Affinity in Electrophoresis

Computational Methods and Deep Learning for Elucidating Protein Interaction Networks

Protein interactions play a critical role in all biological processes, but experimental identification of protein interactions is a time- and resource-intensive process. The advances in next-generation sequencing and multi-omics technologies have greatly benefited large-scale predictions of protein interactions using machine learning methods. A wide range of tools have been developed to predict protein-protein, protein-nucleic acid, and protein-drug interactions. Here, we discuss the applications, methods, and challenges faced when employing the various prediction methods. We also briefly describe ways to overcome the challenges and prospective future developments in the field of protein interaction biology.

Capillary electrophoresis as a fragment screening tool to cross-validate hits from chromogenic assay: Application to FXIIa

In this study, a partial-filling affinity capillary electrophoresis (pf-ACE) method was developed for the cross-validation of fragment hits revealed by chromogenic factor XIIa (FXIIa) assay. Chromogenic assay produces false positives, mainly due to spectrophotometric interferences and sample purity issues. pf-ACE was selected as counter-screening technology because of its separative character and the fact that the target does not have to be attached or tagged. The effects of protein plug length, applied voltage and composition of the running buffer were examined and optimized. Detection limit in terms of dissociation constant was estimated at 400 μM. The affinity evaluation was performed close to physiological conditions (pH 7.4, ionic strength 0.13 mol L^-1) in a poly (ethylene oxide)-coated capillary of 75 μm internal diameter x 33 cm length with an applied voltage of 3 kV. This method uncovered chromogenic assay's false positives due to zinc contamination. Moreover, pf-ACE supported the evaluation of compounds absorbing at 405 nm.

Toward an automated workflow for the study of plasma protein-drug interactions based on capillary electrophoresis-frontal analysis combined with in-capillary mixing of interacting partners

Capillary electrophoresis-frontal analysis (CE-FA) together with mobility shift affinity CE is the most frequently used mode of affinity CE for a study of plasma protein-drug interactions, which is a substantial part of the early stage of drug discovery. Whereas in the classic CE-FA setup the sample is prepared by off-line mixing of the interaction partners in the sample vial outside the CE instrument and after a short incubation period loaded into the capillary and analysed, in this work a new methodological approach has been developed that combines CE-FA with the mixing of interacting partners directly inside the capillary. This combination gives rise to a fully automated and versatile methodology for the characterization of these binding interactions besides a substantial reduction in the amounts of sample compounds used. The minimization of possible experimental errors due to the full involving of sophisticated CE instrument in the injection procedure, mixing and separation instead of manual manipulation is another fundamental benefit. The in-capillary mixing is based on the transverse diffusion of laminar flow profile methodology introduced by Krylov et al. using its multi-zone injection modification presented by Řemínek at al.. Actually, after the method optimization, the alternate introduction of six plugs of drug and six plugs of bovine serum protein in BGE, each injected for 3 s at a pressure of -10 mbar (-1 kPa) into the capillary filled by BGE, was found to be the best injection procedure. The method repeatability calculated as RSDs of plateau highs of bovine serum albumin and propranolol as model sample compounds were better than 3.44 %. Its applicability was finally demonstrated on the determination of apparent binding parameters of bovine serum albumin for basic drugs propranolol and lidocaine and acid drug phenylbutazone. The values obtained by a new on-line CE-FA methodology are in agreement with values estimated by classic off-line CE-FA, as well as with literature data obtained using different techniques.

Predictive and Experimental Approaches for Elucidating Protein-Protein Interactions and Quaternary Structures

The elucidation of protein-protein interactions is vital for determining the function and action of quaternary protein structures. Here, we discuss the difficulty and importance of establishing protein quaternary structure and review in vitro and in silico methods for doing so. Determining the interacting partner proteins of predicted protein structures is very time-consuming when using in vitro methods, this can be somewhat alleviated by use of predictive methods. However, developing reliably accurate predictive tools has proved to be difficult. We review the current state of the art in predictive protein interaction software and discuss the problem of scoring and therefore ranking predictions. Current community-based predictive exercises are discussed in relation to the growth of protein interaction prediction as an area within these exercises. We suggest a fusion of experimental and predictive methods that make use of sparse experimental data to determine higher resolution predicted protein interactions as being necessary to drive forward development.

