https://pubs.rsc.org/en/content/articlepdf/2019/NP/C8NP00092A

Marine natural products.

The potential of the diverse chemistries present in natural products (NP) for biotechnology and medicine remains untapped because NP databases are not searchable with raw data and the NP community has no way to share data other than in published papers. Although mass spectrometry (MS) techniques are well-suited to high-throughput characterization of NP, there is a pressing need for an infrastructure to enable sharing and curation of data. We present Global Natural Products Social Molecular Networking (GNPS; http://gnps.ucsd.edu), an open-access knowledge base for community-wide organization and sharing of raw, processed or identified tandem mass (MS/MS) spectrometry data. In GNPS, crowdsourced curation of freely available community-wide reference MS libraries will underpin improved annotations. Data-driven social-networking should facilitate identification of spectra and foster collaborations. We also introduce the concept of 'living data' through continuous reanalysis of deposited data.

/pdf/sharing-and-community-curation-of-mass-spectrometry-data-11cqx1k38i.pdf

Sharing and community curation of mass spectrometry data with Global Natural Products Social Molecular Networking

9-Fluorenylmethoxycarbonyl (Fmoc) amino acids were first used for solid phase peptide synthesis a little more than a decade ago. Since that time, Fmoc solid phase peptide synthesis methodology has been greatly enhanced by the introduction of a variety of solid supports, linkages, and side chain protecting groups, as well as by increased understanding of solvation conditions. These advances have led to many impressive syntheses, such as those of biologically active and isotopically labeled peptides and small proteins. The great variety of conditions under which Fmoc solid phase peptide synthesis may be carried out represents a truly "orthogonal" scheme, and thus offers many unique opportunities for bioorganic chemistry.

Solid phase peptide synthesis utilizing 9‐fluorenylmethoxycarbonyl amino acids

Iron is a limiting nutrient for primary production in large areas of the oceans. Dissolved iron(III) in the upper oceans occurs almost entirely in the form of complexes with strong organic ligands presumed to be of biological origin. Although the importance of organic ligands to aquatic iron cycling is becoming clear, the mechanism by which they are involved in this process remains uncertain. Here we report observations of photochemical reactions involving Fe(III) bound to siderophores--high-affinity iron(III) ligands produced by bacteria to facilitate iron acquisition. We show that photolysis of Fe(III)-siderophore complexes leads to the formation of lower-affinity Fe(III) ligands and the reduction of Fe(III), increasing the availability of siderophore-bound iron for uptake by planktonic assemblages. These photochemical reactions are mediated by the alpha-hydroxy acid moiety, a group which has generally been found to be present in the marine siderophores that have been characterized. We suggest that Fe(III)-binding ligands can enhance the photolytic production of reactive iron species in the euphotic zone and so influence iron availability in aquatic systems.

Photochemical cycling of iron in the surface ocean mediated by microbial iron(III)-binding ligands.

Structure and Biosynthesis of the Jamaicamides, New Mixed Polyketide-Peptide Neurotoxins from the Marine Cyanobacterium Lyngbya majuscula

1-fluoro-2,4-dinitrophenyl-5-l-alanine amide has been synthesized in high yield (76%) from 1,5-difluoro-2,4-dinitrobenzene andl-Ala-NH2. This compound contains a reactive fluorine atom which can be used for the reaction with a mixture ofl- andd-amino acids. The resulting diastereomers which are obtained in quantitative yield can be separated and estimated by HPLC. With the five amino acids studied (Ala, Asp, Glu, Met and Phe),l-diastereomers were eluted from the reverse-phase column befored-diastereomers. This behavior can be explained by a stronger intramolecular hydrogen bonding in the latter diastereomer. When artificial mixtures of the five amino acids containing known proportions ofl- andd-isomers were derivatized with the reagent and the reaction products analyzed by HPLC, it was possible to determine the relative content of each isomer in nanomole range.

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Determination ofD-amino acids. II. Use of a bifunctional reagent, 1,5-difluoro-2,4-dinitrobenzene

l- andd-amino acids were treated with fluoroniditrobenzene to form DNP-derivatives. The latter were esterified with methanol in the presence of dry HCl gas to the corresponding methyl esters. Treatment of the ester mixture with carboxypeptidase-Y resulted in the hydrolysis of onlyl-esters. Alld-esters and somel-esters were unaffected. The produced DNP-l-amino acids could be separated from DNP-d-amino acid methyl esters by high performance liquid chromatography allowing quantitation of thed-isomers. When a test mixture consisting of Ala, Asp, Glu, Met and Phe, present in different proportions asl- andd-isomers, was subjected to the above procedure, alld-amino acids could be quantitated. The method allows detection ofd-amino acids in the nanomole range.

/pdf/determination-ofd-amino-acids-i-hydrolysis-of-dnp-l-amino-200fgvu11u.pdf

Determination ofd-amino acids. I. Hydrolysis of DNP-l-amino acid methyl esters with carboxypeptidase-Y

Treatment of a flocculent (strain 201) and a non-flocculent (strain 116) cell suspension of Saccharomyces carlsbergensis with trypsin, followed by β-mercaptoethanol and a second trypsin treatment solubilized approximately 15% of material from both types of cells based on dry weight. The solubilized fractions were resolved by Sephadex gel filtration into high mol. wt. (40,000 to 200,000) and low mol.wt. (less than 4,000) components. High mol.wt. components from the flocculent cells contained more carbohydrate and less protein than the corresponding components isolated from the non-flocculent cells. Furthermore, the polypeptide material from the flocculent cells had a higher content of proline, lysine, and arginine than that from non-flocculent cells. High mol.wt. material contained antigenic determinants similar to those previously found in beer fractions. Yeast-derived antigens were found in all fractions while antigens of barley origin were found only in the tryptic digests.

/pdf/studies-on-yeast-flocculation-comparison-of-enzymatic-1v4raz1c26.pdf

Peter Marfey

Papers

Determination ofD-amino acids. II. Use of a bifunctional reagent, 1,5-difluoro-2,4-dinitrobenzene

Determination ofd-amino acids. I. Hydrolysis of DNP-l-amino acid methyl esters with carboxypeptidase-Y

Studies on yeast flocculation. comparison of enzymatic digests of flocculent and non-flocculent cells of saccharomyces carlsbergensis