicas, Universidade Estadual de Londrina, CEP 86 057-970 Londrina, Brazil; [email protected] * Correspondence: [email protected] Received: 9 October 2020; Accepted: 25 November 2020; Published: 10 December 2020 Abstract: The peptides/proteins of all living beings on our planet are mostly made up of 19 L-amino acids and glycine, an achiral amino acid. Arising from endogenous and exogenous sources, the seas of the prebiotic Earth could have contained a huge diversity of biomolecules (including amino acids), and precursors of biomolecules. Thus, how were these amino acids selected from the huge number of available amino acids and other molecules? What were the peptides of prebiotic Earth made up of? How were these peptides synthesized? Minerals have been considered for this task, since they can preconcentrate amino acids from dilute solutions, catalyze their polymerization, and even make the chiral selection of them. However, until now, this problem has only been studied in compartmentalized experiments. There are separate experiments showing that minerals preconcentrate amino acids by adsorption or catalyze their polymerization, or separate L-amino acids from D-amino acids. Based on the [GADV]-protein world hypothesis, as well as the relative abundance of amino acids on prebiotic Earth obtained by Zaia, several experiments are suggested. -
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. -
Proteins, Peptides, and Amino Acids
Proteins, Peptides, and Amino Acids Chandra Mohan, Ph.D. Calbiochem-Novabiochem Corp., San Diego, CA The Chemical Nature of Amino Acids Peptides and polypeptides are polymers of α-amino acids. There are 20 α-amino acids that make-up all proteins of biological interest. The α-amino acids in peptides and proteins α consist of a carboxylic acid (-COOH) and an amino (-NH2) functional group attached to the same tetrahedral carbon atom. This carbon is known as the -carbon. The type of R- group attached to this carbon distinguishes one amino acid from another. Several other amino acids, also found in the body, may not be associated with peptides or proteins. These non-protein-associated amino acids perform specialized functions. Some of the α-amino acids found in proteins are also involved in other functions in the body. For example, tyrosine is involved in the formation of thyroid hormones, and glutamate and aspartate act as neurotransmitters at fast junctions. R Amino acids exist in either D- or L- enantiomorphs or stereoisomers. The D- and L-refer to the absolute confirmation of optically active compounds. With the exception of glycine, all other amino acids are mirror images that can not be superimposed. Most of the amino acids found in nature are of the L-type. Hence, eukaryotic proteins are always composed of L-amino acids although D-amino acids are found in bacterial cell walls and in some peptide antibiotics. All biological reactions occur in an aqueous phase. Hence, it is important to know how the R-group of any given amino acid dictates the structure-function relationships of peptides and proteins in solution. -
COMPILATION of AMINO ACIDS, DRUGS, METABOLITES and OTHER COMPOUNDS in MASSTRAK AMINO ACID ANALYSIS SOLUTION Paula Hong, Kendon S
COMPILATION OF AMINO ACIDS, DRUGS, METABOLITES AND OTHER COMPOUNDS IN MASSTRAK AMINO ACID ANALYSIS SOLUTION Paula Hong, Kendon S. Graham, Alexandre Paccou, T homas E. Wheat and Diane M. Diehl INTRODUCTION LC conditions Physiological amino acid analysis is commonly performed to LC System: Waters ACQUITY UPLC® System with TUV monitor and study a wide variety of metabolic processes. A wide Column: MassTrak AAA Column 2.1 x 150 mm, 1.7 µm variety of drugs, foods, and metabolic intermediates that may Column Temp: 43 ˚C be present in biological fluids can appear as peaks in amino Flow Rate: 400 µL/min. acid analysis, therefore, it is important to be able to identify Mobile Phase A: MassTrak AAA Eluent A