> Phenomena > Natural Phenomenon or Process > Glycosylation

← Glare

Glycosylation

Glycosylation is the enzymatic process that attaches glycan chains to proteins, lipids, or other organic molecules.
This post-translational modification plays a crucial role in numerous biological processes, including protein folding, stability, and function.
Researchers can leverage PubCompare.ai's AI-driven platform to optimize their glycosylation studies, locate the best protocols, and improve reproducibility.
The tool's intelligent comparisons help identify the most effective approaches, streamlining research and unlocking new insights.
With PubCompare.ai, scientists can easily access glycosylation-related literature, preprints, and patents, supporting their efforts to enhance this fundamental area of biological chemistry.

Most cited protocols related to «Glycosylation»

Establishing a Keyword Library for Herbal Compound-Protein Interactions

Establishing a key word library is critically important to retrieve the related literatures. We randomly choose individual compound and checked the full-text review papers to establish this library. Fifty nine keywords are listed in Table 2, which are frequently used to describe the interaction between compound and proteins. The keywords are divided into two types. One is the nouns describing the interaction (Type A), while the other (Type B) is the phrases describing the specific effect such as inhibit the activity of some proteins.

Table 2.

Keyword library to describe the interaction between herbal ingredients and proteins

	Interaction			Effect
	Positive	Negative	General
Type A	Agonist; activator	Antagonist; inhibitor	Bind; target; bound
Type B	Activate; Augment; Ameliorate; Derepress; Elevate; Enhance; Hasten; Increase; Induce; Incitate; Initiate Potentiate; Promote; Raise; Stimulate; Up-regulate	Abrogate; Abolish; Against; Attenuate; Antagonize; Block; Blunt; Down regulate; Decrease; Degrade; Diminish; Impair; Inhibit; Reduce; Repress; Suppress	Affect; Interact; Disturb; Regulate; Impact; Influence; Interfere; Modify; Modulate	Activity; Activation; Expression; Level; Pathway; Cleavage; Methylation; Phosphorylation; Severance; Glycosylation; Acetylation

Ye H., Ye L., Kang H., Zhang D., Tao L., Tang K., Liu X., Zhu R., Liu Q., Chen Y.Z., Li Y, & Cao Z. (2010). HIT: linking herbal active ingredients to targets. Nucleic Acids Research, 39(Database issue), D1055-D1059.

Publication 2010

Acetylation Cardiac Arrest cDNA Library Cytokinesis Glycosylation Lanugo Methylation Phosphorylation Proteins

Curated C. elegans Secreted Proteins for Germline Studies

All candidate genes encode secreted or membrane-associated proteins as judged by the presence of a signal peptide or a predicted transmembrane or signal anchor domain (SignalP 3.0, www.cbs.dtu.dk/services/SignalP; PSORT II, psort.hgc.jp/form2.html) and were selected from a curated list of C. elegans secreted proteins provided by Brian Ackley and Andrew Chisholm. For the majority of candidates, we also required at least one line of prior evidence for a role in the germline. Our candidate gene set included all of the germline enriched [13] (link), [14] (link) and maternal sterile genes [5] (link) that had a signal peptide. Since the set of genes previously found to be expressed in dissected germlines that have a signal peptide is large (Serial Analysis of Gene Expression database, Genome BC C. elegans Gene Expression Consortium, http://elegans.bcgsc.bc.ca), germline expressed genes were only included if they had previously been shown to result in embryonic lethality when inhibited by RNAi (Wormbase release WS199). Genes with domains found in proteins previously implicated in the formation of extra-embryonic layers (chitin binding, glycosylation, protease, peroxidase, lipid binding, or LDLR domains; Wormbase release WS202) were included regardless of whether there was prior evidence for a germline role. Due to redundancy, the total number of candidate genes was 310 (see Spreadsheet S1.xlsx for a breakdown of genes by identification method).

Carvalho A., Olson S.K., Gutierrez E., Zhang K., Noble L.B., Zanin E., Desai A., Groisman A, & Oegema K. (2011). Acute Drug Treatment in the Early C. elegans Embryo. PLoS ONE, 6(9), e24656.

