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1.
Food Chem ; 451: 139295, 2024 Sep 01.
Article in English | MEDLINE | ID: mdl-38729042

ABSTRACT

Information regarding protein expression and phosphorylation modifications in the bovine milk fat globule membrane is scarce, particularly throughout various lactation periods. This study employed a complete proteome and phosphoproteome between bovine colostrum and mature milk. A total of 11 proteins were seen in both protein expression and phosphorylation levels. There were 400 proteins identified in only protein expression, and 104 phosphoproteins identified in only phosphorylation levels. A total of 232 significant protein characteristics were identified within the proteome and significant phosphorylation sites within 86 phosphoproteins of the phosphoproteome. Biological activities and pathways primarily exhibited associations with the immune system. Simultaneously, a comprehensive analysis of proteins and phosphorylation sites using a multi-omics approach. Hence, the data we have obtained has the potential to expand our understanding of how the bovine milk fat globule membrane might be utilized as a beneficial component in dairy products.


Subject(s)
Glycolipids , Glycoproteins , Lactation , Lipid Droplets , Milk , Phosphoproteins , Proteomics , Animals , Cattle , Glycoproteins/chemistry , Glycoproteins/immunology , Glycoproteins/metabolism , Lipid Droplets/chemistry , Lipid Droplets/metabolism , Glycolipids/chemistry , Glycolipids/metabolism , Female , Phosphoproteins/chemistry , Phosphoproteins/metabolism , Phosphoproteins/genetics , Phosphoproteins/immunology , Milk/chemistry , Milk Proteins/chemistry , Milk Proteins/metabolism , Milk Proteins/immunology , Phosphorylation , Proteome/chemistry , Proteome/immunology , Proteome/analysis
2.
J Transl Med ; 22(1): 454, 2024 May 13.
Article in English | MEDLINE | ID: mdl-38741158

ABSTRACT

BACKGROUND: Glycosylation is an enzyme-catalyzed post-translational modification that is distinct from glycation and is present on a majority of plasma proteins. N-glycosylation occurs on asparagine residues predominantly within canonical N-glycosylation motifs (Asn-X-Ser/Thr) although non-canonical N-glycosylation motifs Asn-X-Cys/Val have also been reported. Albumin is the most abundant protein in plasma whose glycation is well-studied in diabetes mellitus. However, albumin has long been considered a non-glycosylated protein due to absence of canonical motifs. Albumin contains two non-canonical N-glycosylation motifs, of which one was recently reported to be glycosylated. METHODS: We enriched abundant serum proteins to investigate their N-linked glycosylation followed by trypsin digestion and glycopeptide enrichment by size-exclusion or mixed-mode anion-exchange chromatography. Glycosylation at canonical as well as non-canonical sites was evaluated by liquid chromatography-tandem mass spectrometry (LC-MS/MS) of enriched glycopeptides. Deglycosylation analysis was performed to confirm N-linked glycosylation at non-canonical sites. Albumin-derived glycopeptides were fragmented by MS3 to confirm attached glycans. Parallel reaction monitoring was carried out on twenty additional samples to validate these findings. Bovine and rabbit albumin-derived glycopeptides were similarly analyzed by LC-MS/MS. RESULTS: Human albumin is N-glycosylated at two non-canonical sites, Asn68 and Asn123. N-glycopeptides were detected at both sites bearing four complex sialylated glycans and validated by MS3-based fragmentation and deglycosylation studies. Targeted mass spectrometry confirmed glycosylation in twenty additional donor samples. Finally, the highly conserved Asn123 in bovine and rabbit serum albumin was also found to be glycosylated. CONCLUSIONS: Albumin is a glycoprotein with conserved N-linked glycosylation sites that could have potential clinical applications.


Subject(s)
Glycopeptides , Glycoproteins , Glycosylation , Glycoproteins/metabolism , Glycoproteins/chemistry , Humans , Glycopeptides/metabolism , Glycopeptides/chemistry , Amino Acid Sequence , Tandem Mass Spectrometry , Animals , Molecular Sequence Data , Albumins/metabolism , Cattle , Chromatography, Liquid
3.
J Agric Food Chem ; 72(19): 11268-11277, 2024 May 15.
Article in English | MEDLINE | ID: mdl-38695399