Concentrate, unknown compounds.1,2,3 The reproducibility and robustness of diluted 1:10 the MassTrak Amino Acid Analysis Solution make this method well Mobile Phase B: MassTrak AAA Eluent B suited to such a study as well.4 Weak Needle Wash: 5/95 Acetonitrile/Water Strong Needle Wash: 95/5 Acetonitrile/Water Gradient: MassTrak AAA Standard Gradient (as provided in kit) Detection: UV @ 260 nm Injection Volume: 1 µL EXPERIMENTAL Injection Mode: Partial Loop with Needle Overfill (PLNO) Compound sample preparation A library of compounds was assembled. Each compound was derivatized individually and spiked into the MassTrak™ AAA Solution Standard prior to chromatographic analysis. The elution RESULTS AND DISCUSSION position of each tested compound could be related to known amino acids. A wide variety of antibiotics, pharmaceutical compounds and metabolite by-products are found in biological fluids. The reten- 1. -
Supplementary File 1 (PDF, 650 Kib)
Preliminary Zinc and boscalid sub lethal concentrations Zinc and boscalid sub lethal concentrations were determined by running preliminary 72‐hour LC50 exposures. A range of concentrations, resulting in 100% survival to 100% mortality was run for both chemicals in water only exposures. Filtered seawater was used as a control and to dilute stock concentrations of zinc and boscalid. Six treatments with three replicates were run for both chemicals including a control (seawater only). The zinc chloride (ZnCl2) exposure concentrations were: 62mg/L; 125mg/L; 250mg/L; 500mg/L and 1000mg/L. The commercial fungicide Filan® has 500g/kg active ingredient of boscalid, concentrations of 100mg/L; 250mg/L; 500mg/L; 750mg/L and 1000mg/L. Acid‐ rinsed 600ml glass beakers were randomly placed in a temperature‐controlled incubator at 20oC (+/‐ 1oC) with added aeration and a one ply sheet of ethanol rinsed toilet paper in each beaker as substratum. No food was added; the average pH of the water was 7.5 across treatments. The dissolved oxygen remained between 70‐100%. Zinc chloride LC50 = 125mg/L and boscalid LC50 = 750mg/L. Table S1. –Concentrations of boscalid and zinc at 0 h and one week. Measured concentrations of boscalid and zinc detected in estuaries in Victoria, Australia. Exposure at Control Exposure at 0 hr Environmental dose 1 week Boscalid 0 N/A 75 mg/L 3.3 mg/L (Vu et al. 2016) Zinc 0.026 – 0.034 mg/L 12.5 mg/L 3.4 mg/L (Long et al. 2015) Table S2. Water Quality Parameters. Date Sample Dissolved oxygen (%) pH Conductivity (µS/cm) Ammonia 15/05/17 Control 98.36 8.44 59464.4 0.25 15/05/17 Zinc 99.10 8.31 59379.1 0.25 15/05/17 Boscalid 99.18 8.28 59656.8 0.25 15/05/17 Mixture 94.81 8.25 59386.0 0.25 30/05/17 Control 101.90 8.16 59332.4 0.5 30/05/17 Zinc 102.47 8.11 59536.7 0.5 30/05/17 Boscalid 92.17 8.15 59489.3 0.5 30/05/17 Mixture 101.57 8.14 59593.2 0.5 Supplementary Material . -
Vitamin K Dependent Modifications of Glutamic Acid Residues In
Proc. Nat. Acad. Sci. USA Vol. 71, No. 7, pp. 2730-2733, July 1974 Vitamin K Dependent Modifications of Glutamic Acid Residues in Prothrombin (proton magnetic resonance spectroscopy/mass spectrometry) JOHAN STENFLO*, PER FERNLUND*, WILLIAM EGANt, AND PETER ROEPSTORFFt * Department of Clinical Chemistry, University of Lund, Malm6 General Hospital, 8-214 01 Malm6, Sweden; t Department of Physical Chemistry II, Lund Institute of Technology, Chemical Center, S-220 07 Lund, Sweden; and t The Danish Institute of Protein Chemistry, DK-2970 Horsholm, Denmark Communicated by Sune Bergstrom, May 9, 1974 ABSTRACT A tetrapeptide, residues 6 to 9 in normal hydrogen on the -y carbon atom by a carboxyl group. This prothrombin, was isolated from the NH2-terminal, Ca2+- work will be described in greater detail elsewhere. binding part of normal prothrombin. The electrophoretic mobility of the peptide was too high to be explained en- tirely by its amino-acid composition. According to 1H MATERIALS AND METHODS nuclear magnetic