Publication 2011

Catabolism Chitin Embryo Gene Expression Gene Expression Profiling Genes Genome Germ Line Glycosylation LDLR protein, human Lipids Membrane Proteins Mothers Peptide Hydrolases Peroxidase Protein C Proteins RNA Interference Signal Peptides Staphylococcal Protein A Sterility, Reproductive

Identifying Candida glabrata Virulence Genes

Genes of different functional categories were manually selected based on potential function in virulence and drug resistance. The categories involved genes of signaling pathways, kinases, ABC transporters and permeases, GPI-anchored proteins, cell wall associated genes, genes involved in glycosylation, phospholipid biosynthesis, histone modification, iron metabolism, and several genes with no obvious homologue in S. cerevisiae. The genes were selected by their homology to S. cerevisiae based on these functional categories (SGD annotations; http://www.yeastgenome.org). C. glabrata orthologues of the selected genes were first identified using a BLAST approach. The three best-aligned hits for each gene were saved and the C. glabrata homologue with the highest P-value was arbitrarily defined as the C. glabrata orthologue of a given gene in baker's yeast and named accordingly. In addition, a complete catalogue of orthology and paralogy relationships between C. glabrata genes and their homologues in 16 other fully-sequenced fungi was derived using a phylogenetic approach [128] (link). For this a complete collection of Maximum Likelihood phylogenetic trees for all C. glabrata genes, the so-called phylome, was generated using the automated pipeline described elsewhere [129] (link). Gene phylogenies, alignments and orthology and paralogy predictions are publicly available through PhylomeDB (http://www.phylomedb.org).

Schwarzmüller T., Ma B., Hiller E., Istel F., Tscherner M., Brunke S., Ames L., Firon A., Green B., Cabral V., Marcet-Houben M., Jacobsen I.D., Quintin J., Seider K., Frohner I., Glaser W., Jungwirth H., Bachellier-Bassi S., Chauvel M., Zeidler U., Ferrandon D., Gabaldón T., Hube B., d'Enfert C., Rupp S., Cormack B., Haynes K, & Kuchler K. (2014). Systematic Phenotyping of a Large-Scale Candida glabrata Deletion Collection Reveals Novel Antifungal Tolerance Genes. PLoS Pathogens, 10(6), e1004211.

Publication 2014

Anabolism ATP-Binding Cassette Transporters Candida glabrata Cell Wall Fungi Genes Glycosylation GPI-Linked Proteins Histones Iron Metabolism Permease Phospholipids Phosphotransferases Resistance, Drug Saccharomyces cerevisiae Signal Transduction Pathways Virulence

Fab Fragment Generation from Plasma IgG

Protocol full text hidden due to copyright restrictions

Open the protocol to access the free full text link

Publication 2021

Centrifugation Endopeptidases Glycosylation IgG1 Immunoglobulins, Fab Monoclonal Antibodies Plasma

WGCNA Analysis of Uveal Melanoma

The systems biological method WGCNA was applied to the gene co-expression network of TCGA-UM (23 (link)). The following outlines the steps are taken: exclusion of genes with missing values using the “goodSamplesGenes” function, grouping of tumor samples, deletion of outliers, and establishment of a cut line of 100. The optimal soft threshold for adjacency calculation was determined using graphical methods. An adjacency matrix was generated from the expression matrix to determine the genetic interconnectedness of the network. The topological overlap matrix (TOM) was then constructed from the adjacency matrix. Hierarchical clustering was performed using an average linkage approach and the differences in TOM. The hierarchical clustering tree was dynamically pruned to identify similar modules with high correlation coefficients (r > 0.25). Pearson’s correlation test was applied to examine the relationship between eigengenes and clinical characteristics. The modules containing genes with the most significant correlations to clinical traits, such as glycosylation score, survival status, and survival time were selected for further investigation.

Liu J., Zhang P., Yang F., Jiang K., Sun S., Xia Z., Yao G, & Tang J. (2023). Integrating single-cell analysis and machine learning to create glycosylation-based gene signature for prognostic prediction of uveal melanoma. Frontiers in Endocrinology, 14, 1163046.

Publication 2023

Biopharmaceuticals Deletion Mutation Gene Regulatory Networks Genes Glycosylation Neoplasms Trees

Most recents protocols related to «Glycosylation»

Synthesis of 2-Azidoethylgentiotetrose Compound

Not available on PMC !

Example 29

Scheme 7 illustrates the incorporation of the azido moiety into building block 2, prepared as described in example 7.

[Figure (not displayed)]

Compound 5 (building block 2) was reacted with Cl₃CCN in the presence of a catalytic amount of DBU in the presence of dichloromethane to give trichloroimidate 8. Trichloroimidate 8 was reacted under Schmidt glycosylation conditions to give compound 14. Compound 14 was synthesized in 70% overall yield.

Scheme 8 illustrates the synthesis of 2-azidoethylgentiotetrose.