ABSTRACT

Buttermilk is a potential material for the production of a milk fat globule membrane (MFGM) and can be mainly classified into two types: whole cream buttermilk and cheese whey cream buttermilk (WCB). Due to the high casein micelle content of whole cream buttermilk, the removal of casein micelles to improve the purity of MFGM materials is always required. This study investigated the effects of rennet and acid coagulation on the lipid profile of buttermilk rennet-coagulated whey (BRW) and buttermilk acid-coagulated whey (BAW) and compared them with WCB. BRW has significantly higher phospholipids (PLs) and ganglioside contents than BAW and WCB. The abundance of arachidonic acid (ARA)- and eicosapentaenoic acid (EPA)-structured PLs was higher in WCB, while docosahexaenoic acid (DHA)-structured PLs were higher in BRW, indicating that BRW and WCB intake might have a greater effect on improving cardiovascular conditions and neurodevelopment. WCB and BRW had a higher abundance of plasmanyl PL and plasmalogen PL, respectively. Phosphatidylcholine (PC) (28:1), LPE (20:5), and PC (26:0) are characteristic lipids among BRW, BAW, and WCB, and they can be used to distinguish MFGM-enriched whey from different sources.


Subject(s)
Buttermilk , Cheese , Goats , Lipidomics , Whey , Animals , Buttermilk/analysis , Cheese/analysis , Whey/chemistry , Phospholipids/analysis , Phospholipids/chemistry , Glycolipids/chemistry , Milk/chemistry , Lipid Droplets/chemistry , Glycoproteins/chemistry , Glycoproteins/analysis , Lipids/chemistry , Lipids/analysis
4.
Int J Mol Sci ; 25(9)2024 Apr 28.
Article in English | MEDLINE | ID: mdl-38732045

ABSTRACT

In the absence of naturally available galactofuranose-specific lectin, we report herein the bioengineering of GalfNeoLect, from the first cloned wild-type galactofuranosidase (Streptomyces sp. strain JHA19), which recognises and binds a single monosaccharide that is only related to nonmammalian species, usually pathogenic microorganisms. We kinetically characterised the GalfNeoLect to confirm attenuation of hydrolytic activity and used competitive inhibition assay, with close structural analogues of Galf, to show that it conserved interaction with its original substrate. We synthetised the bovine serum albumin-based neoglycoprotein (GalfNGP), carrying the multivalent Galf units, as a suitable ligand and high-avidity system for the recognition of GalfNeoLect which we successfully tested directly with the galactomannan spores of Aspergillus brasiliensis (ATCC 16404). Altogether, our results indicate that GalfNeoLect has the necessary versatility and plasticity to be used in both research and diagnostic lectin-based applications.


Subject(s)
Galactose , Galactose/analogs & derivatives , Galactose/metabolism , Galactose/chemistry , Aspergillus/metabolism , Aspergillus/genetics , Lectins/metabolism , Lectins/chemistry , Glycoproteins/chemistry , Glycoproteins/metabolism , Mannans/chemistry , Animals , Serum Albumin, Bovine/chemistry
5.
Langmuir ; 40(20): 10405-10413, 2024 May 21.
Article in English | MEDLINE | ID: mdl-38723020

ABSTRACT

Glycosylated proteins or glycoproteins make up a large family of glycoconjugates, and they participate in a variety of fundamental biological events. Glycoproteins have become important biomarkers in the diagnosis and treatment of a number of tumors. Biosensors are quite suitable for glycoprotein detection. The design and fabrication of a functional sensing interface play a crucial role in the biosensor construction to target glycoproteins. The functional interface, particularly receptors, typically determines the key characteristics of a biosensor, such as selectivity and sensitivity. Antibody, peptide, aptamer, boronic acid derivative, lectin, and molecularly imprinted polymer are all capable receptors for glycoprotein recognition, and each of these will be discussed. Most glycoproteins exist in low abundance, thus rendering signal amplification techniques indispensable. Nucleic acid-mediated and nanomaterial-mediated signal amplification for the detection of glycoproteins will be focused on herein. This review aims to highlight these different functional interfaces for glycoprotein sensing.


