Boronate affinity chromatography

Preoperative HbA1c and Blood Glucose Measurements in Diabetes Mellitus before Oral Surgery and Implantology Treatments

Diabetes mellitus has become a worldwide epidemic and is frequently accompanied by a number of complications proportional to the duration of hyperglycemia. The aim of this narrative review is to assess the most up-to-date guidelines on DM provided by both diabetes and dental associations. Furthermore, to gather evidence on the uni/bidirectional relationships of elevated HbA1c levels on dental surgery, implantology, bone augmentation, and periodontology and to demonstrate the importance of measuring HbA1c levels before invasive dental treatments. HbA1c and blood glucose measurements are a minimally invasive method for preventing complications in diabetes mellitus. The authors conducted a literature review to determine which oral conditions are affected by diabetes mellitus. MEDLINE served as a source with the use of a specific search key. Regarding oral complications of diabetes, prevention is the most vital factor. With this publication, we hope to assist physicians and dentists to make prompt diagnoses and to help in recognizing various oral manifestations of diabetes and follow the existing guidelines.

Facile Capture of Recombinant Human Erythropoietin on Mesoporous Affinity Hydrogel Matrix Functionalized with Azoboronate

Boronate affinity ligands (BALs) have gained attention for glycoproteins capture and recognition due to their unique affinity interaction with glycans. In this paper, the effect of azo immobilization of phenylboronic acid on the reduction of adsorption pH of a recombinant glycoprotein (i.e., rhEPO) on hydrogel microparticles was investigated. To evaluate the influence of intraparticle porosity on protein adsorption, microporous (MicroBead) and mesoporous (MesoBead) agarose beads carrying two levels of amine densities were functionalized with azoboronate ligand. Affinity adsorption of the glycoprotein during static and dynamic adsorptions at relatively low pHs of 8 and 7 was studied. Results revealed successful adsorption of rhEPO at pH = 8 through affinity capture of glycans by azoboronate ligands. Increased amine density provided 1.1 and 1.5 times higher static adsorption capacities and dynamic performance efficiencies, respectively. In addition, adsorption capacities and initial adsorption rates of rhEPO on MesoBeads were respectively 1.4 and 2.5-2.8 times of MicroBeads. Also, at pH = 8, MesoBeads recorded higher dynamic recoveries (59 and 91%) compared with microporous ones (46 and 69%) since mesoporosity facilitates intraparticle mass transfer. Reduction of binding pH from 8 to 7 resulted in a sharp decrease in dynamic recovery (14%), indicating the appropriate binding pH of azoPBA to be above 7. The azoboronate affinity ligand is a leading candidate for capturing glycoproteins at relatively low pH. Also, mesoporous microparticles are appropriate tools in more efficient medium-sized protein binding applications.

Rheological analysis of a novel phenylboronic acid-closomer gel

This study aims to characterize the rheological behavior of a novel phenylboronic acid (PBA)-based closomer nanoconjugate (Closogel) with potential application in pharmaceutical formulation. PBA was used as a cross-linking agent and model (antiviral) drug. The PBA loaded Closogel chemical structure was analyzed by boron (¹¹B) NMR and Fourier transform infrared (FTIR) spectroscopy. The Closogel and control hydroxyethyl cellulose (HEC) gel were analyzed under oscillatory and continuous shear rheometry followed by mathematical modeling to characterize the gel flow behavior. The chemical analysis confirmed the existence of characteristic borate esters peaks and Boron chemical shifts within Closogel spectra. Due to its more flexible molecular structure, undiluted Closogel exhibited lower, yield stress, viscosity and relaxation time (30 Pa &163 Pa.s & 0.21 s vs 45 Pa &301 Pa.s & 0.39 s for HEC). Both Closogel and HEC gels exhibited a thixotropic behavior. The plastic undiluted and pseudoplastic 2.5 % w/v aqueous Closogels were more viscous than elastic (tan (δ) > 1) in the linear viscoelastic range. The Herschel-Bulkley model showed a significant fitting to all experimental data (R² > 0.95). The 0.25 % w/v aqueous Closogel nearly exhibited a Newtonian behavior with a flow index of 0.93. These data suggest that PBA loaded Closomer-based gels have similar rheological behavior, with lower complex modulus than that of HEC gels, and they can be a promising platform used for delivery of topical antiviral or other bioactive agents.