Advances in capillary electrophoresis and the implications for drug discovery

INTRODUCTION

Many screening platforms are prone to assay interferences that can be avoided by directly measuring the target or enzymatic product. Capillary electrophoresis (CE) and microchip electrophoresis (MCE) have been applied in a variety of formats to drug discovery. CE provides direct detection of the product allowing for the identification of some forms of assay interference. The high efficiency, rapid separations, and low volume requirements make CE amenable to drug discovery. Areas covered: This article describes advances in capillary electrophoresis throughput, sample introduction, and target assays as they pertain to drug discovery and screening. Instrumental advances discussed include integrated droplet microfluidics platforms and multiplexed arrays. Applications of CE to assays of diverse drug discovery targets, including enzymes and affinity interactions are also described. Expert opinion: Current screening with CE does not fully take advantage of the throughputs or low sample volumes possible with CE and is most suitable as a secondary screening method or for screens that are inaccessible with more common platforms. With further development, droplet microfluidics coupled to MCE could take advantage of the low sample requirements by performing assays on the nanoliter scale at high throughput.

Analysis of proteins and peptides by electromigration methods in microchips

This review presents the developments and applications of microchip electromigration methods in the separation and analysis of peptides and proteins in the period 2011-mid-2016. The developments in sample preparation and preconcentration, microchannel material, and surface treatment are described. Separations by various microchip electromigration methods (zone electrophoresis in free and sieving media, affinity electrophoresis, isotachophoresis, isoelectric focusing, electrokinetic chromatography, and electrochromatography) are demonstrated. Advances in detection methods are reported and novel applications in the areas of proteomics and peptidomics, quality control of peptide and protein pharmaceuticals, analysis of proteins and peptides in biomatrices, and determination of physicochemical parameters are shown.

Protein Cross-Linking Capillary Electrophoresis for Protein-Protein Interaction Analysis

Capillary electrophoresis (CE) has been identified as a useful platform for detecting, quantifying, and screening for modulators of protein-protein interactions (PPIs). In this method, one protein binding partner is labeled with a fluorophore, the protein binding partners are mixed, and then, the complex is separated from free protein to allow direct determination of bound to free ratios. Although it possesses many advantages for PPI studies, the method is limited by the need to have separation conditions that both prevent protein adsorption to capillary and maintain protein interactions during the separation. In this work, we use protein cross-linking capillary electrophoresis (PXCE) to overcome this limitation. In PXCE, the proteins are cross-linked under binding conditions and then separated. This approach eliminates the need to maintain noncovalent interactions during electrophoresis and facilitates method development. We report PXCE methods for an antibody-antigen interaction and heterodimer and homodimer heat shock protein complexes. Complexes are cross-linked by short treatments with formaldehyde after reaching binding equilibrium. Cross-linked complexes are separated by electrophoretic mobility using free solution CE or by size using sieving electrophoresis of SDS complexes. The method gives good quantitative results; e.g., a lysozyme-antibody interaction was found to have Kd = 24 ± 3 nM by PXCE and Kd = 17 ± 2 nM using isothermal calorimetry (ITC). Heat shock protein 70 (Hsp70) in complex with bcl2 associated athanogene 3 (Bag3) was found to have Kd = 25 ± 5 nM by PXCE which agrees with Kd values reported without cross-linking. Hsp70-Bag3 binding site mutants and small molecule inhibitors of Hsp70-Bag3 were characterized by PXCE with good agreement to inhibitory constants and IC50 values obtained by a bead-based flow cytometry protein interaction assay (FCPIA). PXCE allows rapid method development for quantitative analysis of PPIs.

Affinity Capillary Electrophoresis for Selective Control of Electrophoretic Mobility of Sialic Acid Using Lanthanide-Hexadentate Macrocyclic Polyazacarboxylate Complexes

It is difficult to control the electrophoretic mobility in order to obtain high resolution among saccharides in complex samples. We report herein on a new affinity capillary electrophoresis (ACE) method for an anionic monosaccharide, N-acetylneuraminic acid (Neu5Ac), which is important in terms of pathological diagnosis, using lanthanide-hexadentate macrocyclic polyazacarboxylate complexes (Ln-NOTA) as affinity reagents. It was shown that Ln-NOTA complexes increased the anionic mobility of Neu5Ac by approximately 40% through selective complexation with Neu5Ac. The extent of change in the mobility strongly depended on the type of central metal ion of Ln-NOTA. The stability constant (K) of Lu-NOTA with Neu5Ac was determined by ACE to be log Kb = 3.62 ± 0.04, which is the highest value among artificial receptors for Neu5Ac reported so far. Using this ACE, the Neu5Ac content in a glycoprotein sample, α1-acid glycoprotein (AGP), was determined after acid hydrolysis. Complete separation between Neu5Ac and hydrolysis products was successful by controlling the mobility to determine the concentration of Neu5Ac.