Subject(s)
Biosensing Techniques , Glycoproteins , Biosensing Techniques/methods , Glycoproteins/analysis , Glycoproteins/chemistry , Humans
6.
J Mass Spectrom ; 59(6): e5034, 2024 Jun.
Article in English | MEDLINE | ID: mdl-38726698

ABSTRACT

Glycosylation is an incredibly common and diverse post-translational modification that contributes widely to cellular health and disease. Mass spectrometry is the premier technique to study glycoproteins; however, glycoproteomics has lagged behind traditional proteomics due to the challenges associated with studying glycosylation. For instance, glycans dissociate by collision-based fragmentation, thus necessitating electron-based fragmentation for site-localization. The vast glycan heterogeneity leads to lower overall abundance of each glycopeptide, and often, ion suppression is observed. One of the biggest issues facing glycoproteomics is the lack of reliable software for analysis, which necessitates manual validation and serves as a massive bottleneck in data processing. Here, I will discuss each of these challenges and some ways in which the field is attempting to address them, along with perspectives on how I believe we should move forward.


Subject(s)
Glycomics , Glycoproteins , Mass Spectrometry , Proteomics , Proteomics/methods , Glycomics/methods , Mass Spectrometry/methods , Glycoproteins/analysis , Glycoproteins/chemistry , Humans , Glycosylation , Polysaccharides/analysis , Polysaccharides/chemistry , Glycopeptides/analysis , Glycopeptides/chemistry , Software , Protein Processing, Post-Translational , Animals
7.
J Nanobiotechnology ; 22(1): 278, 2024 May 23.
Article in English | MEDLINE | ID: mdl-38783363

ABSTRACT

Amyloid-ß (Aß) readily misfolds into neurotoxic aggregates, generating high levels of reactive oxygen species (ROS), leading to progressive oxidative damage and ultimately cell death. Therefore, simultaneous inhibition of Aß aggregation and scavenging of ROS may be a promising therapeutic strategy to alleviate Alzheimer's disease pathology. Based on the previously developed antibody 1F12 that targets all forms of Aß42, we developed an Aß42 and ROS dual-targeting nanocomposite using biodegradable mesoporous silica nanoparticles as carriers to load ultra-small cerium oxide nanocrystals (bMSNs@Ce-1F12). By modifying the brain-targeted rabies virus glycoprotein 29 (RVG29-bMSNs@Ce-1F12), this intelligent nanocomposite can efficiently target brain Aß-rich regions. Combined with peripheral and central nervous system treatments, RVG29-bMSNs@Ce-1F12 can significantly alleviate AD symptoms by inhibiting Aß42 misfolding, accelerating Aß42 clearance, and scavenging ROS. Furthermore, this synergistic effect of ROS scavenging and Aß clearance exhibited by this Aß42 and ROS dual-targeted strategy also reduced the burden of hyperphosphorylated tau, alleviated glial cell activation, and ultimately improved cognitive function in APP/PS1 mice. Our findings indicate that RVG29-bMSNs@Ce-1F12 is a promising nanodrug that can facilitate multi-target treatment of AD.


Subject(s)
Alzheimer Disease , Amyloid beta-Peptides , Cerium , Nanocomposites , Reactive Oxygen Species , Alzheimer Disease/drug therapy , Alzheimer Disease/metabolism , Animals , Reactive Oxygen Species/metabolism , Amyloid beta-Peptides/metabolism , Nanocomposites/chemistry , Mice , Cerium/chemistry , Cerium/pharmacology , Mice, Transgenic , Silicon Dioxide/chemistry , Peptide Fragments/chemistry , Peptide Fragments/pharmacology , Humans , Brain/metabolism , Nanoparticles/chemistry , Glycoproteins/chemistry , Glycoproteins/pharmacology , Glycoproteins/metabolism , Disease Models, Animal , Viral Proteins
8.
Int J Biol Macromol ; 269(Pt 1): 132022, 2024 Jun.
Article in English | MEDLINE | ID: mdl-38697414

ABSTRACT

Edible bird's nest (EBN) is made up of sialylated-mucin glycoprotein with various health benefits due to its high antioxidative activity. However, as a macromolecule with distinct charged sialic acid and amino acids, fractions with different charges would have varied physicochemical properties and antioxidant activity, which have not been studied. Therefore, this study aimed to fractionate and purify the enzymatic hydrolysed of cleaned EBN (EBNhc) and EBN by-product (EBNhbyp) through anion exchange chromatography (AEC), and determine their molecular weights, physicochemical properties, and antioxidative activities. Overall, 26 fractionates were collected from enzymatic hydrolysate by AEC, which were classified into 5 fractions. It was found that the positively charged fraction of EBNhc (CF 1) and EBNhbyp (DF 1) showed the significantly highest (p < 0.05) soluble protein contents (22.86 and 18.40 mg/g), total peptide contents (511.13 and 800.47 mg/g) and ferric reducing antioxidant power (17.44 and 6.96 mg/g) among the fractionates. In conclusion, a positively charged fraction (CF 1 and DF 1) showed more desired physicochemical properties and antioxidative activities. This research suggests the potential of AEC fractionation as a technology to purify EBN and produce positively charged EBN fractionates with antioxidative potential that could be applied as food components to provide health benefits.