Molecularly imprinted polymers for selective extraction/microextraction of cancer biomarkers: A review

Over recent years, great efforts have been extensively documented in top scientific journals on the development of methods for early diagnosis, treatment, and monitoring of cancers which are prevalent critical diseases with a high mortality rate among men and women. The determination of cancer biomarkers using different optimum methodologies is one of the finest options for achieving these goals with more precision, speed, and at a lower cost than traditional clinical procedures. In this regard, while focusing on specific biomarkers, molecularly imprinted technology has enabled novel diagnostic techniques for a variety of diseases. Due to the well-known advantages of molecularly imprinted polymers (MIPs), this review focuses on the current trends of MIPs-based extraction/microextraction methods, specifically targeting cancer biomarkers from various matrices. These optimized methods have demonstrated high selectivity, accuracy, sorbent reusability, extraction recovery, and low limits of detection and quantification for a variety of cancer biomarkers, which are a powerful tool to provide early diagnosis, prognosis, and treatment monitoring, with potential clinical application expected soon. This review highlights the key progress, specific modifications, and strategies used for MIP synthesis. The future perspectives for cancer biomarkers purification and determination by fabricating MIP-based techniques are also discussed.

An HPF1/PARP1-Based Chemical Biology Strategy for Exploring ADP-Ribosylation

Strategies for installing authentic ADP-ribosylation (ADPr) at desired positions are fundamental for creating the tools needed to explore this elusive post-translational modification (PTM) in essential cellular processes. Here, we describe a phospho-guided chemoenzymatic approach based on the Ser-ADPr writer complex for rapid, scalable preparation of a panel of pure, precisely modified peptides. Integrating this methodology with phage display technology, we have developed site-specific as well as broad-specificity antibodies to mono-ADPr. These recombinant antibodies have been selected and characterized using multiple ADP-ribosylated peptides and tested by immunoblotting and immunofluorescence for their ability to detect physiological ADPr events. Mono-ADPr proteomics and poly-to-mono comparisons at the modification site level have revealed the prevalence of mono-ADPr upon DNA damage and illustrated its dependence on PARG and ARH3. These and future tools created on our versatile chemical biology-recombinant antibody platform have broad potential to elucidate ADPr signaling pathways in health and disease.

Determination of Adenylate Nucleotides in Amphipod Gammarus fossarum by Ion-Pair Reverse Phase Liquid Chromatography: Possibilities of Positive Pressure Micro-Solid Phase Extraction

Adenine nucleotides—adenosine monophosphate, diphosphate, and triphosphate—are of utmost importance to all living organisms, where they play a critical role in the energy metabolism and are tied to allosteric regulation in various regulatory enzymes. Adenylate energy charge represents the precise relationship between the concentrations of adenosine monophosphate, diphosphate, and triphosphate and indicates the amount of metabolic energy available to an organism. The experimental conditions of adenylate extraction in freshwater amphipod Gammarus fossarum are reported here for the first time and are crucial for the qualitative and quantitative determination of adenylate nucleotides using efficient and sensitive ion-pair reverse phase LC. It was shown that amphipod calcified exoskeleton impeded the neutralization of homogenate. The highest adenylate yield was obtained by homogenization in perchloric acid and subsequent addition of potassium hydroxide and phosphate buffer to achieve a pH around 11. This method enables separation and accurate detection of adenylates. Our study provides new insight into the complexity of adenylate extraction and quantification that is crucial for the application of adenylate energy charge as a confident physiological measure of environmental stress and as a health index of G. fossarum.

Glucose-Responsive Gene Delivery at Physiological pH through Tertiary-Amine Stabilized Boronate-PVA Particles Synthesized by One-Pot Reaction

We report a physiologically stable and cytocompatible glucose-responsive nonviral gene delivery system made up of boronate functionalized polymeric material. Herein, we utilize boronate cis-diol interactions to develop a glucose-responsive submicron particle (SMP) system. The stability of the boronate interaction at a physiological pH was achieved by copolymerization of dimethyl aminoethyl methacrylate (DMAEMA) with acrylamidophenylboronic acid (AAPBA) and the formation of a complex with polyvinylalcohol (PVA) which is governed by cis-diol interactions. The shift in hydrodynamic diameter of SMPs was observed and correlated with increasing glucose concentrations at a physiological pH. Optimal transfection was observed for a 5 µg dose of the gaussia luciferase reporter gene in NIH3T3 cells without any adverse effect on cellular viability. The destabilization of the AAPBA–PVA complex by interacting with glucose allowed the release of encapsulated bovine serum albumin (BSA) in a glucose-responsive manner. In total, 95% of BSA was released from SMPs at a 50 mM glucose concentration after 72 h. A two-fold increase in transfection was observed in 50 mM glucose compared to that of 10 mM glucose.