resonance spectroscopy and mass Isolation of Tetrapeptide. The heptapeptide from normal spectrometry, the peptide contained two residues of modi- fied glutamic acid, -y-carboxyglutamic acid (3-amino-1,1,3- prothrombin (residues 4 to 10) (ref. 13) was first thoroughly propanetricarboxylic acid), a hitherto unidentified amino digested with aminopeptidase M (Sigma) and afterwards with acid. This amino acid gives normal prothrombin the Ca2 +_ carboxypeptidase B (Sigma). A tetrapeptide was isolated binding ability that is necessary for its activation. Obser- from the digest by gel chromatography on Sephadex G-25 vations indicate that abnormal prothrombin, induced by the vitamin K antagonist, dicoumarol, lacks these modi- superfine and obtained in pure form as judged by high voltage fied glutamic acid residues and that this is the reason why electrophoresis at pH 6.5 (electrophoretic mobility relative to abnormal prothrombin does not bind Ca2+ and is non- that of aspartic acid 1.09) and amino-acid analysis (14), which functioning in blood coagulation. -
N,N-Diprotected Dehydroamino Acid Derivatives: Versatile Substrates for the Synthesis of Novel Amino Acids
N,N-DIPROTECTED DEHYDROAMINO ACID DERIVATIVES: VERSATILE SUBSTRATES FOR THE SYNTHESIS OF NOVEL AMINO ACIDS Paula M. T. Ferreira and Luís S. Monteiro Department of Chemistry, University of Minho, Gualtar, 4710-057 Braga, Portugal (e-mail: [email protected]) Abstract. Non-proteinogenic amino acids are an important class of organic compounds that can have intrinsic biological activity or can be found in peptides with antiviral, antitumor, anti-inflammatory or immunosuppressive activities. This type of compounds is also important in drug development, in the elucidation of biochemical pathways and in conformational studies. Therefore, research towards efficient methods that allow the synthesis of these compounds constitutes an important area of peptide chemistry. In our laboratories we have developed a new and high yielding method for the synthesis of N,N-diprotected dehydroamino acid derivatives using tert-butyl pyrocarbonate and 4-dimethylaminopyridine. These compounds were used as substrates in several types of reactions, allowing the synthesis of a variety of new amino acid derivatives. Some of these new compounds are heterocyclic systems or contain heterocyclic moieties such as pyrazole, indole, or imidazole. Thus, several nitrogen heterocycles were reacted with N,N-diprotected dehydroalanine to give new β-substituted alanines and dehydroalanines. Furanic amino acids were obtained treating the methyl ester of N-(4-toluenesulfonyl), N-(tert-butoxycarbonyl) dehydroalanine with carbon nucleophiles of the β-dicarbonyl type having at least one methyl group attached to one of the carbonyl groups. Treatment of these furanic amino acids with trifluoracetic acid afforded pyrrole derivatives in good to high yields. A N,N-diprotected 1,4-dihydropyrazine was obtained reacting the methyl ester of N-(4-toluenesulfonyl), N-(tert-butoxycarbonyl)dehydroalanine with 4-dimethylaminopyridine and an excess of potassium carbonate. -
Dissociation Constants of Organic Acids and Bases
DISSOCIATION CONSTANTS OF ORGANIC ACIDS AND BASES This table lists the dissociation (ionization) constants of over pKa + pKb = pKwater = 14.00 (at 25°C) 1070 organic acids, bases, and amphoteric compounds. All data apply to dilute aqueous solutions and are presented as values of Compounds are listed by molecular formula in Hill order. pKa, which is defined as the negative of the logarithm of the equi- librium constant K for the reaction a References HA H+ + A- 1. Perrin, D. D., Dissociation Constants of Organic Bases in Aqueous i.e., Solution, Butterworths, London, 1965; Supplement, 1972. 2. Serjeant, E. P., and Dempsey, B., Ionization Constants of Organic Acids + - Ka = [H ][A ]/[HA] in Aqueous Solution, Pergamon, Oxford, 1979. 