Subject(s)
Antioxidants , Birds , Glycoproteins , Animals , Chromatography, Ion Exchange/methods , Antioxidants/chemistry , Antioxidants/isolation & purification , Antioxidants/pharmacology , Glycoproteins/chemistry , Glycoproteins/isolation & purification , Hydrolysis , Molecular Weight , N-Acetylneuraminic Acid/chemistry , Chemical Fractionation/methods
9.
Anal Chem ; 96(22): 8956-8964, 2024 Jun 04.
Article in English | MEDLINE | ID: mdl-38776126

ABSTRACT

Glycoproteins play important roles in numerous physiological processes and are often implicated in disease. Analysis of site-specific protein glycobiology through glycoproteomics has evolved rapidly in recent years thanks to hardware and software innovations. Particularly, the introduction of parallel accumulation serial fragmentation (PASEF) on hybrid trapped ion mobility time-of-flight mass spectrometry instruments combined deep proteome sequencing with separation of (near-)isobaric precursor ions or converging isotope envelopes through ion mobility separation. However, the reported use of PASEF in integrated glycoproteomics workflows to comprehensively capture the glycoproteome is still limited. To this end, we developed an integrated methodology using timsTOF Pro 2 to enhance N-glycopeptide identifications in complex mixtures. We systematically optimized the ion optics tuning, collision energies, mobility isolation width, and the use of dopant-enriched nitrogen gas (DEN). Thus, we obtained a marked increase in unique glycopeptide identification rates compared to standard proteomics settings, showcasing our results on a large set of glycopeptides. With short liquid chromatography gradients of 30 min, we increased the number of unique N-glycopeptide identifications in human plasma samples from around 100 identifications under standard proteomics conditions to up to 1500 with our optimized glycoproteomics approach, highlighting the need for tailored optimizations to obtain comprehensive data.


Subject(s)
Glycopeptides , Proteomics , Proteomics/methods , Humans , Glycopeptides/analysis , Glycopeptides/chemistry , Glycopeptides/blood , Workflow , Glycoproteins/analysis , Glycoproteins/chemistry , Glycoproteins/blood , Chromatography, Liquid , Tandem Mass Spectrometry
10.
J Proteome Res ; 23(6): 2137-2147, 2024 Jun 07.
Article in English | MEDLINE | ID: mdl-38787631

ABSTRACT

N-glycosylation is one of the most universal and complex protein post-translational modifications (PTMs), and it is involved in many physiological and pathological activities. Owing to the low abundance of N-glycoproteins, enrichment of N-glycopeptides for mass spectrometry analysis usually requires a large amount of peptides. Additionally, oocyte protein N-glycosylation has not been systemically characterized due to the limited sample amount. Here, we developed a glycosylation enrichment method based on lectin and a single-pot, solid-phase-enhanced sample preparation (SP3) technology, termed lectin-based SP3 technology (LectinSP3). LectinSP3 immobilized lectin on the SP3 beads for N-glycopeptide enrichment. It could identify over 1100 N-glycosylation sites and 600 N-glycoproteins from 10 µg of mouse testis peptides. Furthermore, using the LectinSP3 method, we characterized the N-glycoproteome of 1000 mouse oocytes in three replicates and identified a total of 363 N-glycosylation sites from 215 N-glycoproteins. Bioinformatics analysis revealed that these oocyte N-glycoproteins were mainly enriched in cell adhesion, fertilization, and sperm-egg recognition. Overall, the LectinSP3 method has all procedures performed in one tube, using magnetic beads. It is suitable for analysis of a low amount of samples and is expected to be easily adaptable for automation. In addition, our mouse oocyte protein N-glycosylation profiling could help further characterize the regulation of oocyte functions.


