Monitoring carbohydrate 3D structure quality with the Privateer database

• Jordan S. Dialpuri,
• Haroldas Bagdonas,
• Lucy C. Schofield,
• Phuong Thao Pham,
• Lou Holland and
• Jon Agirre

Beilstein J. Org. Chem. 2024, 20, 931–939, doi:10.3762/bjoc.20.83

• complement the growing glycan content of the PDB. Keywords: carbohydrates; database; N-glycans; N-glycosylation; polysaccharides; validation; website; Introduction Carbohydrate modelling is an important but often cumbersome stage in the macromolecular X-ray structure solution workflow. The accurate

• interface on the Privateer database homepage, carbohydrate-containing PDB entries can easily be found and filtered. Privateer database entries for specific glycosylation types, namely, N-glycosylation, O-glycosylation, S-glycosylation, or C-glycosylation can be filtered quickly and easily. Additional

Synthetic strategies toward 1,3-oxathiolane nucleoside analogues

• Umesh P. Aher,
• Dhananjai Srivastava,
• Girij P. Singh and
• Jayashree B. S

Beilstein J. Org. Chem. 2021, 17, 2680–2715, doi:10.3762/bjoc.17.182

• accompanied by coupling nucleobases via N-glycosylation. However, over the last three decades, efforts were made for the synthesis of 1,3-oxathiolane nucleosides by selective N-glycosylation of carbohydrate precursors at C-1, and this approach has emerged as a strong alternative that allows simple

• -oxathiolane ring with different nucleobases in a way that only one isomer is produced in a stereoselective manner via N-glycosylation. An emphasis has been placed on the C–N-glycosidic bond constructed during the formation of the nucleoside analogue. The third focus is on the separation of enantiomers of 1,3

• -oxathiolane nucleosides via resolution methods. The chemical as well as enzymatic procedures are reviewed and segregated in this review for effective synthesis of 1,3-oxathiolane nucleoside analogues. Keywords: chiral auxiliaries; enzymes; Lewis acids; N-glycosylation; 1,3-oxathiolane sugar and nucleosides

A systems-based framework to computationally describe putative transcription factors and signaling pathways regulating glycan biosynthesis

• Theodore Groth,
• Rudiyanto Gunawan and
• Sriram Neelamegham

Beilstein J. Org. Chem. 2021, 17, 1712–1724, doi:10.3762/bjoc.17.119

• reticulum. The enzymes involved is such synthesis include the ALG (asparagine-linked N-glycosylation) enzymes and additional proteins (part of OSTA and OSTB) involved in the transfer of the glycan to the nascent protein. 5) Complex N-glycans: This pathway includes glycogenes responsible for processing the N

Semiautomated glycoproteomics data analysis workflow for maximized glycopeptide identification and reliable quantification

• Steffen Lippold,
• Arnoud H. de Ru,
• Jan Nouta,
• Peter A. van Veelen,
• Magnus Palmblad,
• Manfred Wuhrer and
• Noortje de Haan

Beilstein J. Org. Chem. 2020, 16, 3038–3051, doi:10.3762/bjoc.16.253

• relying only on oxonium ions and precursor mass, using a score above 30 were also described recently [15]. A suitable cut-off score should always be carefully evaluated for each (glyco)peptide moiety with respect to the glycoform coverage and accuracy [11]. Byonic identified the relevant N-glycosylation

A consensus-based and readable extension of Linear Code for Reaction Rules (LiCoRR)

• Benjamin P. Kellman,
• Yujie Zhang,
• Emma Logomasini,
• Eric Meinhardt,
• Karla P. Godinez-Macias,
• Austin W. T. Chiang,
• James T. Sorrentino,
• Chenguang Liang,
• Bokan Bao,
• Yusen Zhou,
• Sachiko Akase,
• Isami Sogabe,
• Thukaa Kouka,
• Elizabeth A. Winzeler,
• Iain B. H. Wilson,
• Matthew P. Campbell,
• Sriram Neelamegham,
• Frederick J. Krambeck,
• Kiyoko F. Aoki-Kinoshita and
• Nathan E. Lewis

Beilstein J. Org. Chem. 2020, 16, 2645–2662, doi:10.3762/bjoc.16.215

• implementations. Here we propose possible solutions as described by the original prescription for Linear Code, the consensus of the community, and our recommendation following this survey. We have demonstrated the LiCoRR representation of all N-glycosylation reaction rules discussed in this paper in Table 9