Analysis of quantum dots and their conjugates by capillary electrophoresis with detection of laser-induced luminescence

In many bioanalytical applications, important molecules such as DNA, proteins, and antibodies are routinely conjugated with fluorescent tags to reach an extraordinary sensitivity of analyses. Semiconductor nanoparticles, quantum dots, have already proved to be suitable components of highly luminescent tags, probes, and sensors with a broad applicability in analytical chemistry. Quantum dots provide high extinction coefficients together with a wide range of excitation wavelengths, size- and composition-tunable emissions, narrow and symmetric emission spectra, good quantum yields, relatively long size-dependent luminescence lifetime, and practically no photobleaching. Most of these properties are superior when compared with conventional organic fluorescent dyes. In this chapter, optimized procedures for the preparation of water-dispersed cadmium telluride (CdTe) quantum dots, conjugating reactions with antibodies, DNA, and macrocycles as well as their analyses by capillary electrophoresis are described. The potential of capillary electrophoresis for fast analyses of nanoparticles, their conjugates with antibodies, and immunocomplexes with targeted antigens is demonstrated on examples.

Study of deoxyribonucleic acid-ligand interactions by partial filling affinity capillary electrophoresis

In this work, a new partial filling affinity capillary electrophoresis (PF-ACE) method has been developed and applied to investigation of non-covalent molecular interactions between double stranded DNA oligonucleotide (Dickerson dodecamer) and classical DNA intercalator ligand-ethidiumbromide (EtBr) or oligophenylene derivatives-based potential new type of DNA ligands. Binding constants of DNA-ligand complexes were determined from the dependence of migration time changes of DNA oligomer (applied as analyte) on the length of ligand zones introduced beforehand as plugs of various lengths (0-75mm with 12.5mm step) in hydroxypropylcellulose coated fused silica capillary of 50/375μm I.D./O.D. and 400/300mm total/effective length. PF-ACE experiments were performed in two background electrolytes, Tris-borate, pH 8.0, ionic strength 14.3mM (BGE1), and sodium phosphate, pH 7.5, ionic strength 133mM (BGE2). Binding constants of DNA-EtBr complex (ca 15300L/mol in the BGE1 and 4200L/mol in the BGE2) were found to be significantly higher than those of DNA complexes with oligophenylene derivatives (ca 2200-3600L/mol in the BGE1 and 1600-2300L/mol in the BGE2).

Quantitative SNP genotyping by affinity capillary electrophoresis using PEG-oligodeoxyribonucleotide block copolymers with electroosmotic flow

Quantitative SNP detection was demonstrated with an ACE using a PEG-oligodeoxyribonucleotide block copolymer (PEG-b-ODN) as a probe in the presence of an EOF. The probe's PEG segment with large molecular weight and small polydispersity yielded a high resolution in the separation of a chemically synthesized 60-base ssDNA (WT) and its single-base-substituted mutant (MT). A mixture of WT and MT was clearly separated within 10 min by simultaneously using two types of PEG-b-ODN probes whose ODN segments were complementary to WT and MT and whose PEG segments were of different lengths. The peak area ratio between WT and MT was in good agreement with the feed ratio. The averaged difference between the feed and observed ratio of MT was determined to be 0.23%, which is lower than that of any other methods. The ACE using the PEG-b-ODN probes in the presence of EOF could be utilized as a facile method for estimating SNP allele frequency in various research fields.

Applications of reversible covalent chemistry in analytical sample preparation

Reversible covalent chemistry (RCC) adds another dimension to commonly used sample preparation techniques like solid-phase extraction (SPE), solid-phase microextraction (SPME), molecular imprinted polymers (MIPs) or immuno-affinity cleanup (IAC): chemical selectivity. By selecting analytes according to their covalent reactivity, sample complexity can be reduced significantly, resulting in enhanced analytical performance for low-abundance target analytes. This review gives a comprehensive overview of the applications of RCC in analytical sample preparation. The major reactions covered include reversible boronic ester formation, thiol-disulfide exchange and reversible hydrazone formation, targeting analyte groups like diols (sugars, glycoproteins and glycopeptides, catechols), thiols (cysteinyl-proteins and cysteinyl-peptides) and carbonyls (carbonylated proteins, mycotoxins). Their applications range from low abundance proteomics to reversible protein/peptide labelling to antibody chromatography to quantitative and qualitative food analysis. In discussing the potential of RCC, a special focus is on the conditions and restrictions of the utilized reaction chemistry.