Subject(s)
Glycopeptides , Glycoproteins , Lectins , Oocytes , Proteomics , Animals , Oocytes/metabolism , Mice , Glycosylation , Glycoproteins/metabolism , Glycoproteins/chemistry , Glycoproteins/analysis , Lectins/chemistry , Lectins/metabolism , Proteomics/methods , Female , Glycopeptides/analysis , Glycopeptides/chemistry , Protein Processing, Post-Translational , Male , Testis/metabolism , Testis/chemistry , Proteome/analysis , Proteome/metabolism
11.
PLoS One ; 19(5): e0300507, 2024.
Article in English | MEDLINE | ID: mdl-38728300

ABSTRACT

According to the 2018 WHO R&D Blueprint, Nipah virus (NiV) is a priority disease, and the development of a vaccine against NiV is strongly encouraged. According to criteria used to categorize zoonotic diseases, NiV is a stage III disease that can spread to people and cause unpredictable outbreaks. Since 2001, the NiV virus has caused annual outbreaks in Bangladesh, while in India it has caused occasional outbreaks. According to estimates, the mortality rate for infected individuals ranges from 70 to 91%. Using immunoinformatic approaches to anticipate the epitopes of the MHC-I, MHC-II, and B-cells, they were predicted using the NiV glycoprotein and nucleocapsid protein. The selected epitopes were used to develop a multi-epitope vaccine construct connected with linkers and adjuvants in order to improve immune responses to the vaccine construct. The 3D structure of the engineered vaccine was anticipated, optimized, and confirmed using a variety of computer simulation techniques so that its stability could be assessed. According to the immunological simulation tests, it was found that the vaccination elicits a targeted immune response against the NiV. Docking with TLR-3, 7, and 8 revealed that vaccine candidates had high binding affinities and low binding energies. Finally, molecular dynamic analysis confirms the stability of the new vaccine. Codon optimization and in silico cloning showed that the proposed vaccine was expressed to a high degree in Escherichia coli. The study will help in identifying a potential epitope for a vaccine candidate against NiV. The developed multi-epitope vaccine construct has a lot of potential, but they still need to be verified by in vitro & in vivo studies.


Subject(s)
Glycoproteins , Nipah Virus , Viral Vaccines , Nipah Virus/immunology , Viral Vaccines/immunology , Glycoproteins/immunology , Glycoproteins/chemistry , Humans , Henipavirus Infections/prevention & control , Henipavirus Infections/immunology , Computer Simulation , Epitopes/immunology , Epitopes/chemistry , Molecular Dynamics Simulation , Nucleocapsid/immunology , Molecular Docking Simulation
12.
Anal Methods ; 16(22): 3475-3485, 2024 Jun 06.
Article in English | MEDLINE | ID: mdl-38780482

ABSTRACT

Sialylation is an important modification of proteins, related to protein life and bioactivity. However, the evaluation of sialylation is only based on the average molecular composition by peptide mapping and glycan profiling because sialylated proteins are usually too heterogeneous to obtain good quality mass spectra by conventional intact mass analysis methods. In this study, a simple strong cation exchange-mass spectroscopy (SCX-MS) method was developed for intact mass analysis of sialylated glycoproteins. The developed SCX-MS method provided good separation for sialylated glycoproteins and had an inherent characteristic of native MS. Thus, the intact mass analysis of highly heterogeneous glycoprotein, which cannot be obtained by reversed-phase liquid chromatography (RPLC)-MS and size exclusion chromatography (SEC)-MS methods, can be well analyzed using the current SCX-MS method. First, the method was developed and optimized using the etanercept monomer. Conditions including MS parameters, flow rate, and gradient were investigated. Then, the developed method was used to analyze a new recombinant vaccine, protein 1. Similar to the etanercept monomer, the intact molecular information of protein 1, which cannot be obtained by RPLC-MS and SEC-MS, can be achieved using SCX-MS. Combined with information obtained on peptide mapping and glycan profiles obtained by LC-MS, the new vaccine was well characterized. Finally, the SCX-MS method was used to quickly evaluate the batch-to-batch reproducibility of protein 1. It was much faster than peptide mapping and glycan profiling methods and can provide information complementary to these strategies. It should be useful for many applications where speed and comprehensive characterization are required, such as recombinant sialylated vaccines and fusion proteins.


