Quantitative analysis of N-glycans from human alfa-acid-glycoprotein using stable isotope labeling and zwitterionic hydrophilic interaction capillary liquid chromatography electrospray mass spectrometry as tool for pancreatic disease diagnosis

In this work we demonstrate the potential of glycan reductive isotope labeling (GRIL) using [¹²C]- and [¹³C]-coded aniline and zwitterionic hydrophilic interaction capillary liquid chromatography electrospray mass spectrometry (μZIC-HILIC-ESI-MS) for relative quantitation of glycosylation variants in selected glycoproteins present in samples from cancer patients. Human α₁-acid-glycoprotein (hAGP) is an acute phase serum glycoprotein whose glycosylation has been described to be altered in cancer and chronic inflammation. However, it is not clear yet whether some particular glycans in hAGP can be used as biomarker for differentiating between these two pathologies. In this work, hAGP was isolated by immunoaffinity chromatography (IAC) from serum samples of healthy individuals and from those suffering chronic pancreatitis and different stages of pancreatic cancer, respectively. After de-N-glycosylation, relative quantitation of the hAGP glycans was carried out using stable isotope labeling and μZIC-HILIC-ESI-MS analysis. First, protein denaturing conditions prior to PNGase F digestion were optimized to achieve quantitative digestion yields, and the reproducibility of the established methodology was evaluated with standard hAGP. Then, the proposed method was applied to the analysis of the clinical samples (control vs. pathological). Pancreatic cancer samples clearly showed an increase in the abundance of fucosylated glycans as the stage of the disease increases and this was unlike to samples from chronic pancreatitis. The results gained here indicate the mentioned glycan in hAGP as a candidate structure worth to be corroborated by an extended study including more clinical cases; especially those with chronic pancreatitis and initial stages of pancreatic cancer. Importantly, the results demonstrate that the presented methodology combining an enrichment of a target protein by IAC with isotope coded relative quantitation of N-glycans can be successfully used for targeted glycomics studies. The methodology is assumed being suitable as well for other such studies aimed at finding novel cancer associated glycoprotein biomarkers.     

Resolving and assigning N-linked glycan structural isomers from ovalbumin by IMS-MS

Ion mobility-mass spectrometry (IMS-MS) and molecular modeling techniques have been used to characterize ovalbumin N-linked glycans. Some glycans from this glycoprotein exist as multiple isomeric forms. The gas-phase separation makes it possible to resolve some isomers before MS analysis. Comparisons of experimental cross sections for selected glycan isomers with values that are calculated for iterative structures generated by molecular modeling techniques allow the assignment of sharp features to specific isomers. We focus here on an example glycan set, each having a m/z value of 1046.52 with formula [H₅N₄+2Na]²⁺, where H corresponds to a hexose, and N to a N-acetylglucosamine. This glycan appears to exist as three different isomeric forms that are assignable based on comparisons of measured and calculated cross sections. We estimate the relative ratios of the abundances of the three isomers to be in the range of ∼1.0:1.35:0.85 to ∼1.0:1.5:0.80. In total, IMS-MS analysis of ovalbumin N-linked glycans provides evidence for 19 different glycan structures corresponding to high-mannose and hybrid type carbohydrates with a total of 42 distinct features related to isomers and/or conformers.     

Synthesis and Binding of Mannose-Specific Synthetic Carbohydrate Receptors

Synthetic carbohydrate receptors (SCRs) that selectively recognize cell-surface glycans could be used for detection, drug delivery, or as therapeutics. Here we report the synthesis of seven new C_2h symmetric tetrapodal SCRs. The structures of these SCRs possess a conserved biaryl core, and they vary in the four heterocyclic binding groups that are linked to the biaryl core via secondary amines. Supramolecular association between these SCRs and five biologically relevant C¹-O-octyloxy glycans, α/β-glucoside ( α/β-Glc ), α/β-mannoside ( α/β-Man ), and β-galactoside ( β-Gal ), was studied by mass spectrometry, ¹H NMR titrations, and molecular modeling. These studies revealed that selectivity can be achieved in these tetrapodal SCRs by varying the heterocyclic binding group. We found that SCR017 (3-pyrrole), SCR021 (3-pyridine), and SCR022 (2-phenol) bind only to β-Glc. SCR019 (3-indole) binds only to β-Man. SCR020 (2-pyridine) binds β-Man and α-Man with a preference to the latter. SCR018 (2-indole) binds α-Man and β-Gal with a preference to the former. The glycan guests bound within their SCR hosts in one of three supramolecular geometries: center-parallel, center-perpendicular, and off-center. Many host–guest combinations formed higher stoichiometry complexes, 2:1 glycan⋅SCR or 1:2 glycan⋅SCR , where the former are driven by positive allosteric cooperativity induced by glycan–glycan contacts.     