[Figure (not displayed)]

Compound 14 was deprotected by treatment of borontrifluoride etherate complex in methanol to give compound 15. Compound 3 (building block 1) was treated with trichloroacetonitrile and catalytic DBU to give compound 11. Compound 14 and compound 11 then subjected to the Schmidt glycosylation conditions to afford the gentiotetrose product 16. The overall yield of the sequence was 60%.

US11865135B2. ß-1,6-glucan therapeutic antibody conjugates (2024-01-09). Innate Biotherapeutics, LLC [US]. Inventors: Gabriel Oscar Reznik [US], John James Kane [US], James Michael Siedlecki [US], Zuzana Dostalova [US], Isabelle Sansal-Castellano [US], Ifat Rubin-Bejerano [US], Hua Miao [US], Eric Steven Furfine [US].

Patent 2024

Anabolism Catalysis Glycosylation Methanol Methylene Chloride trichloroacetonitrile

Antibody Purity and Identity Analysis

Not available on PMC !

Example 5

Non-reducing and reducing SDS-PAGE is used to analyze purity and identity of an antibody. The band pattern in non-reducing gels shows the major band at about 160 kDa and methodical artefacts of heavy and light chains and combinations thereof (˜25, 50-55, 75, 110, 135 kDa). Reducing gels show distinct light and heavy chain bands at and 50-55 kDa. Due to lack of the Fab glycosylation PM-N54Q has a smaller heavy chain, as expected (see FIG. 4, right).

The charge profile is clearly different, as shown by isoelectric focusing (IEF; see FIG. 5). The Fab glycosylation is considerably sialylated, whereas the Fc glycosylation is only minimally sialylated. Thus PankoMab-GEX® has more charged isoforms than PM-N54Q, reflecting its higher level of negatively charged sialic acids in the Fab part.

US11872289B2. Anti-MUC1 antibody-drug conjugate (2024-01-16). DAIICHI SANKYO CO., LTD. [JP]. Inventors: Johanna Gellert [DE], Anke Flechner [DE], Doreen Weigelt [DE], Antje Danielczyk [DE], Akiko Nagase [JP].

Patent 2024

Gels Glycosylation Immunoglobulins Light PankoMab-GEX Protein Isoforms SDS-PAGE Sialic Acids

Conformational Analysis of GCS Substrates

To
analyze the location and conformation of the GCS substrates, an FM
protocol was used.^{20 (link)} A starting ceramide
conformation inside the enzyme was chosen between those found after
preliminary MD runs to be compatible with glycosylation, i.e., when
the distance d_C1-Oc between the terminal
hydroxyl oxygen of the ceramide’s polar head and the carbon
C1 of glucose in UDP-glucose (atoms involved in the glycosylation
reaction were minimal). The starting system is shown in Figure S3. According to FM, biased CVs chosen
were the position along the rotation axis of the funnel (CV1), its
distance from the axis (CV2), and the distance d_C1-Oc (CV3). The funnel parameters that were used are Zcc =
3.0 nm, Alpha = 0.5 rad, and R_cyl = 0.6
nm. Gaussian functions with a height of 2 kJ/mol and a sigma value
of 0.05 were deposited every 1 ps.

Canini G., Lo Cascio E., Della Longa S., Cecconi F, & Arcovito A. (2023). Human Glucosylceramide Synthase at Work as Provided by “In Silico” Molecular Docking, Molecular Dynamics, and Metadynamics. ACS Omega, 8(9), 8755-8765.

Publication 2023

Ceramides Enzymes Epistropheus Glucose Glycosylation Head Oxygen Uridine Diphosphate Glucose

Cloning and Expression of CMAH and GGTA1

Gene fragments for the mouse genes encoding CMAH and GGTA1, the glycosylation enzymes were synthesized (Geneart, Thermo Fisher). The gene fragments were designed such that the CMAH and GGTA1 genes would be expressed in a bi-cistronic vector configuration, with or without fluorescent tags added to either the N-terminus or the C-terminus of the genes for convenient expression monitoring. Tags were also needed for immunofluorescence, as there were no commercially available CMAH or GGTA1 specific antibodies. Green fluorescent protein (GFP) with a 5′IRES (internal ribosome entry site) was incorporated into all constructs to select GFP-positive cells expressing the genes of interest and monitor their cellular localization. Lyophilized DNA fragments in an intermediate cloning vector were reconstituted in 8 µL of water and digested with SalI and NotI restriction endonucleases to release the desired fragment, then separated on an agarose gel (1%). Each fragment was ligated into the vector between SalI and NotI sites. The ligation reaction was used to transform chemically competent E. coli TOP10 cells. Two to four individual colonies were picked for Qiagen miniprep. After positive sequence verification of the miniprep, one clone was selected for large-scale plasmid preparation (Qiagen maxiprep). The whole plasmid was sequenced and confirmed to have the correct orientation. Additionally, a control vector with GFP expression cassette-only was generated.