Subject(s)
Glycoproteins , Mass Spectrometry , Glycoproteins/chemistry , Glycoproteins/analysis , Mass Spectrometry/methods , Chromatography, Ion Exchange/methods , Etanercept/chemistry , Glycosylation , N-Acetylneuraminic Acid/chemistry , N-Acetylneuraminic Acid/analysis , Humans , Animals , Cations/chemistry , Recombinant Proteins/chemistry , Recombinant Proteins/analysis
13.
Carbohydr Res ; 538: 109094, 2024 Apr.
Article in English | MEDLINE | ID: mdl-38564900

ABSTRACT

Human diseases often correlate with changes in protein glycosylation, which can be observed in serum or plasma samples. N-glycosylation, the most common form, can provide potential biomarkers for disease prognosis and diagnosis. However, glycoproteins constitute a relatively small proportion of the total proteins in human serum and plasma compared to the non-glycosylated protein albumin, which constitutes the majority. The detection of microheterogeneity and low glycan abundance presents a challenge. Mass spectrometry facilitates glycoproteomics research, yet it faces challenges due to interference from abundant plasma proteins. Therefore, methods have emerged to enrich N-glycans and N-linked glycopeptides using glycan affinity, chemical properties, stationary phase chemical coupling, bioorthogonal techniques, and other alternatives. This review focuses on N-glycans and N-glycopeptides enrichment in human serum or plasma, emphasizing methods and applications. Although not exhaustive, it aims to elucidate principles and showcase the utility and limitations of glycoproteome characterization.


Subject(s)
Glycopeptides , Glycoproteins , Humans , Glycopeptides/chemistry , Glycoproteins/chemistry , Glycosylation , Mass Spectrometry/methods , Polysaccharides
14.
Glycobiology ; 34(6)2024 Apr 24.
Article in English | MEDLINE | ID: mdl-38590172

ABSTRACT

Human noroviruses, globally the main cause of viral gastroenteritis, show strain specific affinity for histo-blood group antigens (HBGA) and can successfully be propagated ex vivo in human intestinal enteroids (HIEs). HIEs established from jejunal stem cells of individuals with different ABO, Lewis and secretor geno- and phenotypes, show varying susceptibility to such infections. Using bottom-up glycoproteomic approaches we have defined and compared the N-linked glycans of glycoproteins of seven jejunal HIEs. Membrane proteins were extracted, trypsin digested, and glycopeptides enriched by hydrophilic interaction liquid chromatography and analyzed by nanoLC-MS/MS. The Byonic software was used for glycopeptide identification followed by hands-on verifications and interpretations. Glycan structures and attachment sites were identified from MS2 spectra obtained by higher-energy collision dissociation through analysis of diagnostic saccharide oxonium ions (B-ions), stepwise glycosidic fragmentation of the glycans (Y-ions), and peptide sequence ions (b- and y-ions). Altogether 694 unique glycopeptides from 93 glycoproteins were identified. The N-glycans encompassed pauci- and oligomannose, hybrid- and complex-type structures. Notably, polyfucosylated HBGA-containing glycopeptides of the four glycoproteins tetraspanin-8, carcinoembryonic antigen-related cell adhesion molecule 5, sucrose-isomaltase and aminopeptidase N were especially prominent and were characterized in detail and related to donor ABO, Lewis and secretor types of each HIE. Virtually no sialylated N-glycans were identified for these glycoproteins suggesting that terminal sialylation was infrequent compared to fucosylation and HBGA biosynthesis. This approach gives unique site-specific information on the structural complexity of N-linked glycans of glycoproteins of human HIEs and provides a platform for future studies on the role of host glycoproteins in gastrointestinal infectious diseases.


Subject(s)
Glycoproteins , Humans , Glycoproteins/metabolism , Glycoproteins/chemistry , Proteomics/methods , Blood Group Antigens/metabolism , Blood Group Antigens/chemistry , Polysaccharides/chemistry , Polysaccharides/metabolism , Fucose/metabolism , Fucose/chemistry , Phenotype , Glycosylation , ABO Blood-Group System/metabolism , ABO Blood-Group System/chemistry
15.
Anal Chem ; 96(15): 5741-5745, 2024 Apr 16.
Article in English | MEDLINE | ID: mdl-38573003

ABSTRACT

Fucosylation is an important structural feature of glycans and plays an essential role in the regulation of glycoprotein functions. Fucosylation can be classified into core- (CF) and antenna-fucosylation (AF, also known as (sialyl-) Lewis) based on the location on N-glycans, and they perform distinct biological functions. In this study, core- and antenna-fucosylated N-glycans on human serum glycoproteins that hold great clinical application values were systematically characterized at the site-specific level using StrucGP combined with the recently developed fucosylation assignment method. The results showed that fucosylation was widely distributed on serum glycoproteins, with 50% of fucosylated glycopeptides modified by AF N-glycans, 37% by CF N-glycans, and 13% by dual-fucosylated N-glycans. Interestingly, CF and AF N-glycans preferred to modify different groups of serum glycoproteins with different tissue origins and were involved in distinctive biological processes. Specifically, AF N-glycoproteins are mainly from the liver and participated in complement activation, blood coagulation, and endopeptidase activities, while CF N-glycoproteins originate from diverse tissues and are mainly involved in cell adhesion and signaling transduction. These data further enhanced our understanding of fucosylation on circulation glycoproteins.