Biomimetic nanochannels for the discrimination of sialylated glycans via a tug-of-war between glycan binding and polymer shrinkage

Sialylated glycans that are attached to cell surface mediate diverse cellular processes such as immune responses, pathogen binding, and cancer progression. Precise determination of sialylated glycans, particularly their linkage isomers that can trigger distinct biological events and are indicative of different cancer types, remains a challenge, due to their complicated composition and limited structural differences. Here, we present a biomimetic nanochannels system integrated with the responsive polymer polyethyleneimine-g-glucopyranoside (Glc-PEI) to solve this problem. By using a dramatic “OFF–ON” change in ion flux, the nanochannels system achieves specific recognition for N-acetylneuraminic acid (Neu5Ac, the predominant form of sialic acid) from various monosaccharides and sialic acid species. Importantly, different “OFF–ON” ratios of the conical nanochannels system allows the precise and sensitive discrimination of sialylated glycan linkage isomers, α2–3 and α2–6 linkage (the corresponding ion conductance increase ratios are 96.2% and 264%, respectively). Analyses revealed an unusual tug-of-war mechanism between polymer-glycan binding and polymer shrinkage. The low binding affinity of Glc-PEI for the α2–6-linked glycan caused considerable shrinkage of Glc-PEI layer, but the high affinity for the α2–3-linked glycan resulted in only a slight shrinkage. This competition mechanism provides a simple and versatile materials design principle for recognition or sensing systems that involve negatively charged target biomolecules. Furthermore, this work broadens the application of nanochannel systems in bioanalysis and biosensing, and opens a new route to glycan analysis that could help to uncover the mysterious and wonderful glycoworld.

A glycan-responsive polymer-modified nanochannels system enables the precise discrimination of sialylated glycan linkage isomers via the different “OFF–ON” changes resulting from a “tug-of-war” between polymer-glycan binding and polymer shrinkage.     

Recognition of sialylated poly-N-acetyllactosamine chains on N- and O-linked glycans by human and avian influenza A virus hemagglutinins

Human influenza viruses are proposed to recognize sialic acids (pink diamonds) on glycans extended with poly-LacNAc chains (LacNAc=(yellow circle+blue square)). N- and O-linked glycans were extended with different poly-LacNAc chains with α2-3- and α2-6-linked sialic acids recognized by human and avian influenza viruses, respectively. The specificity of recombinant hemagglutinins (receptors in green) was investigated by using glycan microarray technology.     

Altered Glycosylation of Human Alpha-1-Acid Glycoprotein as a Biomarker for Malignant Melanoma

A high-resolution HILIC-MS/MS method was developed to analyze anthranilic acid derivatives of N-glycans released from human serum alpha-1-acid glycoprotein (AGP). The method was applied to samples obtained from 18 patients suffering from high-risk malignant melanoma as well as 19 healthy individuals. It enabled the identification of 102 glycan isomers separating isomers that differ only in sialic acid linkage (α-2,3, α-2,6) or in fucose positions (core, antenna). Comparative assessment of the samples revealed that upregulation of certain fucosylated glycans and downregulation of their nonfucosylated counterparts occurred in cancer patients. An increased ratio of isomers with more α-2,6-linked sialic acids was also observed. Linear discriminant analysis (LDA) combining 10 variables with the highest discriminatory power was employed to categorize the samples based on their glycosylation pattern. The performance of the method was tested by cross-validation, resulting in an overall classification success rate of 96.7%. The approach presented here is significantly superior to serological marker S100B protein in terms of sensitivity and negative predictive power in the population studied. Therefore, it may effectively support the diagnosis of malignant melanoma as a biomarker.     

Isomerization and fragmentation of aliphatic ether radical cations: Interconversion of distonic ions and cyclopropane intermediates

The reactions of propyl ether radical cations close to threshold are initiated by (reversible) formation of γ-disitonic isomers, R$ \mathop {\rm O}\limits^ + $ (H)CH₂CH₂CH₂^·. The three methylene groups in these ions lose their positional identity by ring closure/ring opening via [cyclopropane + alcohol]^+· intermediates. Extensive hydrogen exchange occurs within the C₃-chain. When R is not methyl the γ-distonic isomer undergoes further intramolecular hydrogen atom transfer reactions that lead to formation of α- and β-distonic ions. The α-distonic isomers expel ethyl and propyl radicals by C? O bond cleavage.     