Affinity chromatography: A review of trends and developments over the past 50 years

The field of affinity chromatography, which employs a biologically-related agent as the stationary phase, has seen significant growth since the modern era of this method began in 1968. This review examines the major developments and trends that have occurred in this technique over the past five decades. The basic principles and history of this area are first discussed. This is followed by an overview of the various supports, immobilization strategies, and types of binding agents that have been used in this field. The general types of applications and fields of use that have appeared for affinity chromatography are also considered. A survey of the literature is used to identify major trends in these topics and important areas of use for affinity chromatography in the separation, analysis, or characterization of chemicals and biochemicals.

Site-specific analysis of the Asp- and Glu-ADP-ribosylated proteome by quantitative mass spectrometry

ADP-ribosylation is a protein post-translational modification that is critically involved in a wide array of biological processes connected to cell stress responses. Enzymes known as poly-ADP-ribose polymerases (PARPs) catalyze the addition of the ADP-ribose units to amino acids with various side chain chemistries. In particular, the PARP family member PARP1 is responsible for the modification of a large number of proteins and is involved in initiation of the DNA damage response, although the mechanisms through which PARP1 functions are still incompletely understood. The analysis of protein ADP-ribosylation is challenging because PARylation is a low-abundance, labile and heterogeneous protein modification. Recently, we developed an integrative proteomic platform for the site-specific analysis of protein ADP-ribosylation on Asp and Glu residues. Herein, we describe the method, and demonstrate its utility in quantitative characterization of the human Asp- and Glu-ADP-ribosylated proteome.

Metabolomics and Biomarker Discovery

Recently, metabolomics-the study of metabolite profiles within biological samples-has found a wide range of applications. This chapter describes the different techniques available for metabolomic analysis, the various samples that can be utilised for analysis and applications of both global and targeted metabolomic analysis to biomarker discovery in medicine.

An inorganic boronate affinity in-needle monolithic device for specific capture of cis-diol containing compounds

In this work, inorganic boronate affinity monolith was prepared by in situ synthesis in 0.33mm i.d. stainless steel needle through sol-gel process using tetraethoxysilane and tetrabutyl orthotitanate as the co-precursors. The morphology, structure and composition of the monolith were characterized. In contrast to conventional boronate affinity materials, inorganic boric acid was used as affinity ligand. Different compounds were used for the evaluation of the boronate affinity of this inorganic monolithic material. The monolith exhibited good selectivity towards cis-diol containing compounds. Recovery of greater than 90% was achieved for in-needle extraction of catechol under neutral conditions. Owing to the hydrophilic property of the monolith, the procedure of affinity chromatography could be performed in aqueous solution. This monolithic in-needle device will be useful for boronate affinity extraction of small-volume samples.

Boronate affinity materials for separation and molecular recognition: structure, properties and applications

Boronate affinity materials, as unique sorbents, have emerged as important media for the selective separation and molecular recognition of cis-diol-containing compounds. With the introduction of boronic acid functionality, boronate affinity materials exhibit several significant advantages, including broad-spectrum selectivity, reversible covalent binding, pH-controlled capture/release, fast association/desorption kinetics, and good compatibility with mass spectrometry. Because cis-diol-containing biomolecules, including nucleosides, saccharides, glycans, glycoproteins and so on, are the important targets in current research frontiers such as metabolomics, glycomics and proteomics, boronate affinity materials have gained rapid development and found increasing applications in the last decade. In this review, we critically survey recent advances in boronate affinity materials. We focus on fundamental considerations as well as important progress and new boronate affinity materials reported in the last decade. We particularly discuss on the effects of the structure of boronate ligands and supporting materials on the properties of boronate affinity materials, such as binding pH, affinity, selectivity, binding capacity, tolerance for interference and so on. A variety of promising applications, including affinity separation, proteomics, metabolomics, disease diagnostics and aptamer selection, are introduced with main emphasis on how boronate affinity materials can solve the issues in the applications and what merits boronate affinity materials can provide.