Synthesis and characterization of a hydrogel with controllable electroosmosis: a potential brain tissue surrogate for electrokinetic transport

Electroosmosis is the bulk fluid flow initiated by application of an electric field to an electrolyte solution in contact with immobile objects with a nonzero ζ-potential such as the surface of a porous medium. Electroosmosis may be used to assist analytical separations. Several gel-based systems with varying electroosmotic mobilities have been made in this context. A method was recently developed to determine the ζ-potential of organotypic hippocampal slice cultures (OHSC) as a representative model for normal brain tissue. The ζ-potential of the tissue is significant. However, determining the role of the ζ-potential in solute transport in tissue in an electric field is difficult because the tissue's ζ-potential cannot be altered. We hypothesized that mass transport properties, namely the ζ-potential and tortuosity, could be modulated by controlling the composition of a set of hydrogels. Thus, poly(acrylamide-co-acrylic acid) gels were prepared with three compositions (by monomer weight percent): acrylamide/acrylic acid 100/0, 90/10, and 75/25. The ζ-potentials of these gels at pH 7.4 are distinctly different, and in fact vary approximately linearly with the weight percent of acrylic acid. We discovered that the 25% acrylic acid gel is a respectable model for brain tissue, as its ζ-potential is comparable to the OHSC. This series of gels permits the experimental determination of the importance of electrokinetic properties in a particular experiment or protocol. Additionally, tortuosities were measured electrokinetically and by evaluating diffusion coefficients. Hydrogels with well-defined ζ-potential and tortuosity may find utility in biomaterials and analytical separations, and as a surrogate model for OHSC and living biological tissues.

Capillary electrophoresis immunoassays with conjugated quantum dots

Water-soluble CdTe quantum dots (QDs) and their conjugates with antibodies and antigenes were prepared by optimized procedures for applications in CE immunoassays. The QD size of 3.5 nm, excitation spectrum in the range of 300-500 nm, the maximum wavelength of the emission spectrum at 610 nm, quantum yield of 0.25 and luminescence lifetimes in the range of 3.6-43 ns were determined. The 0.1 M solution of TRIS/TAPS (pH 8.3) was found to be the optimum buffer for the separation of the antiovalbumin-ovalbumin immunocomplex from the free conjugates of QDs.

Varying nanoparticle pseudostationary phase plug length during capillary electrophoresis

Capillary electrophoresis based separations of the hypothesized Parkinson's disease biomarkers dopamine, epinephrine, pyrocatechol, L-3,4-dihydroxyphenylalanine (L-DOPA), glutathione, and uric acid are performed in the presence of a 1 nM 11-mercaptoundecanoic acid functionalized gold (Au@MUA) nanoparticle pseudostationary phase plug. Au@MUA nanoparticles are monitored in the capillary and remain stable in the presence of electrically-driven flow. Migration times, peak areas, and relative velocity changes (vs. no pseudostationary) are monitored upon varying (1) the Au@MUA nanoparticle pseudostationary phase plug length at a fixed separation voltage and (2) the separation voltage for a fixed Au@MUA nanoparticle pseudostationary phase plug length. For instance, the migration times of positively charged dopamine and epinephrine increase slightly as the nanoparticle pseudostationary phase plug length increases with concomitant decreases in peak areas and relative velocities as a result of attractive forces between the positively charged analytes and the negatively charged nanoparticles. Migration times for neutral pyrocatechol and slightly negative L-DOPA did not exhibit significant changes with increasing nanoparticle pseudostationary plug length; however, reduction in peak areas for these two molecules were evident and attributed to non-specific interactions (i.e. hydrogen bonding and van der Waals interactions) between the biomarkers and nanoparticles. Moreover, negatively charged uric acid and glutathione displayed progressively decreasing migration times and peak areas and as a result, increased relative velocities with increasing nanoparticle pseudostationary phase plug length. These trends are attributed to partitioning and exchanging with 11-mercaptoundecanoic acid on nanoparticle surfaces for uric acid and glutathione, respectively. Similar trends are observed when the separation voltage decreased thereby suggesting that nanoparticle-biomarker interaction time dictates these trends. Understanding these analyte migration time, peak area, and velocity trends will expand our insight for incorporating nanoparticles in separations.