Quantitative estimation of trans-1,4 and cis-1,4 isomers in polychloroprene by high-resolution NMR

In the ¹H-NMR spectrum of polychloroprene dissolved in C₆D₆, the ?CH proton signal was separated into two triplet peaks. These triplet signals were assigned to the ?CH proton in the trans-1,4 and cis-1,4 isomers by measurement of ¹H-NMR spectra of 3-chloro-1-butene and a mixture of trans- and cis-2-chloro-2-butene as model compounds for the 1,2, trans-1,4 and cis-1,4 isomers. In ¹H-NMR spectra (220 Mcps) of polychloroprene dissolved in C₆D₆, two triplet signals were separated completely from which the relative concentrations of trans-1,4 and cis-1,4 isomers could be obtained quantitatively.     

Study of the Conformational Variety of the Oligosaccharide Substrates of Neuraminidases from Pathogens using Molecular Modeling

Analysis of the conformational variety of the oligosaccharide fragments of the human glycan receptors LSTa (α-D-Neu5Ac-(2-3)-β-D-Gal-(1-3)-β-D-GlcNAc-(1-3)-β-D-Gal(1-4)-D-Glc) and LSTc (α-D-Neu5Ac-(2-6)-β-D-Gal-(1-3)-β-D-GlcNAc-(1-3)-β-D-Gal(1-4)-D-Glc) in aqueous solution has been performed with the comprehensive use of molecular modeling and statistical data processing followed by determination of major and minor stabilized conformers and selection of relevant topologies. The sialic acid ring conformational free energy landscape for both pentasaccharides has been reconstructed and analyzed giving a specification of the most probable distorted ring conformations of the basic chair ¹C₄ structure. The obtained results are in a good agreement with experimental data generated by nuclear magnetic resonance spectroscopy and X-ray crystallography.     

(Hydroxyimino)Phosphonoacetic Acids: Synthesis,Stereochemistry and Reactivity

Abstract

Individual E/Z isomers of the C-methyl ester 1 of α-(hydroxyimino)phosphonoacetic acid (“troika acid”) were recently prepared as dicyclohexylammonium salts and found to be stable at neutral pH.¹ On alkaline demethylation followed by pH adjustment to 6–7, E?1 and Z?1 stereospecifically undergo P-C_αand C_α-C_β cleavage, respectively.¹ Herein we report synthesis of the corresponding P-methyl ester from trimethyl phos-phonoacetate 2. The product was isolated as its bis-DCHA⁺ salt E-3, with stereochemistry assigned by NMR.²     

Molecular fragmentations: Part VII. Structures and energies of mass spectral fragments derived from benzene

Molecular structures and energies have been calculated, using MINDO/3, of the mass spectral ions arising from benzene: (C₆H₆)⁺ (three non-valence isomers); (C₆H₅⁺); (C₅H₃⁺) (four isomers); (C₄H₄)⁺ (three isomers); (C₄H₃)⁺ (two isomers); (C₄H₂)⁺ (four isomers); (C₃H₃)⁺; and (C₂H₂)⁺. Calculations have been made for the conjugate neutral fragments, allowing calculation of appearance potentials, and also for the ion (C₆H₇)⁺.     

Assigning the major isomers of fullerene C88 by theoretical 13C NMR spectra

The IPR isomers of fullerene C₈₈ have been studied using density functional theory. Structures of all C₈₈ isomers with non-zero HOMO–LUMO gaps were optimized at the B3LYP/STO-3G level. Those isomers having energies lower than 25 kcal/mol were subjected to geometry optimization using the 6-31G basis set. Isomer 17 has the lowest energy, followed by 7 and 33. All three isomers have large HOMO–LUMO gaps. ¹³C NMR chemical shifts were obtained employing the GIAO method. The comparison between predicted and measured NMR spectra strongly supports the observed C₈₈-1(C_s) as isomer 17, and isomers C₈₈-2(C₂) and C₈₈-3(C₂) as 7 and 33, respectively.     

Modulating Cell‐Surface Receptor Signaling and Ion Channel Functions by In Situ Glycan Editing

Glycans anchored on cell‐surface receptors are active modulators of receptor signaling. A strategy is presented that enforces transient changes to cell‐surface glycosylation patterns to tune receptor signaling. This approach, termed in situ glycan editing, exploits recombinant glycosyltransferases to incorporate monosaccharides with linkage specificity onto receptors in situ. α2,3‐linked sialic acid or α1,3‐linked fucose added in situ suppresses signaling through epidermal growth factor receptor and fibroblast growth factor receptor. We also applied the same strategy to regulate the electrical signaling of a potassium ion channel–human ether‐à‐go‐go‐related gene channel. Compared to gene editing, no long‐term perturbations are introduced to the treated cells. In situ glycan editing therefore offers a promising approach for studying the dynamic role of specific glycans in membrane receptor signaling and ion channel functions.     