Subject(s)
Glycoproteins , Liver , Humans , Glycoproteins/chemistry , Glycosylation , Liver/metabolism , Polysaccharides/chemistry , Fucose/chemistry
16.
Cell Rep Methods ; 4(4): 100744, 2024 Apr 22.
Article in English | MEDLINE | ID: mdl-38582075

ABSTRACT

A comprehensive analysis of site-specific protein O-glycosylation is hindered by the absence of a consensus O-glycosylation motif, the diversity of O-glycan structures, and the lack of a universal enzyme that cleaves attached O-glycans. Here, we report the development of a robust O-glycoproteomic workflow for analyzing complex biological samples by combining four different strategies: removal of N-glycans, complementary digestion using O-glycoprotease (IMPa) with/without another protease, glycopeptide enrichment, and mass spectrometry with fragmentation of glycopeptides using stepped collision energy. Using this workflow, we cataloged 474 O-glycopeptides on 189 O-glycosites derived from 79 O-glycoproteins from human plasma. These data revealed O-glycosylation of several abundant proteins that have not been previously reported. Because many of the proteins that contained unannotated O-glycosylation sites have been extensively studied, we wished to confirm glycosylation at these sites in a targeted fashion. Thus, we analyzed selected purified proteins (kininogen-1, fetuin-A, fibrinogen, apolipoprotein E, and plasminogen) in independent experiments and validated the previously unknown O-glycosites.


Subject(s)
Glycoproteins , Proteome , Proteomics , Workflow , Humans , Glycosylation , Glycoproteins/metabolism , Glycoproteins/chemistry , Proteomics/methods , Proteome/metabolism , Proteome/analysis , Glycopeptides/analysis , Glycopeptides/chemistry , Glycopeptides/metabolism , Kininogens/metabolism , Kininogens/chemistry , Polysaccharides/metabolism , Apolipoproteins E/metabolism , Apolipoproteins E/chemistry , Fibrinogen/metabolism , Fibrinogen/chemistry , alpha-2-HS-Glycoprotein/metabolism , alpha-2-HS-Glycoprotein/analysis
17.
Biomacromolecules ; 25(5): 3001-3010, 2024 May 13.
Article in English | MEDLINE | ID: mdl-38598264

ABSTRACT

Glycosylation is a valuable tool for modulating protein solubility; however, the lack of reliable research strategies has impeded efficient progress in understanding and applying this modification. This study aimed to bridge this gap by investigating the solubility of a model glycoprotein molecule, the carbohydrate-binding module (CBM), through a two-stage process. In the first stage, an approach involving chemical synthesis, comparative analysis, and molecular dynamics simulations of a library of glycoforms was employed to elucidate the effect of different glycosylation patterns on solubility and the key factors responsible for the effect. In the second stage, a predictive mathematical formula, innovatively harnessing machine learning algorithms, was derived to relate solubility to the identified key factors and accurately predict the solubility of the newly designed glycoforms. Demonstrating feasibility and effectiveness, this two-stage approach offers a valuable strategy for advancing glycosylation research, especially for the discovery of glycoforms with increased solubility.


Subject(s)
Machine Learning , Molecular Dynamics Simulation , Solubility , Glycosylation , Glycoproteins/chemistry
18.
J Proteome Res ; 23(5): 1571-1582, 2024 May 03.
Article in English | MEDLINE | ID: mdl-38594959

ABSTRACT

Reproducibility is a "proteomic dream" yet to be fully realized. A typical data analysis workflow utilizing extracted ion chromatograms (XICs) often treats the information path from identification to quantification as a one-way street. Here, we propose an XIC-centric approach in which the data flow is bidirectional: identifications are used to derive XICs whose information is in turn applied to validate the identifications. In this study, we employed liquid chromatography-mass spectrometry data from glycoprotein and human hair samples to illustrate the XIC-centric concept. At the core of this approach was XIC-based monoisotope repicking. Taking advantage of the intensity information for all detected isotopes across the whole range of an XIC peak significantly improved the accuracy and uncovered misidentifications originating from monoisotope assignment mistakes. It could also rescue non-top-ranked glycopeptide hits. Identification of glycopeptides is particularly susceptible to precursor mass errors for their low abundances, large masses, and glycans differing by 1 or 2 Da easily confused as isotopes. In addition, the XIC-centric strategy significantly reduced the problem of one XIC peak associated with multiple unique identifications, a source of quantitative irreproducibility. Taken together, the proposed approach can lead to improved identification and quantification accuracy and, ultimately, enhanced reproducibility in proteomic data analyses.