Carbon nanotubes-assisted polyacrylamide gel electrophoresis for enhanced separation of human serum proteins and application in liverish diagnosis

The application of pore-gradient polyacrylamide gel electrophoresis (PG-PAGE) incorporated with carbon nanotube modified by Triton X-100 and carboxylation so as to improve the separation of human serum proteins is reported. The novel PG-PAGE was made by adding water-soluble single-walled carbon nanotubes (CNTs) when preparing the polyacrylamide gel. Significant improvements in separation of complement C3 protein and haptoglobin (Hp) in human serum were achieved. It was estimated that the interactions between the hydrophilic groups on the proteins and the surface of the CNTs result in different adsorption kinetics of complement C3 and Hp subtype on the nanoparticles incorporated in the gel, thus enhancing the separation of the two proteins in serum. This new CNT matrix-assisted PG-PAGE method for enhanced separation of complement C3 and Hp in human serum was successfully applied to distinguish the samples from liverish patients and healthy people.

Universal method for determining electrolyte temperatures in capillary electrophoresis

Temperature increase in capillary electrophoresis (CE) due to Joule heating is an inherent limitation of this powerful separation technique. Active cooling systems can decrease the temperature of a large part of the capillary but they leave "hot spots" at the capillary ends which can completely ruin some CE analyses despite their short lengths. Here, we introduce a "universal method for determining electrolyte temperatures" (UMET) that can determine temperatures in both efficiently- and inefficiently-cooled parts of the capillary. UMET can be applied to all electrolytes, as it does not involve any probe; it requires only measuring current versus voltage for different voltages and processing the data using an iterative algorithm. To demonstrate the universality of UMET, we measured temperatures for electrolytes of different ionic strengths as well as for different capillary diameters. We further propose a "simplified universal method for predicting electrolyte temperatures" (SUMET) which only requires one measurement of current and voltage (that can be completed in 1 min) and uses two empirical equations to predict temperatures in the efficiently- and inefficiently-cooled parts of the capillary. The equations include several instrument-specific empirical parameters that are determined using a large set of current-voltage data obtained with UMET for a range of electrolytes and different capillaries. To demonstrate the utility of SUMET, we obtained the required data set for a Beckman MDQ CE instrument and produced all required empirical parameters that enable a user of this instrument to predict the temperature for every new experimental set in a matter of minutes. We confirmed the accuracy of SUMET by measuring the temperature-sensitive dissociation rate constant of a protein-DNA complex. We foresee that UMET will be used to produce instrument-specific empirical parameters for all CE instruments and then SUMET will be routinely used for temperature prediction in CE.

Electrophoresis today and tomorrow: Helping biologists' dreams come true

Intensive research and development of electrophoresis methodology and instrumentation during past decades has resulted in unique methods widely implemented in bioanalysis. While two-dimensional electrophoresis and denaturing polyacrylamide gel electrophoresis in sodium dodecylsulfate are still the most frequently used electrophoretic methods applied to analyses of proteins, new miniaturized capillary and microfluidic versions of electromigrational methods have been developed. High-throughput electrophoretic instruments with hundreds of capillaries for parallel separations and laser-induced fluorescence detection of labeled DNA strands have been of key importance for the scientific and commercial success of the Human Genome Project. Another powerful method, capillary isoelectric focusing with pressurized and pH-driven mobilization, provides efficient separations and on-line sensitive detection of proteins, bacteria and viruses. Electrophoretic microfluidic devices can integrate single-cell injection, cell lysis, separation of its components and fluorescence or mass spectrometry detection. These miniaturized devices also proved the capability of single-molecule detection.

Affinity-trap polyacrylamide gel electrophoresis: a novel method of capturing specific proteins by electro-transfer

A method for the affinity capture of specific proteins from a complex mixture using a polyacrylamide gel technique is described. The approach is based on the orthogonal electro-transfer of proteins separated by ordinary polyacrylamide gel electrophoresis (PAGE) to a ligand-coupled polyacrylamide gel (Li-PAG), which is placed under the PAGE gel. Upon electro-transfer, the proteins orthogonally migrate from the PAGE into the Li-PAG, based on the net charge. During migration to the Li-PAG, proteins that specifically interact with a ligand can be transiently trapped in the Li-PAG, while those that do not interact with a ligand pass through it. This method permits the separation of the proteins that can specifically interact with a ligand, even when present in a complex mixture. The method is demonstrated by applying it to the one-step isolation of a trypsin inhibitor from a crude extract of soybean flour.