Gupta S., Shah B., Fung C.S., Chan P.K., Wakefield D.L., Kuhns S., Goudar C.T, & Piret J.M. (2023). Engineering protein glycosylation in CHO cells to be highly similar to murine host cells. Frontiers in Bioengineering and Biotechnology, 11, 1113994.

Publication 2023

Antibodies Cells Cistron Clone Cells Cloning Vectors DNA Restriction Enzymes Enzymes Escherichia coli Genes Glycosylation Green Fluorescent Proteins Immunofluorescence Internal Ribosome Entry Sites Ligation Mus Plasmids Sepharose

Generation of GlyRα1 N38Q Mutant

Site-directed mutagenesis was used to create the non-glycosylation mutant GlyRα1^N38Q. The human GlyRα1 cDNA in pRK5 vector (gift †P. Seeburg) was used as template. Sequence correctness was verified (Eurofins Genomics Germany GmbH, Ebersberg, Germany). For transfection with GFP, the eGFP-N1 plasmid (Takara Bio Europe, Saint-Germain-en-Laye, France) was used.

Rauschenberger V., Piro I., Kasaragod V.B., Hörlin V., Eckes A.L., Kluck C.J., Schindelin H., Meinck H.M., Wickel J., Geis C., Tüzün E., Doppler K., Sommer C, & Villmann C. (2023). Glycine receptor autoantibody binding to the extracellular domain is independent from receptor glycosylation. Frontiers in Molecular Neuroscience, 16, 1089101.

Publication 2023

Cloning Vectors DNA, Complementary Glycosylation Homo sapiens Mutagenesis, Site-Directed Plasmids Transfection

Top products related to «Glycosylation»

Pngase f by New England Biolabs

Sourced in United States, United Kingdom, Germany, Japan, Canada, France, China, Morocco, Italy

PNGase F is an enzyme that cleaves the bond between the asparagine residue and the N-acetylglucosamine residue in N-linked glycoproteins. It is commonly used in the analysis and characterization of glycoproteins.

Rt2 first strand kit by Qiagen

Sourced in Germany, United States, United Kingdom, Netherlands, Canada, China, Spain, France, Australia, Italy, Japan

The RT2 First Strand Kit is a laboratory reagent used for the reverse transcription of RNA to cDNA. It provides the necessary components for the conversion of RNA to cDNA, which is a crucial step in various molecular biology applications, such as gene expression analysis and real-time PCR.

Tskgel g3000sw by Tosoh

Sourced in Japan

Tskgel G3000SW is a gel permeation chromatography (GPC) column designed for the size-exclusion chromatography (SEC) analysis of macromolecules. The column is packed with a silica-based stationary phase and is suitable for the separation of polymers, proteins, and other large molecules based on their size and molecular weight.

Ppic9k vector by Thermo Fisher Scientific

Sourced in United States

The PPIC9K vector is a circular DNA plasmid used for gene expression and protein production in various cell lines. It contains the necessary genetic elements for cloning and expressing target genes, including a promoter, multiple cloning site, and selectable marker. The core function of the PPIC9K vector is to facilitate the introduction and expression of recombinant DNA in host cells for research and experimental purposes.

Tsk gel guard sw xl by Tosoh

The TSK® gel Guard SW xl is a size-exclusion chromatography (SEC) column used for the separation and analysis of macromolecules. It is designed to protect the main analytical column from contamination and extends the lifetime of the system.

Endo h by New England Biolabs

Sourced in United States, United Kingdom, Germany, Canada, Switzerland, France

Endo H is a glycosidase enzyme that cleaves the chitobiose core of high mannose and some hybrid-type oligosaccharides from N-linked glycoproteins. It removes the N-linked glycans from glycoproteins, allowing the study of the effects of glycosylation on protein structure and function.

Immunoradiometric assay by Fujirebio

Sourced in Japan

An immunoradiometric assay (IRMA) is a type of immunoassay that uses radioactive isotopes to quantify the concentration of a specific analyte in a sample. It involves the use of antibodies labeled with radioactive elements to detect and measure the target analyte in a sample.