Identification and analysis of ADP-ribosylated proteins

The analysis of ADP-ribosylated proteins is a challenging task, on the one hand because of the diversity of the target proteins and the modification sites, on the other hand because of the particular problems posed by the analysis of ADP-ribosylated peptides. ADP-ribosylated proteins can be detected in in vitro experiments after the incorporation of radioactively labeled or chemically modified ADP-ribose. Endogenously ADP-ribosylated proteins may be detected and enriched by antibodies directed against the ADP-ribosyl moiety or by ADP-ribosyl binding macro domains. The determination of the exact attachment site of the modification, which is a prerequisite for the understanding of the specificity of the various ADP-ribosyl transferases and the structural consequences of ADP-ribosylation, necessitates the proteolytic cleavage of the proteins. The resulting peptides can afterwards be enriched either by IMAC (using the affinity of the pyrophosphate group for heavy metal ions) or by immobilized boronic acid beads (using the affinity of the vicinal ribose hydroxy groups for boronic acid). The identification of the modified peptides usually requires tandem mass spectrometric measurements. Problems that hamper the mass spectrometric analysis by collision-induced decay (CID) can be circumvented either by the application of different fragmentation techniques (electron transfer or electron capture dissociation; ETD or ECD) or by enzymatic cleavage of the ADP-ribosyl group to ribosyl-phosphate.

Proteomics approaches to identify mono-(ADP-ribosyl)ated and poly(ADP-ribosyl)ated proteins

ADP-ribosylation refers to the addition of one or more ADP-ribose units onto protein substrates and this protein modification has been implicated in various cellular processes including DNA damage repair, RNA metabolism, transcription, and cell cycle regulation. This review focuses on a compilation of large-scale proteomics studies that identify ADP-ribosylated proteins and their associated proteins by MS using a variety of enrichment strategies. Some methods, such as the use of a poly(ADP-ribose)-specific antibody and boronate affinity chromatography and NAD(+) analogues, have been employed for decades while others, such as the use of protein microarrays and recombinant proteins that bind ADP-ribose moieties (such as macrodomains), have only recently been developed. The advantages and disadvantages of each method and whether these methods are specific for identifying mono(ADP-ribosyl)ated and poly(ADP-ribosyl)ated proteins will be discussed. Lastly, since poly(ADP-ribose) is heterogeneous in length, it has been difficult to attain a mass signature associated with the modification sites. Several strategies on how to reduce polymer chain length heterogeneity for site identification will be reviewed.

Kinetic approach for the purification of nucleotides with magnetic separation

The isolation of β-nicotinamide adenine dinucleotide is of great importance since it is widely used in different scientific and technologic fields such as biofuel cells, sensor technology, and hydrogen production. In order to isolate β-nicotinamide adenine dinucleotide, first 3-aminophenyboronic acid functionalized magnetic nanoparticles were prepared to serve as a magnetic solid support and subsequently they were used for reversible adsorption/desorption of β-nicotinamide adenine dinucleotide in a batch fashion. The loading capacity of the 3-aminophenyboronic acid functionalized nanoparticles for β-nicotinamide adenine dinucleotide adsorption was 13.0 μmol/g. Adsorption kinetic and isotherm studies showed that the adsorption process followed a pseudo-second-order kinetic model and the experimental data can be represented using Langmuir isotherm model. The 3-aminophenyboronic acid functionalized magnetic nanoparticles were proposed as an alternative support for the β-nicotinamide adenine dinucleotide purification. The results elucidated the significance of magnetic separation as a fast, relatively simple, and low-cost technique. Furthermore, the magnetic supports can be reused at least five times for purification processes.

Pyridinylboronic acid-functionalized organic-silica hybrid monolithic capillary for the selective enrichment and separation of cis-diol-containing biomolecules at acidic pH

Boronate affinity chromatography (BAC) is a unique means for the selective separation and enrichment of 1,2 and 1,3 cis-diol-containing compounds. However, conventional boronate affinity materials require a basic binding pH (usually≥8.5), which gives rise to not only inconvenience in operation but also the risk of degradation of labile compounds. Although the applicable pH has been expanded to 5.0 in recent years, the current boronate affinity materials still fail to meet the acidic pH end of frequently used biosamples, particularly urine (pH 4.5). In this study, we report a 3-pyridylboronic acid-functionalized organic-silica hybrid monolithic capillary that exhibited a binding pH of 4.5, the lowest so far in BAC. Such a binding pH enabled direct extraction of cis-diol-containing biomolecules such as nucleosides from urine samples without pH adjustment. The boronate affinity monolithic capillary showed enhanced affinity toward negatively charged cis-diol-containing analytes such as ribonucleotides. Moreover, it could function as an anion exchanger at acidic pH (∼2). The column was found to retain multiple compounds from urine, which can be assumed to be at least mostly if not entirely cis-diol-containing compounds.

