structural assignment
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Author(s):  
Pedro Y. Kovatch ◽  
Alexsandro E. Ferreira ◽  
Guilherme M. L. Ghizonni ◽  
Sérgio R. Ambrósio ◽  
Antônio E. M. Crotti ◽  
...  

2021 ◽  
Author(s):  
Johannes Helm ◽  
Clemens Gruenwald-Gruber ◽  
Andreas Thader ◽  
Jonathan Urteil ◽  
Johannes Fuehrer ◽  
...  

The importance of protein glycosylation in the biomedical field demands for methods capable of resolving and identifying isomeric structures of N-glycans. However, the unambiguous identification of isomeric structures from complex mixtures is currently not reasonably realized even by the most sophisticated approaches. Here we present a novel approach which uses stable isotope labelled reference N-glycans to establish a retention time grid (glyco-TiGr) on porous graphitized carbon. This furthermore enables retention as the primary criterion for the structural assignment of isomeric N-glycans. Moreover, we biosynthesized forty natural isomers of the fundamental N-glycan type consisting of five hexoses, four N-acetylhexosamines and one fucose residue. Nearly all of these isomers occupied unique positions on the retention time grid. Reference glycan assisted retention time determination with deci-minute accuracy narrowed the assignment space to very few, often only one possible glycan isomer. Application of the glyco-TiGr approach revealed yet undescribed isomers of Lewis x determinants in multimeric human IgA and hybrid type N-glycans in human brain with galactose and even fucose linked to the bisecting N-acetylglucosamine. Thus, the brain N-glycome displayed a degree of sophistication commensurate with this organ's role.


2021 ◽  
Vol 2 (1) ◽  
pp. 105-116
Author(s):  
Alain Ibáñez de Opakua ◽  
Markus Zweckstetter

Abstract. The application of anisotropic nuclear magnetic resonance (NMR) parameters for the correct structural assignment of small molecules requires the use of partially ordered media. Previously we demonstrated that the use of P3D simulations using poly(γ-benzyl-L-glutamate) (PBLG) as an alignment medium allows for the determination of the correct diastereomer from extremely sparse NMR data. Through the analysis of the structural characteristics of small molecules in different alignment media, here we show that when steric or electrostatic factors dominate the alignment, P3D-PBLG retains its diastereomer discrimination power. We also demonstrate that P3D simulations can define the different conformations of a flexible small molecule from sparse NMR data.


Author(s):  
Seoung Rak Lee ◽  
Huijuan Guo ◽  
Jae Sik Yu ◽  
Minji Park ◽  
Hans-Martin Dahse ◽  
...  

Actinobacteria have long served as sources of novel natural products with antibiotic properties, but the isolation of novel derivatives and the determination of their absolute structures have remained a scientific...


2020 ◽  
Vol 22 (1) ◽  
pp. 304
Author(s):  
Bożena Szulc ◽  
Yelyzaveta Zadorozhna ◽  
Mariusz Olczak ◽  
Wojciech Wiertelak ◽  
Dorota Maszczak-Seneczko

Congenital disorders of glycosylation (CDG) are a group of rare genetic and metabolic diseases caused by alterations in glycosylation pathways. Five patients bearing CDG-causing mutations in the SLC35A1 gene encoding the CMP-sialic acid transporter (CST) have been reported to date. In this study we examined how specific mutations in the SLC35A1 gene affect the protein’s properties in two previously described SLC35A1-CDG cases: one caused by a substitution (Q101H) and another involving a compound heterozygous mutation (T156R/E196K). The effects of single mutations and the combination of T156R and E196K mutations on the CST’s functionality was examined separately in CST-deficient HEK293T cells. As shown by microscopic studies, none of the CDG-causing mutations affected the protein’s proper localization in the Golgi apparatus. Cellular glycophenotypes were characterized using lectins, structural assignment of N- and O-glycans and analysis of glycolipids. Single Q101H, T156R and E196K mutants were able to partially restore sialylation in CST-deficient cells, and the deleterious effect of a single T156R or E196K mutation on the CST functionality was strongly enhanced upon their combination. We also revealed differences in the ability of CST variants to form dimers. The results of this study improve our understanding of the molecular background of SLC35A1-CDG cases.


2020 ◽  
Author(s):  
Alain Ibáñez de Opakua ◽  
Markus Zweckstetter

Abstract. The application of anisotropic NMR parameters for the correct structural assignment of small molecules requires the use of partially ordered media. Previously we demonstrated that the use of P3D simulations using PBLG as alignment medium allows the determination of the correct diastereomer from extremely sparse NMR data. Through the analysis of the structural characteristics of small molecules in different alignment media we here show that when steric or electrostatic factors dominate the alignment, P3D-PBLG retains its diastereomer discrimination power. We also demonstrate that P3D simulations can define the different conformations of a flexible small molecule from sparse NMR data.


Author(s):  
Marta Olivares ◽  
Martin Albrecht

Pyridyl-triazolylidene ligands with variable donor properties were used as tunable ligands at a dihydride iridium(III) center. The straightforward synthesis of this type of ligand allows for an easy incorporation of electron donating substituents in different positions of the pyridine ring or different functional groups such as esters, alkoxy or aliphatic chains on the C4 position of the triazole heterocycle. The stability of these hydride metal systems allowed these complexes to be used as models for studying the influence of the ligand modifications on hydride reactivity. Spectroscopic analysis provided unambiguous structural assignment of the dihydride system. Modulation of the electronic properties of the wingtip substituents did not appreciably alter the reactivity of the hydrides. Reactivity studies using acids with a wide range of pKa values indicated a correlation between hydride reactivity and acidity and showed exclusive reactivity towards the less shielded hydride trans to the carbene carbon rather than the more shielded hydride trans to the pyridine ring, suggesting that the trans effect is more relevant in these reactions than the NMR spectroscopically deduced hydridic character.


2020 ◽  
Vol 26 (20) ◽  
pp. 4433-4433
Author(s):  
Jevgenij A. Raskatov ◽  
Scott Virgil ◽  
Hsiau‐Wei Lee ◽  
Lawrence M. Henling ◽  
Ka Chan ◽  
...  

2020 ◽  
pp. 23-28
Author(s):  
A. Antony Muthu Prabhu

The theoretical investigation of inclusion complexation of amide-imidol tautomer of two guest molecules benzanilide (BA) and fast violet B (FVB) with β-cyclodextrin (β-CD) using DFT B3LYP 3-21G  method in the gas phase. Benzanilide has no substitution in the basic skeleton and the other selected compound substituted with three groups such as –NH2, -CH3 and –OCH3 group in the same aromatic ring. The tautomer  of two selected compounds was formed the stable inclusion complexes with the β-CD supramolecule. The theoretically calculated complexation energy was observed the negative value for all the inclusion complexes. This method was applicable to determine the structural assignment of the inclusion complexes between BA, FVB and β-CD.


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