Subject(s)
Hair , Proteomics , Proteomics/methods , Humans , Chromatography, Liquid/methods , Hair/chemistry , Reproducibility of Results , Glycoproteins/analysis , Glycoproteins/chemistry , Glycopeptides/analysis , Glycopeptides/chemistry , Data Analysis , Mass Spectrometry/methods , Tandem Mass Spectrometry/methods
19.
Int J Biol Macromol ; 268(Pt 1): 131511, 2024 May.
Article in English | MEDLINE | ID: mdl-38615867

ABSTRACT

This comprehensive review delves into the intricate landscape of glycans and glycoconjugates, unraveling their multifaceted roles across diverse biological dimensions. From influencing fundamental cellular processes such as signaling, recognition, and adhesion to exerting profound effects at the molecular and genetic levels, these complex carbohydrate structures emerge as linchpins in cellular functions and interactions. The structural diversity of glycoconjugates, which can be specifically classified into glycoproteins, glycolipids, and proteoglycans, underscores their importance in shaping the architecture of cells. Beyond their structural roles, these molecules also play key functions in facilitating cellular communication and modulating recognition mechanisms. Further, glycans and glycoconjugates prove invaluable as biomarkers in disease diagnostics, particularly in cancer, where aberrant glycosylation patterns offer critical diagnostic cues. Furthermore, the review explores their promising therapeutic applications, ranging from the development of glycan-based nanomaterials for precise drug delivery to innovative interventions in cancer treatment. This review endeavors to comprehensively explore the intricate functions of glycans and glycoconjugates, with the primary goal of offering valuable insights into their extensive implications in both health and disease. Encompassing a broad spectrum of biological processes, the focus of the review aims to provide a comprehensive understanding of the significant roles played by glycans and glycoconjugates.


Subject(s)
Glycoconjugates , Polysaccharides , Humans , Polysaccharides/chemistry , Polysaccharides/metabolism , Glycoconjugates/chemistry , Glycoconjugates/metabolism , Animals , Neoplasms/metabolism , Glycosylation , Glycoproteins/chemistry , Glycoproteins/metabolism
20.
Ultrason Sonochem ; 105: 106873, 2024 May.
Article in English | MEDLINE | ID: mdl-38608436

ABSTRACT

Starting from the consideration of the structure of human milk fat globule (MFG), this study aimed to investigate the effects of ultrasonic treatment on milk fat globule membrane (MFGM) and soy lecithin (SL) complexes and their role in mimicking human MFG emulsions. Ultrasonic power significantly affected the structure of the MFGM-SL complex, further promoting the unfolding of the molecular structure of the protein, and then increased solubility and surface hydrophobicity. Furthermore, the microstructure of mimicking MFG emulsions without sonication was unevenly distributed, and the average droplet diameter was large. After ultrasonic treatment, the droplets of the emulsion were more uniformly dispersed, the particle size was smaller, and the emulsification properties and stability were improved to varying degrees. Especially when the ultrasonic power was 300 W, the mimicking MFG emulsion had the highest encapsulation rate and emulsion activity index and emulsion stability index were increased by 60.88 % and 117.74 %, respectively. From the microstructure, it was observed that the spherical droplets of the mimicking MFG emulsion after appropriate ultrasonic treatment remain well separated without obvious flocculation. This study can provide a reference for the screening of milk fat globules mimicking membrane materials and the further utilization and development of ultrasound in infant formula.


Subject(s)
Emulsions , Glycolipids , Glycoproteins , Lecithins , Lipid Droplets , Lecithins/chemistry , Glycolipids/chemistry , Lipid Droplets/chemistry , Glycoproteins/chemistry , Glycoproteins/analysis , Humans , Glycine max/chemistry , Milk, Human/chemistry , Chemical Phenomena , Particle Size , Ultrasonic Waves , Sonication
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