Synthesis of a SiO2/TiO2 hybrid boronate affinity monolithic column for specific capture of glycoproteins under neutral conditions

A unique boronate-functionalized SiO₂/TiO₂ hybrid monolithic column was synthesized by a facile approach. The monolith exhibited specific capacity to capture glycoproteins and antibodies in aqueous solution at neutral pH.

Site-specific characterization of the Asp- and Glu-ADP-ribosylated proteome

Poly(ADP-ribosyl)ation is catalyzed by a family of enzymes known as PARPs. We describe a method to characterize the human aspartic acid- and glutamic acid-ADP-ribosylated proteome. We identified 1,048 ADP-ribosylation sites on 340 proteins involved in a wide array of nuclear functions; among these were many previously unknown PARP downstream targets whose ADP-ribosylation was sensitive to PARP inhibitor treatment. We also confirmed that iniparib had a negligible effect on PARP activity in intact cells.

Characterization of disease-associated N-linked glycoproteins

N-linked glycoproteins play important roles in biological processes, including cell-to-cell recognition, growth, differentiation, and programmed cell death. Specific N-linked glycoprotein changes are associated with disease progression and identification of these N-linked glycoproteins has potential for use in disease diagnosis, prognosis, and prediction of treatments. In this review, we summarize common strategies for N-linked glycoprotein characterization and applications of these strategies to identification of glycoprotein changes associated with disease states. We also review the N-linked glycoproteins altered in diseases such as breast cancer, lung cancer, and prostate cancer. Although assays for these glycoproteins have potential clinical utility, research is needed to translate these glycoproteins to clinical biomarkers.

Advances in purification and separation of posttranslationally modified proteins

Posttranslational modifications (PTMs) of proteins represent fascinating extensions of the dynamic complexity of living cells' proteomes. The results of enzymatically catalyzed or spontaneous chemical reactions, PTMs form a fourth tier in the gene - transcript - protein cascade, and contribute not only to proteins' biological functions, but also to challenges in their analysis. There have been tremendous advances in proteomics during the last decade. Identification and mapping of PTMs in proteins have improved dramatically, mainly due to constant increases in the sensitivity, speed, accuracy and resolution of mass spectrometry (MS). However, it is also becoming increasingly evident that simple gel-free shotgun MS profiling is unlikely to suffice for comprehensive detection and characterization of proteins and/or protein modifications present in low amounts. Here, we review current approaches for enriching and separating posttranslationally modified proteins, and their MS-independent detection. First, we discuss general approaches for proteome separation, fractionation and enrichment. We then consider the commonest forms of PTMs (phosphorylation, glycosylation and glycation, lipidation, methylation, acetylation, deamidation, ubiquitination and various redox modifications), and the best available methods for detecting and purifying proteins carrying these PTMs. This article is part of a Special Issue entitled: Posttranslational Protein modifications in biology and Medicine.

Se-derivatized RNAs for X-ray crystallography

Selenium derivatization of RNA is an important strategy for crystal structure determination and functional studies of noncoding RNAs and protein-RNA interactions. We describe here the synthesis of nucleoside 5'-(α-P-seleno)-triphosphate analogs (Se-NTPs) and their use in vitro transcription and purification of Se-derivatized RNA samples (phosphoroselenoate RNA, PSe-RNA).

Facile synthesis of nucleoside 5'-(α-P-seleno)-triphosphates and phosphoroselenoate RNA transcription

Phosphoroselenoate RNA (PSe-RNA) is nuclease resistant and has great potentials in X-ray crystal structure and function studies of noncoding RNAs and protein-RNA interactions. In order to conveniently synthesize PSe-RNA via transcription, we have developed a one-pot synthetic method for the nucleoside 5'-(α-P-seleno)-triphosphates (NTPαSe) analogs without protecting any functionality of the ribonucleosides. The NTPαSe diastereomers have been purified, fully characterized, and incorporated into RNAs by T7 RNA polymerase. The transcribed RNAs are diastereomerically pure, and the Se-derivatized ribozymes are generally active. Furthermore, we have established an affinity purification strategy by using immobilized boronate to conveniently purify NTPαSe analogs. Though the affinity-purified NTPαSe analogs are diastereomeric mixtures, they can be directly used in transcription without a significant impact on the transcription efficiency. Moreover, we found that the PSe-nucleotide is stable during polyacrylamide gel purification, indicating that the PSe-RNAs can be purified straightforwardly for crystal structural and functional studies.