Leveraging glycomics data in glycoprotein 3D structure validation with Privateer

• Haroldas Bagdonas,
• Daniel Ungar and
• Jon Agirre

Beilstein J. Org. Chem. 2020, 16, 2523–2533, doi:10.3762/bjoc.16.204

• . Furthermore, despite the example showing just N-glycosylation, other kinds of glycosylation are searchable as well, and therefore this tool could shed much needed light on the validity of models representing more obscure types of modifications. Example 2 – 2Z62 Successfully matching the WURCS string to a

GlypNirO: An automated workflow for quantitative N- and O-linked glycoproteomic data analysis

• Toan K. Phung,
• Cassandra L. Pegg and
• Benjamin L. Schulz

Beilstein J. Org. Chem. 2020, 16, 2127–2135, doi:10.3762/bjoc.16.180

• suite of N-glycosylation sites that we were able to identify and measure with GlypNirO. Comparing the site-specific glycoform relative abundance and occupancy, we identified 111 unique glycopeptides with increased and 128 with decreased abundance in HCC compared with healthy controls in depleted plasma

• not imputed. Spectra were manually validated for glycoforms of interest. Evaluation of GlypNirO site-specific N-glycosylation profiling. Site-specific relative glycoform abundance in HCC and healthy controls at (a) immunoglobulin heavy constant gamma 1 (IgG1) N180, and (b) alpha-1-antichymotrypsin

• statistical workflows. We used GlypNirO to analyse a published plasma glycoproteome dataset and identified changes in site-specific N- and O-glycosylation occupancy and structure associated with hepatocellular carcinoma as putative biomarkers of disease. Keywords: glycoproteomics; mass spectrometry; N

Clustering and curation of electropherograms: an efficient method for analyzing large cohorts of capillary electrophoresis glycomic profiles for bioprocessing operations

• Ian Walsh,
• Matthew S. F. Choo,
• Sim Lyn Chiin,
• Amelia Mak,
• Shi Jie Tay,
• Pauline M. Rudd,
• Yang Yuansheng,
• Andre Choo,
• Ho Ying Swan and
• Terry Nguyen-Khuong

Beilstein J. Org. Chem. 2020, 16, 2087–2099, doi:10.3762/bjoc.16.176

• critical process parameters that control the glycosylation critical quality attributes. The advances made in protocols for capillary electrophoresis-laser-induced fluorescence (CE-LIF) measurements of antibody N-glycans have increased the potential for generating large datasets of N-glycosylation values

• to assess how glycans behave under these diverse conditions. During this process development of antibody-based drugs, the N-glycosylation of an antibody can deviate from their expected glycomic profiles as a result of fluctuations in culture conditions and operating parameters. Therefore, to assess

How and why plants and human N-glycans are different: Insight from molecular dynamics into the “glycoblocks” architecture of complex carbohydrates

• Carl A. Fogarty,
• Aoife M. Harbison,
• Amy R. Dugdale and
• Elisa Fadda

Beilstein J. Org. Chem. 2020, 16, 2046–2056, doi:10.3762/bjoc.16.171

• Carl A. Fogarty Aoife M. Harbison Amy R. Dugdale Elisa Fadda Department of Chemistry and Hamilton Institute, Maynooth University, Maynooth, Kildare, Ireland 10.3762/bjoc.16.171 Abstract The N-glycosylation is one of the most abundant and diverse post-translational modifications of proteins

• ][21][22][23]. More specifically, we investigate how core α(1-3)-linked fucose (Fuc) and β(1-2)-linked xylose (Xyl) affect the structure and dynamics of plants N-glycoforms [23] and of hybrid constructs with mammalian N-glycoforms [24]. At first glance plants protein N-glycosylation [23] is quite

• refer to N-glycans as either “plant” or “hybrid” separately. Nevertheless, it is important to underline that some of these motifs, such as β(1-2) xylosylation and difucosylated core are also found in invertebrate N- glycosylation [30]. Finally, we discuss these findings within a framework where the

Nonenzymatic synthesis of anomerically pure, mannosyl-based molecular probes for scramblase identification studies

• Giovanni Picca,
• Markus Probst,
• Simon M. Langenegger,
• Oleg Khorev,
• Peter Bütikofer,
• Anant K. Menon and
• Robert Häner

Beilstein J. Org. Chem. 2020, 16, 1732–1739, doi:10.3762/bjoc.16.145

• glycolipid analogs; scramblase; Introduction Mannosyl phosphoryl dolichol (MPD), an important, multifunctional glycolipid, is used as a mannose donor for protein N-glycosylation, O- and C-mannosylation, and glycosylphosphatidylinositol (GPI) anchoring in the luminal leaflet of the endoplasmic reticulum (ER