The NMR Coupling Constants,and Conformational and Structural Properties of Flexible Aldopyranosyl Rings: α- and β-D-Idopyranose

ABSTRACT

The flexible ring structures of α- and β-D-idopyranose have been investigated by conformational analysis using structures generated by MacroModel and GMMX search protocols. The lowest energy structures found during the conformer search for the ⁴ C ₁, ¹ C ₄, ^O S ₂ and the ³ S ₁ structures were then examined by AM1 and Gaussian ab initio methods at the HF/6-311G** and HF/6-31+G* levels. The B _2,5 conformer found for β-D-idopyranose at 14 kJ/mol by GMMX and 29.5 kJ/mol for α-D-idopyranose by MacroModel would not contribute to Boltzmann-averaged ¹H NMR coupling constants. The Merck MMFF force field tends to overweight the ¹ C ₄ structures, making these the lowest energy conformers for both anomers. Boltzmann-averaged coupling constants are heavily weighted by this structure in the MMFF search conformer ensemble. Averaged proton coupling constants determined using MMFF fit very well for α-D-idopyranose compared to the observed values, but fit poorly for the β-anomer. Ab initio results place the ¹ C ₄ conformer at lowest energy for the α-anomer and place the ⁴ C ₁ conformer at lowest energy for the β-anomer. The GMMX and MM3* force fields find the ⁴ C ₁ conformer to have the lowest energies for both anomers.     

Glycan analysis: scope and limitations of different techniques—a case for integrated use of LC-MS(/MS) and NMR techniques

The structure of glycans from glycoproteins is highly relevant for their function. We tightly integrate liquid chromatography–mass spectrometry (LC-MS), MS/MS, and nuclear magnetic resonance (NMR) data to achieve a complete characterization of even isobaric glycans differing in only one linkage position or in the substitution in one branch. As example, we analyzed ten desialylated underivatized glycans from bovine fibrinogen. The molecules were separated on a PGC column, and LC-MS data allowed an assignment of the compositions of the glycans. MS/MS data of the same glycans allowed elucidation of sequence and to some extent of branching and linkage. All MS/MS fragmentation methods led to multiple dissociations, resulting in several cases in ambiguous data. The MS/MS data were interpreted both by scientists and automatically by software, and the differential results are compared. Additional data from a tight integration of LC-MS and NMR data resulted in a complete structural characterization of the glycans. The acquisition of simple 1D ¹H NMR data led—in combination with LC-MS and MS/MS data—to an unambiguous assignment of the isobaric glycans. Compounds that were not separated in the chromatography could easily be assigned structurally by applying the 3D cross-correlation (3DCC) technology to arrive at NMR spectra of the pure components—without actually separating them. By applying LC-MS, MS/MS, 1D ¹H NMR, and 3DCC together, one can assign glycan structures from glycoconjugates with high confidence affording only 200 pmol of glycan material.     

A Stereoselective Glycosylation Approach to the Construction of 1,2-trans-β-d-Glycosidic Linkages and Convergent Synthesis of Saponins

Conventional syntheses of 1,2-trans-β-d - or α-l -glycosidic linkages rely mainly on neighboring group participation in the glycosylation reactions. The requirement for a neighboring participation group (NPG) excludes direct glycosylation with (1→2)-linked glycan donors, thus only allowing stepwise assembly of glycans and glycoconjugates containing this type of common motif. Here, a robust glycosylation protocol for the synthesis of 1,2-trans-β-d - or α-l -glycosidic linkages without resorting to NPG is disclosed; it employs an optimal combination of glycosyl N-phenyltrifluroacetimidates as donors, FeCl₃ as promoter, and CH₂Cl₂/nitrile as solvent. A broad substrate scope has been demonstrated by glycosylations with 12 (1→2)-linked di- and trisaccharide donors and 13 alcoholic acceptors including eight complex triterpene derivatives. Most of the glycosylation reactions are high yielding and exclusively 1,2-trans selective. Ten representative, naturally occurring triterpene saponins were thus synthesized in a convergent manner after deprotection of the coupled glycosides. Intensive mechanistic studies indicated that this glycosylation proceeds by S_N2-type substitution of the glycosyl α-nitrilium intermediates. Importantly, FeCl₃ dissociates and coordinates with nitrile into [Fe(RCN)_nCl₂]⁺ and [FeCl₄]⁻, and the ferric cationic species coordinates with the alcoholic acceptor to provide a protic species that activates the imidate, meanwhile the poor nucleophilicity of [FeCl₄]⁻ ensures an uninterruptive role for the glycosidation.     