Optimized method for the synthesis and purification of adenosine--folic acid conjugates for use as transcription initiators in the preparation of modified RNA

We present an optimized synthetic strategy for the attachment of molecules to 5'-adenosine monophosphate (AMP), which can then be used to label the 5'-end of RNA by T7 RNA polymerase mediated in vitro transcription. Through the use of a boronate affinity gel, we have developed an efficient route to the preparation of folate conjugated AMP with high yields and purity. Affi-Gel boronate is an affinity resin that selectively binds nucleoside and nucleoside derivatives at pH>7.5 and releases them at pH<6.5. This resin is used to efficiently bind and purify ribonucleotides such as AMP. This allows for the addition of a large excess of reactants and reagents in order to drive the reaction to completion and then allow easy purification without HPLC. The synthesis can be successfully scaled up to produce large quantities of AMP conjugates.

"Clickable" affinity ligands for effective separation of glycoproteins

In this paper, we present a new modular approach to immobilize boronic acid ligands that can offer effective separation of glycoproteins. A new "clickable" boronic acid ligand was synthesized by introducing a terminal acetylene group into commercially available 3-aminophenyl boronic acid. The clickable ligand, 3-(prop-2-ynyloxycarbonylamino)phenylboronic acid (2) could be easily coupled to azide-functionalized hydrophilic Sepharose using Cu(I)-catalyzed 1,3-dipolar cycloaddition reaction under mild condition. Compared to other boronic acid affinity gels, the new affinity gel displayed superior effectiveness in separating model glycoproteins (ovalbumin and RNase B) from closely related bovine serum albumin and RNase A in the presence of crude Escherichia coli proteins. Because of the simplicity of the immobilization through "click chemistry", the new ligand 2 is expected to not only offer improved glycoprotein separation in other formats, but also act as a useful building block to develop new chemical sensors for analysis of other glycan compounds.

Analysis of protein glycation using phenylboronate acrylamide gel electrophoresis

The incorporation of the specialized carbohydrate affinity ligand methacrylamido phenylboronic acid in polyacrylamide gels for SDS-PAGE analysis has been successful for the separation of carbohydrates and has here been adapted for the analysis of post-translationally modified proteins. While conventional SDS-PAGE analysis cannot distinguish between glycated and unglycated proteins, methacrylamido phenylboronate acrylamide gel electrophoresis (mP-AGE) in low loading shows dramatic retention of delta-gluconolactone modified proteins, while the mobility of the unmodified proteins remains unchanged. With gels containing 1% methacrylamido phenylboronate, mP-AGE analysis of gluconoylated recombinant protein Sbi results in the retention of the modified protein at a position expected for a protein that has quadrupled its expected molecular size. Subsequently, mP-AGE was tested on HSA, a protein that is known to undergo glycation under physiological conditions. mP-AGE could distinguish between various carbohydrate-protein adducts, using in vitro glycated HSA, and discriminate early from late glycation states of the protein. Enzymatically glycosylated proteins show no altered retention in the phenylboronate-incorporated gels, rendering this method highly selective for glycated proteins. We reveal that a trident interaction between phenylboronate and the Amadori cis 1,2 diol and amine group provides the molecular basis of this specificity. These results epitomize mP-AGE as an important new proteomics tool for the detection, separation, visualization and identification of protein glycation. This method will aid the design of inhibitors of unwanted carbohydrate modifications in recombinant protein production, ageing, diabetes, cardiovascular diseases and Alzheimer's disease.

Synthesis of hydrophilic boronate affinity monolithic capillary for specific capture of glycoproteins by capillary liquid chromatography

Boronate affinity chromatography is an important tool for specific isolation of cis-diol-containing compounds such as glycoproteins, RNA and carbohydrates. Boronate functionalized monolithic capillaries have been recently developed for specific capture of cis-diol-containing small biomolecules, but the apparent hydrophobicity of the columns prevents them from specific capture of glycoproteins. In this paper, a hydrophilic boronate affinity monolithic capillary was prepared by in situ free radical polymerization, using 4-vinylphenylboronic acid (VPBA) and N, N'-methylenebisacrylamide (MBAA) as functional monomer and cross-linker, respectively. The prepared poly(VPBA-co-MBAA) monolithic capillary exhibited uniform open channel network and high density of accessible boronic acid. Due to the utilization of hydrophilic cross-linker, the prepared column was hydrophilic, allowing for specific capture of glycoproteins.