3. Albert, A., “Ionization Constants of Heterocyclic Substances”, in where [H+], etc. represent the concentrations of the respective Katritzky, A. R., Ed., Physical Methods in Heterocyclic Chemistry, - species in mol/L. It follows that pKa = pH + log[HA] – log[A ], so Academic Press, New York, 1963. 4. Sober, H.A., Ed., CRC Handbook of Biochemistry, CRC Press, Boca that a solution with 50% dissociation has pH equal to the pKa of the acid. Raton, FL, 1968. 5. Perrin, D. D., Dempsey, B., and Serjeant, E. P., pK Prediction for Data for bases are presented as pK values for the conjugate acid, a a Organic Acids and Bases, Chapman and Hall, London, 1981. i.e., for the reaction 6. Albert, A., and Serjeant, E. P., The Determination of Ionization + + Constants, Third Edition, Chapman and Hall, London, 1984. BH H + B 7. Budavari, S., Ed., The Merck Index, Twelth Edition, Merck & Co., Whitehouse Station, NJ, 1996. -
Phenotype Microarrays™
Phenotype MicroArrays™ PM1 MicroPlate™ Carbon Sources A1 A2 A3 A4 A5 A6 A7 A8 A9 A10 A11 A12 Negative Control L-Arabinose N-Acetyl -D- D-Saccharic Acid Succinic Acid D-Galactose L-Aspartic Acid L-Proline D-Alanine D-Trehalose D-Mannose Dulcitol Glucosamine B1 B2 B3 B4 B5 B6 B7 B8 B9 B10 B11 B12 D-Serine D-Sorbitol Glycerol L-Fucose D-Glucuronic D-Gluconic Acid D,L -α-Glycerol- D-Xylose L-Lactic Acid Formic Acid D-Mannitol L-Glutamic Acid Acid Phosphate C1 C2 C3 C4 C5 C6 C7 C8 C9 C10 C11 C12 D-Glucose-6- D-Galactonic D,L-Malic Acid D-Ribose Tween 20 L-Rhamnose D-Fructose Acetic Acid -D-Glucose Maltose D-Melibiose Thymidine α Phosphate Acid- -Lactone γ D-1 D2 D3 D4 D5 D6 D7 D8 D9 D10 D11 D12 L-Asparagine D-Aspartic Acid D-Glucosaminic 1,2-Propanediol Tween 40 -Keto-Glutaric -Keto-Butyric -Methyl-D- -D-Lactose Lactulose Sucrose Uridine α α α α Acid Acid Acid Galactoside E1 E2 E3 E4 E5 E6 E7 E8 E9 E10 E11 E12 L-Glutamine m-Tartaric Acid D-Glucose-1- D-Fructose-6- Tween 80 -Hydroxy -Hydroxy -Methyl-D- Adonitol Maltotriose 2-Deoxy Adenosine α α ß Phosphate Phosphate Glutaric Acid- Butyric Acid Glucoside Adenosine γ- Lactone F1 F2 F3 F4 F5 F6 F7 F8 F9 F10 F11 F12 Glycyl -L-Aspartic Citric Acid myo-Inositol D-Threonine Fumaric Acid Bromo Succinic Propionic Acid Mucic Acid Glycolic Acid Glyoxylic Acid D-Cellobiose Inosine Acid Acid G1 G2 G3 G4 G5 G6 G7 G8 G9 G10 G11 G12 Glycyl-L- Tricarballylic L-Serine L-Threonine L-Alanine L-Alanyl-Glycine Acetoacetic Acid N-Acetyl- -D- Mono Methyl Methyl Pyruvate D-Malic Acid L-Malic Acid ß Glutamic Acid Acid -
Isolation and Characterization of Vitamin K-Dependent Region Of
Proc. Nat. Acad. Sci. USA Vol. 72, No. 4, pp. 1281-1285, April 1975 Isolation and Characterization of Vitamin K-Dependent Region of Bovine Blood Clotting Factor X (protein sequence/homology/calcium binding/-y-carboxyglutamic acid/coagulation) JAMES BRYANT HOWARD* AND GARY L. NELSESTUENt * Department of Biochemistry, College of Medicine 227 Millard Hall, University of Minnesota, Minneapolis, Minn. 55455; and t Department of Biochemistry, College of Biological Sciences, 140 Gortner Hall, University of Minnesota, St. Paul, Minn. 55101 Communicated by Emil L. Smith, January 17, 1975 ABSTRACT A 39-residue peptide from the tryptic di- that 8 of the 10 'y-carboxyglutamic acid residues are found in gestion of bovine blood clotting factor X has been isolated pairs (16, If the vitamin K-dependent blood clotting pro- by specific adsorption on barium citrate. The amino- and 1). carboxyl-terminal sequences of the peptide were deter- teins are related proteins, then homology between these mined and compared to the vitamin K-dependent Ca2+- proteins would be expected for the Ca2+-binding regions. We binding region from bovine prothrombin. The factor X wish to report the isolation and characterization of a peptide peptide was found to contain -y-carboxyglutamic acid resi- from factor X which is similar to the vitamin K-dependent, dues, and the results of independent analysis are con- sistent with all 14 glutamic acid residues as y-carboxy- Ca2+-binding region of prothrombin. Preliminary accounts of glutamic acid. The similarity of the factor X peptide to the some of this work have been presented (18, 20). prothrombin peptide supports the hypothesis that the vitamin K-dependent blood clotting proteins are de- METHODS AND MATERIALS scended from a common ancestral gene. -