Anomeric modification of carbohydrates using the Mitsunobu reaction

• Julia Hain,
• Patrick Rollin,
• Werner Klaffke and
• Thisbe K. Lindhorst

Beilstein J. Org. Chem. 2018, 14, 1619–1636, doi:10.3762/bjoc.14.138

• of indole derivatives were also approached by Zembower et al. employing 2,3,4,6-tetra-O-benzyl glucopyranose in a Mitsunobu reaction [92]. In the same period, Prudhomme’s group followed closely related approaches for the N-glycosylation of indolic structures. Various rebeccamycin analogues were

• a model study directed towards the synthesis of guanofosfocin, Sugimura et al. used the Mitsunobu N-glycosylation to attach a glucopyranosyl donor on either 6-N-trityl-8-oxoadenosine or 6-O-benzyl-8-oxoinosine [108]. Reactions with N–OH acids to yield NO-glycosides Because of its well-suited pKa

AuBr₃-catalyzed azidation of per-O-acetylated and per-O-benzoylated sugars

• Jayashree Rajput,
• Srinivas Hotha and
• Madhuri Vangala

Beilstein J. Org. Chem. 2018, 14, 682–687, doi:10.3762/bjoc.14.56

• -alkynic glycosyl donors, glycosyl halides [18], armed O-methyl glycosides [19], armed and disarmed thioglycosides [20] as well as trichloroacetimidate [21][22] donors were successfully applied to O- and C-glycosylations. Of the gold-catalyzed N-glycosylation reactions, Yu et al. demonstrated the effective

•  2, entries 5 and 6) did not proceed at room temperature and required heating at 55 °C for 2 h to provide the desired products β-D-maltopyranosyl azide and β-D-lactopyranosyl azide 14 and 15 in 91% and 84% yields, respectively. We found these results very intriguing as the rate of N-glycosylation of

Expression, purification and structural analysis of functional GABA transporter 1 using the baculovirus expression system

• Jing Hu,
• Chris Weise,
• Christoph Böttcher,
• Hua Fan and
• Jian Yin

Beilstein J. Org. Chem. 2017, 13, 874–882, doi:10.3762/bjoc.13.88

• GAT1 demonstrates that this single polypeptide contains twelve TM domains connected by hydrophilic loops with the amino and carboxy-termini residing in the cytoplasm [9][10]. Additionally, the GAT1 protein contains three conserved N-glycosylation sites [9]. The role of N-linked glycans in the GABA

• expressed in the baculovirus expression system. The results showed that infected Sf9 cells (0.15 pmol/106 cells) have only slightly higher GABA uptake activity than mock cells (0.1 pmol/106 cells) (Figure S3, Supporting Information File 1). A previous work demonstrated that co-translational N-glycosylation

• but not the terminal trimming of N-glycans is involved in the regulation of the correct membrane glycoprotein folding since the inhibition of N-glycosylation processing by 1-deoxymannojirimycin (dMM) results in a mannose-rich type of N-glycan that does not affect either the protein stability or

Multicomponent reactions in nucleoside chemistry

• Mariola Koszytkowska-Stawińska and
• Włodzimierz Buchowicz

Beilstein J. Org. Chem. 2014, 10, 1706–1732, doi:10.3762/bjoc.10.179

• opinion the method is worth noting since it represents an interesting extension of the Vorbrüggen N-glycosylation process. Thus, the reaction sequence leading to nucleosides 119 was initiated by the titanium(IV) chloride-promoted alkylation of 2,3-dihydrofurane 117 with ethyl pyruvate at −78 °C (1 hour

Carbohydrate PEGylation, an approach to improve pharmacological potency

• M. Eugenia Giorgi,
• Rosalía Agusti and
• Rosa M. de Lederkremer

Beilstein J. Org. Chem. 2014, 10, 1433–1444, doi:10.3762/bjoc.10.147

• pharmacokinetic properties of a protein, N-PEGylation may be used additively to N-glycosylation since both modifications stabilize the protein by different mechanisms [25]. Also, glutamine residues on intact or chimeric proteins can be combined with alkylamino-PEG derivatives by the use of a transglutaminase [26

Synthetic glycopeptides and glycoproteins with applications in biological research

• Ulrika Westerlind

Beilstein J. Org. Chem. 2012, 8, 804–818, doi:10.3762/bjoc.8.90

• ]. EPO consists of 166 amino-acid residues with four glycosylation sites, one O-glycosylation site positioned at serine 126 and three N-glycosylation sites positioned at aspargines 24, 38 and 83. EPO has been found to contain multiple glycoforms and the efficacy of EPO is heavily dependent on the type