Boronate affinity monolith for highly selective enrichment of glycopeptides and glycoproteins

A novel boronate affinity monolith, poly(3-acrylamidophenylboronic acid-co-ethylene dimethacrylate) (AAPBA-co-EDMA), was prepared in 530 microm capillaries by a one-step in situ polymerization procedure using a pre-polymerization mixture consisting of functional monomer 3-acrylamidophenylboronic acid, cross-linker ethylene dimethacrylate, porogenic solvent methanol with added poly(ethylene glycol) 20,000 (PEG 20,000) and initiator azobisisobutyronitrile (AIBN). The preparation of the monolith was optimized by investigating the ratio of functional monomer to cross-linker and the effect of poly(ethylene glycol) molecular weight. The resulting boronate monolith was used as a sorbent for polymer monolith microextraction (PMME). Using nucleosides as the testing analyte, the extraction performance of this boronate monolith towards glycol-containing compounds was examined. Finally, the boronate monolith was applied for selective enrichment of glycopeptides and glycoproteins.

Enrichment of Amadori products derived from the nonenzymatic glycation of proteins using microscale boronate affinity chromatography

Amadori peptides were enriched using boronate affinity tips and measured by matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF/MS). As demonstrated by electrochemical measurements, the tips show the highest binding efficiency for glucose at pH 8.2 employing ammonium chloride/ammonia buffer with ionic strength of 150 mM, exceeding taurine buffer at the same concentration. The bound constituents were released by sorbitol and formic acid. It was also demonstrated that elution with sorbitol at 1.2 M is superior to acidic media. Comparison of results was based on the numbers of detected peptides and their glycated sites. Using sorbitol for elution requires desalting prior to analysis. Therefore, three different sorbents were tested: fullerene-derivatized silica, ZipTip (C18), and C18 silica. Fullerene-derivatized silica and ZipTip showed the same performance regarding the numbers of glycated peptides, and sites were better than C18 silica. The elaborated off-line method was compared with liquid chromatography-tandem mass spectrometry (LC-MS/MS) measurements, by which considerable less modified peptides were detected. Affinity tips used under optimized conditions were tested for the analysis of human serum albumin (HSA) from sera of healthy and diabetic individuals. A peptide with a mass of 1783.9 Da could be detected only in samples of diabetic patients and, therefore, could be a very interesting biomarker candidate.

Synthesis and characterization of a new boronate affinity monolithic capillary for specific capture of cis-diol-containing compounds

Boronate affinity chromatography (BAC) is an important tool for specific capture and separation of cis-diol-containing compounds such as glycoproteins, RNA and carbohydrates. Only a few reports on monolithic column-based BAC have appeared. In this paper, boronate functionalized monolithic capillary column was synthesized by in situ free radical polymerization for the first time. The prepared column was first characterized in terms of morphology, pore properties, capacity and retention mechanisms. The column exhibited uniform open channel network and high capture capacity. Systematical investigation on the retention mechanism revealed that multiple intermolecular interactions occur between the analytes and the boronate affinity monolith, including boronate affinity, reversed-phase, cation-exchange and hydrogen bonding interactions, depending on the conditions used. In addition, the presence of Lewis base such as fluoride ion in the mobile phase was found to be favorable to the complexation between cis-diol-containing compounds with the boronic acid ligand under less basic conditions. On the basis of these fundamental investigations, the prepared monolithic column was then applied to the capture of adenosine and flavin adenine dinucleotide. The investigations in this study provide sound understanding not only on how to manipulate the separation selectivity through selection of appropriate mobile phase composition on the currently prepared columns but also on how to design next-generation columns with desired properties and functions.

N-glycosylation site analysis of human platelet proteins by hydrazide affinity capturing and LC-MS/MS

A starting point for many glycosylation analysis pathways is marked by the determination of the respectivecarbohydrate attachment sites to the polypeptide backbone of proteins. Several methods have been reported for this purpose in the past, commonly divided into a three-step approach (1) affinity purification of glycoproteins/-peptides, (2) processing/trimming of the glycopeptides and (3) elucidation of the glycan attachment site by mass spectrometry. For N-glycosylation site analysis the last two steps are usually similar, while methods differ in the affinity purification step. Here, we describe the oxidative derivatisation of carbohydrate moieties and covalent trapping of glycopeptides on hydrazide functionalized beads. This method is suitable for large scale analysis of glycoproteins as well as isolated glycoproteins and can be applied readily to a number of different samples. In the described protocol, the elucidation of N-glycosylation sites of human platelet proteins is demonstrated as an example.