These Lanthionine FINALE
FACULTÉ DES SCIENCES – DÉPARTEMENT DE CHIMIE CENTRE DE RECHERCHES DU CYCLOTRON SYNTHESIS AND BIOLOGICAL STUDIES OF LANTHIONINE DERIVATIVES Promoteur: Professeur André LUXEN Dissertation présentée par Thibaut DENOËL pour l’obtention du grade de Docteur en Sciences Année académique 2013 - 2014 Membres du Jury : Promoteur : Professeur André Luxen (Université de Liège) Président : Professeur Albert Demonceau (Université de Liège) Autres membres : Docteur Didier Blanot (Université Paris-Sud) Docteur David Thonon (Uteron Pharma) Professeur Bernard Joris (Université de Liège) Docteur Christian Lemaire (Université de Liège) Remerciements Les travaux présentés dans cette thèse ont été réalisés sous la direction du Professeur André Luxen dans les laboratoires du Centre de Recherches du Cyclotron de l’Université de Liège. Je voudrais tout d’abord remercier le Professeur André Luxen pour son accueil au sein du Cyclotron, sa grande patience et son exigence. Il a aussi inspiré nombre de manipulations et m’a guidé dans mes recherches. En outre, il a mis à ma disposition tout le matériel et la quantité de produits chimiques nécessaires à la réalisation de ce travail. Je tiens également à remercier Messieurs les membres du Jury pour m’avoir fait l’honneur d’accepter d’examiner ce travail, en l’occurrence le Docteur Didier Blanot (Université Paris-Sud), le Docteur David Thonon (Uteron Pharma), le Professeur Bernard Joris, le Docteur Christian Lemaire et le Professeur Albert Demonceau dans le rôle de Président. Je remercie aussi les Docteurs Didier Blanot et Mireille Hervé pour la réalisation des essais in vitro avec l’enzyme Mpl et l’aide dans les publications. Je remercie grandement le Docteur Astrid Zervosen pour la réalisation des manipulations biochimiques, ses conseils, sa disponibilité et la correction lors de la rédaction. -
WO 2010/037397 Al
(12) INTERNATIONALAPPLICATION PUBLISHED UNDER THE PATENT COOPERATION TREATY (PCT) (19) World Intellectual Property Organization International Bureau (10) International Publication Number (43) International Publication Date 8 April 2010 (08.04.2010) WO 2010/037397 Al (51) International Patent Classification: (81) Designated States (unless otherwise indicated, for every A61K 38/17 (2006.01) C07K 14/705 (2006.01) kind of national protection available): AE, AG, AL, AM, A61K 47/48 (2006.01) GOlN 33/50 (2006.01) AO, AT, AU, AZ, BA, BB, BG, BH, BR, BW, BY, BZ, CA, CH, CL, CN, CO, CR, CU, CZ, DE, DK, DM, DO, (21) International Application Number: DZ, EC, EE, EG, ES, FI, GB, GD, GE, GH, GM, GT, PCT/DK2009/050257 HN, HR, HU, ID, IL, IN, IS, JP, KE, KG, KM, KN, KP, (22) International Filing Date: KR, KZ, LA, LC, LK, LR, LS, LT, LU, LY, MA, MD, 1 October 2009 (01 .10.2009) ME, MG, MK, MN, MW, MX, MY, MZ, NA, NG, NI, NO, NZ, OM, PE, PG, PH, PL, PT, RO, RS, RU, SC, SD, (25) Filing Language: English SE, SG, SK, SL, SM, ST, SV, SY, TJ, TM, TN, TR, TT, (26) Publication Language: English TZ, UA, UG, US, UZ, VC, VN, ZA, ZM, ZW. (30) Priority Data: (84) Designated States (unless otherwise indicated, for every PA 2008 0 1381 1 October 2008 (01 .10.2008) DK kind of regional protection available): ARIPO (BW, GH, 61/101,898 1 October 2008 (01 .10.2008) US GM, KE, LS, MW, MZ, NA, SD, SL, SZ, TZ, UG, ZM, ZW), Eurasian (AM, AZ, BY, KG, KZ, MD, RU, TJ, (71) Applicant (for all designated States except US): DAKO TM), European (AT, BE, BG, CH, CY, CZ, DE, DK, EE, DENMARK A/S [DK/DK]; Produktionsvej 42, DK-2600 ES, FI, FR, GB, GR, HR, HU, IE, IS, IT, LT, LU, LV, Glostrup (DK).