Mass spectra of halogenated esters 5—Chloromethyl esters of aliphatic C2?C12 n-carboxylic acids and their monochlorinated derivatives

A study has been made of the mass spectral fragmentation upon electron impact of aliphatic C₂? C₁₂ chloromethyl esters and all their 66 monochlorinated derivatives. The fragmentation pathways of the parent chloromethyl esters were elucidated with the aid of the 1st FFR metastable ions. A McLafferty rearrangement gives the base peak in the C₆? C₁₁ parent esters and in almost all the 4-chloro and ω-chloro isomers. The subsequent loss of HCl gives a very characteristic peak of the chloromethyl esters and their (3-ω)-chloro derivatives at m/z 72, [C₃H₄O₂]⁺. The 2-chloro isomers have the corresponding chlorine-containing fragment ion at m/z 106/108. The mass spectra of 2-, 3-, 4-, 5- and ω-chloro isomers give the characteristic fragment ions, the mass spectra of the other isomers being very similar.     

Selective Hydrolysis of Terminal Glycosidic Bond in α-1-Acid Glycoprotein Promoted by Keggin and Wells–Dawson Type Heteropolyacids

The reactivity of a range of Keggin and Wells–Dawson type heteropolyacids (HPAs): H₃PW₁₂O₄₀ H₄SiW₁₂O₄₀, H₃PMo₁₂O₄₀, K₆P₂W₁₈O₆₂, and NaH₂W₁₂O₄, towards the heavily glycosylated α-1-acid glycoprotein (AGP) is reported. Sodium dodecyl sulfate polyacrylamide gel electrophoresis (SDS-PAGE) and high-performance anion exchange chromatography with pulsed amperometric detection (HPAEC-PAD) show that after incubation of the protein with HPAs at 80 °C and pH 2.8 complete hydrolysis of terminal glycosidic bond has been achieved, resulting in the removal of sialic acids with no observed destruction of the protein core or the residual glycan chains. The ¹H NMR spectroscopy confirmed that the released sialic acids preserve intact structure upon their excision from the protein, which makes the reported method suitable for the analysis of sialic acid modifications which play an important role in numerous biological processes. The presence of other sugars was not detected by ¹H NMR and HPAEC-PAD, suggesting that HPAs hydrolyze only the terminal glycosidic bond in the glycoprotein, resulting in the selective release of sialic acid from AGP. The kinetic results have shown that under equal temperature and pH conditions, the hydrolysis of the terminal glucosidic bond occurred faster in the presence of HPAs compared to conventional mineral acids. The observed rate constants were in the range 6,7×10⁻² −11,9×10⁻² min⁻¹ and the complete and selective excision of sialic acids could be achieved within 60 min of incubation. The Trp fluorescence and CD spectroscopy show that non-covalent interaction between HPA and protein takes place in solution which could lead to stabilization of the sialosyl cation that is formed during the glycosidic bond hydrolysis by anionic HPA cluster.     

Studies on molecular motion of polysaccharides in the solid state by broad-line nuclear magnetic resonance

Broad-line NMR measurements have been carried out on solid amylose, pullulan, and dextran in order to shed light upon the relations between different modes of linkage of glucose residues and physical properties. Rotation of the methylol group attached to the C₅ atom around the C₅? C₆ linkage and the libration of glucose residues around the α-1,6 linkage are suggested as the origins of the observed decrease of the second moment with increasing temperature.     

NMR Spectroscopic Characterization of the C-Mannose Conformation in a Thrombospondin Repeat Using a Selective Labeling Approach

Despite the great interest in glycoproteins, structural information reporting on conformation and dynamics of the sugar moieties are limited. We present a new biochemical method to express proteins with glycans that are selectively labeled with NMR-active nuclei. We report on the incorporation of ¹³C-labeled mannose in the C-mannosylated UNC-5 thrombospondin repeat. The conformational landscape of the C-mannose sugar puckers attached to tryptophan residues of UNC-5 is characterized by interconversion between the canonical ¹C₄ state and the B₀₃ / ¹S₃ state. This flexibility may be essential for protein folding and stabilization. We foresee that this versatile tool to produce proteins with selectively labeled C-mannose can be applied and adjusted to other systems and modifications and potentially paves a way to advance glycoprotein research by unravelling the dynamical and conformational properties of glycan structures and their interactions.