Sequential affinity purification of peroxidase tagged bispecific anti-SARS-CoV antibodies on phenylboronic acid agarose

Hybrid hybridomas (quadromas) are derived by fusing at least two hybridomas, each producing a different antibody of predefined specificity. The resulting cell secretes not only the immunoglobulins of both parents but also hybrid molecules manifesting the binding characteristics of the individual fusion partners. Purification of the desired bispecific immunoprobe with high specific activity from a mixture of bispecific and monospecific monoclonal antibodies requires special strategies. Using a dual, sequential affinity chromatography (Protein-G chromatography followed by m-aminophenyleboronic acid agarose column), we have purified bispecific monoclonal antibodies (BsMAb) as a preformed HRPO (Horseradish Peroxidase) complex (BsMAb-HRPO). The quadroma culture supernatant was initially processed on a Protein-G column to isolate all the species of immunoglobulins. This pre-enriched fraction was subsequently passed through the aminophenyleboronic acid column super saturated with HRPO. The column matrix has the ability to bind to proteins such as HRPO with vicinal diols. The enzyme loaded column captures the desired bispecific anti-SARS-CoVxanti-HRPO species with the elimination of the monospecific anti-SARS-CoV MAb to result in a high specific activity diagnostic probe. The presence of anti-HRPO MAb is an acceptable impurity as it will not bind to the target SARS-CoV NP antigen and will get washed out during the ELISA procedure.

Modification of aluminum chips for LDI mass spectrometry of proteins

Matrix-assisted laser desorption ionization time-of-flight mass spectroscopy (MALDI TOFMS) combined with affinity chromatography on immobilized phenylboronic acid agarose gels was used for selective enrichment and detection of specifically modified proteins such as glycated proteins in complex biological samples. Physicochemical grafting of hydrophilic polymers on aluminum surface was developed to reduce nonspecific protein sorption and to create a proper support layer for a three-dimensional affinity hydrogel. Grafted agarose allowed the fixation of three-dimensional agarose hydrogel on the chip surface. Both pinched polymers and hydrogels were effectively derivatized. 3-Aminophenylboronic acid (mPBA) was covalently immobilized as an affinity ligand to achieve specific binding of glycated plasma proteins. Alternatively, the affinity sorbent was immersed into the hydrogel to increase binding capacity. MALDI TOFMS was used to evaluate binding efficiency and molecular mass changes of human serum albumin due to glycation. Glycated proteins were captured directly on the chip with high selectivity and efficacy, and low nonspecific binding. Thus they could easily be characterized by MALDI TOFMS.

Protein-RNA cross-linking in the ribosomes of yeast under oxidative stress

Living systems have efficient degradative pathways for dealing with the fact that reactive oxygen species (ROS) derived from cellular metabolism and the environment oxidatively damage proteins and DNA. But aggregation and cross-linking can occur as well, leading to a series of problems including disruption of cellular regulation, mutations, and even cell death. The mechanism(s) by which protein aggregation occurs and the macromolecular species involved are poorly understood. In the study reported here, evidence is provided for a new type of aggregate between proteins and RNA in ribosomes. While studying the effect of oxidative stress induced in the yeast proteome it was noted that ribosomal proteins were widely oxidized. Eighty six percent of the proteins in yeast ribosomes were found to be carbonylated after stressing yeast cell cultures with hydrogen peroxide. Moreover, many of these proteins appeared to be cross-linked based on their coelution patterns during RPC separation. Since they were not in direct contact, it was not clear how this could occur unless it was through the RNA separating them in the ribosome. This was confirmed in a multiple-step process, the first being derivatization of all carbonylated proteins in cell lysates with biotin hydrazide through Schiff base formation. Following reduction of Schiff bases with sodium cyanoborohydride, biotinylated proteins were selected from cell lysates with avidin affinity chromatography. Oxidized proteins thus captured were then selected again using boronate affinity chromatography to capture vicinal diol-containing proteins. This would include proteins cross-linked to an RNA fragment containing a ribose residue with 2',3'-hydroxyl groups. Some glycoproteins would also be selected by this process. LC/MS/MS analyses of tryptic peptides derived from proteins captured by this process along with MASCOT searches resulted in the identification of 37 ribosomal proteins that appear to be cross-linked to RNA. Aggregation of proteins with ribosomal RNA has not been previously reported. The probable impact of this phenomenon cells is to diminish the protein synthesis capacity.