Asserachrom fix antigen kit by Diagnostica Stago

Sourced in France

The Asserachrom FIX: Antigen Kit is a laboratory equipment product manufactured by Diagnostica Stago. It is used for the quantitative determination of factor IX antigen in human plasma.

7500 fast real time pcr system by Thermo Fisher Scientific

Sourced in United States, China, Japan, Germany, United Kingdom, Switzerland, Canada, Italy, Singapore, France, Poland, Spain, Australia, Luxembourg, Lithuania, Sweden, Denmark, Netherlands, India

The 7500 Fast Real-Time PCR System is a thermal cycler designed for fast and accurate real-time PCR analysis. It features a 96-well format and supports a variety of sample volumes and chemistries. The system is capable of rapid thermal cycling and provides precise temperature control for reliable results.

Accuprime pfx supermix by Thermo Fisher Scientific

Sourced in United States

AccuPrime Pfx SuperMix is a high-fidelity, thermostable DNA polymerase formulation designed for accurate and efficient DNA amplification. It provides robust performance across a wide range of templates and applications.

What are the different types or variations of Glycosylation?

Glycosylation can occur in several forms, including N-linked glycosylation, O-linked glycosylation, and C-linked glycosylation. N-linked glycans are attached to the asparagine residues of proteins, while O-linked glycans are attached to serine or threonine residues. C-linked glycosylation involves the attachment of a mannose residue to a tryptophan residue. Each type of glycosylation can have unique impacts on protein folding, stability, and function.

How can Glycosylation impact biological processes?

Glycosylation plays a crucial role in numerous biological processes, including protein folding, stability, and function. This post-translational modification can affect the tertiary structure of proteins, influencing their interactions with other molecules and their overall activity. Glycosylation is also implicated in cell-cell signaling, immune response, and disease pathogenesis, making it an important area of study for researchers.

What are some common applications of Glycosylation research?

Glycosylation research has numerous applications, including the development of biomarkers for disease diagnosis, the production of therapeutic proteins with enhanced stability and efficacy, and the understanding of pathogenic mechanisms. Researchers may also leverage glycosylation data to engineer novel biomolecules or optimize existing ones for specific functions, such as improved drug delivery or increased resistance to proteolytic degradation.

How can PubCompare.ai assist with Glycosylation research?

PubCompare.ai's AI-driven platform can be a valuable tool for optimizing Glycosylation research. The platform allows researchers to screen protocol literature more efficiently, leveraging artificial intelligence to pinoint critical insights. By comparing the effectiveness of different Glycosylation protocols, PubCompare.ai can help researchers identify the most effective approaches for their specific research goals, enhancing reproducibility and accuracy. This can be particularly useful when trying to choose the best protocol for your Glycolysation studies and unlock new insights in this fundamental area of biological chemistry.

More about "Glycosylation"

Glycosylation is the enzymatic process of attaching glycan chains, also known as carbohydrate moieties, to proteins, lipids, or other organic molecules.
This post-translational modification plays a crucial role in numerous biological processes, including protein folding, stability, and function.
Researchers can leverage advanced tools like PubCompare.ai's AI-driven platform to optimize their glycosylation studies, locate the best protocols, and improve reproducibility.
The tool's intelligent comparisons help identify the most effective approaches, streamlining research and unlocking new insights.
Scientists can easily access glycosylation-related literature, preprints, and patents, supporting their efforts to enhance this fundamental area of biological chemistry.
PNGase F is an enzyme that cleaves the bond between the asparagine residue and the N-linked glycan, allowing for the analysis of glycosylation patterns.
The RT2 First Strand Kit is a tool used for reverse transcription of RNA to cDNA, which can be used to study gene expression related to glycosylation.
Tskgel G3000SW is a size exclusion chromatography column used for the separation and analysis of glycoproteins, while the PPIC9K vector is a plasmid used for the expression of glycosylated proteins.
TSK® gel Guard SW xl is a guard column used to protect the main analytical column from contamination, and Endo H is an enzyme that cleaves high-mannose and some hybrid type N-linked glycans.
Immunoradiometric assay and Asserachrom FIX: Antigen Kit are used for the quantitative detection and measurement of glycosylated proteins, while the 7500 Fast Real-Time PCR System and AccuPrime Pfx SuperMix are tools used for the amplification and analysis of genes involved in glycosylation pathways.
By leveraging these techniques and technologies, researchers can gain deeper insights into the complex processes of glycosylation and its impact on biological systems.