Model Protein Mixture Research Articles

Trypsin Encapsulation in the Zeolitic Imidazolate Framework for Low-Molecular Weight Protein Analysis with High Selectivity and Efficiency.

Low-molecular weight proteins (LWPs) are important sources of biological information in biomarkers, signaling molecules, and pathology. However, the separation and analysis of LWPs in complex biological samples are challenging, mainly due to their low abundance and the complex sample pretreatment procedure. Herein, trypsin modified by poly(acrylic acid) (PAA) was encapsulated by a zeolitic imidazolate framework (ZIF-L). Mesopores were formed on the ZIF-L with the introduction of PAA. An alternative strategy for separation and pretreatment of LWPs was developed based on the prepared ZIF-L-encapsulated trypsin with adjustable pore size. The mesoporous structure of the prepared materials selectively excluded high-molecular weight proteins from the reaction system, allowing LWPs to enter the pores and react with the internal trypsin, resulting in an improved separation efficiency. The hydrophobicity of the ZIF-L simplified the digestion process by inducing significant structural changes in substrate proteins. In addition, the enzymatic activity was significantly enhanced by the developed encapsulation method that maintained the enzyme conformation, allowed low mass transfer resistance, and possessed a high enzyme-to-substrate ratio. As a result, the ZIF-L-encapsulated trypsin can achieve highly selective separation, valid denaturation, and efficient digestion of LWPs in a short time by simply mixing with substrate proteins, greatly simplifying the separation and pretreatment process of the traditional hydrolysis method. The prepared materials and the developed strategy demonstrated an excellent size-selective assay performance in model protein mixtures, showing great potential in the application of proteomics analysis.

Improved process design for monoclonal antibody charge variants separation with multicolumn counter-current solvent gradient purification

The multicolumn counter-current solvent gradient purification (MCSGP) method has proven effective in addressing the issue of elution profile overlap for difficult-to-separate proteins, leading to improved purity and recovery. However, during the MCSGP process, the flow rate and proportion of loaded proteins undergo changes, causing a significant discrepancy between the elution profiles of batch process design and the actual MCSGP process. This mismatch negatively impacts the purity and recovery of the target protein. To address this challenge, an improved process design (reDesign) was proposed with the first-run MCSGP to mimic the actual continuous process and obtain elution profiles that closely resemble the real ones. The reDesign was demonstrated with both a model protein mixture and a sample of monoclonal antibody (mAb) with charge variants. For model protein mixture, the reDesign-based MCSGP process (reMCSGP) showed a remarkable improvement in recovery, increasing from 83.6% to 97.8% while maintaining a purity of more than 95%. For mAb sample, the recovery of reMCSGP improved significantly to 93.9%, surpassing the performance of normal MCSGP processes at a given purity level of more than 84%. In general, the new process design strategy developed in this work could generate a more representative elution profile that closely mirrors actual conditions in continuous processes, which enhances the separation performance of MCSGP.

Cationic Covalent Organic Framework as an Ion Exchange Material for Efficient Adsorptive Separation of Biomolecules.

Although covalent organic frameworks (COFs) have earned significant interest in separation applications, the use of COFs in biomolecule separation remains unexplored. We examined the ionic COF Py-BPy2+-COF as an ion exchange material for biomolecule separation. After characterizing the properties of the synthesized COF with a variety of techniques, binding experiments with both large and small biomolecules were performed. High adsorption capacities of amino acids with different hydrophobicity and charge, as well as proteins of different isoelectric points and molecular weights, were determined in batch equilibrium experiments. Desorption experiments with mixtures of model proteins demonstrated an ability to successfully separate one protein from another with the selectivity hypothesized to be a combination of the isoelectric point, hydrophobicity, and ability to penetrate the crystalline material. Overall, the results demonstrated that Py-BPy2+-COF can be exploited as a robust crystalline anion exchange biomolecule separation material.

High Performance Countercurrent Membrane Purification for protein separations

Although pressure-driven membrane filtration is used extensively in bioprocessing, protein purification is currently performed by chromatographic separations due to the difficulty in achieving high selectivity for similarly sized species using commercially available ultrafiltration membranes in the absence of fouling. This work examines a novel approach for protein separations based on High Performance Countercurrent Membrane Purification (HPCMP), which exploits highly selective diffusive transport across the thin walls of a hollow fiber membrane. Experiments were performed using commercially available hemodialysis membranes using both polydisperse dextrans and a model protein mixture of bovine serum albumin (BSA) and myoglobin (Mb). Dextran transport data obtained using diffusive transport showed significantly greater selectivity than that for pressure-driven filtration. The HPCMP system was then used to separate BSA and Mb, achieving greater than 98% yield of both proteins with purification factors greater than 100-fold. The Mb product obtained in the draw (dialysate) solution had undetectable levels of BSA. Stable operation was achieved for 96 h without any evidence of membrane fouling due to the absence of any significant pressure-driven flow. These results demonstrate the feasibility of using HPCMP for high resolution separations in the preparation of biopharmaceuticals and natural protein products.

Selective adsorption of bovine hemoglobin by Ni2+-functionalized silica nanoparticles

In this work, we have used Stöber method to prepare 200 nm SiO 2 particles and then immobilized metal affinity ligand iminodiacetic acid (IDA) and charged them with Ni 2+ ions. The particles show high absorption efficiency to bovine hemoglobin and the maximum extraction amounts reached 43.4 mg/g. The particles have been applied to separate a model protein mixture of bovine hemoglobin (BHb) and bovine serum albumin (BSA). They can be separated and showed low non-specific adsorption. Then we have used these particles to extract BHb from the mixture of BHb and DNA. They have potential applications in removing abundant protein in proteomic analysis, and we hope it may become a simple, convenient, and potentially effective way to purify hemoglobin in serum.

On the analysis of chromatographic biopharmaceutical data by curve resolution techniques in the framework of the area of feasible solutions.

Monitoring preparative protein chromatographic steps by in-line spectroscopic tools or fraction analytics results in medium or large sized data matrices. Multivariate Curve Resolution (MCR) serve to compute or to estimate the concentration values of the pure components only from these data matrices. However, MCR methods often suffer from an inherent solution ambiguity which underlies the factorization problem. The typical unimodality of the chromatographic profiles of pure components can support the chemometric analysis. Here we present the pure components estimation process within the framework of the area of feasible solutions, which is a systematic approach to represent the range of all possible solutions. The unimodality constraint in combination with Pareto optimization is shown to be an effective method for the pure component calculation. Applications are presented for chromatograms on a model protein mixture containing ribonuclease A, cytochrome c and lysozyme and on a two-dimensional chromatographic separation of a monoclonal antibody from its aggregate species. The root mean squared errors of the first case study are 0.0373, 0.0529 and 0.0380 g/L compared to traditional off-line analytics. The second case study illustrates the potential of recovering hidden components with MCR from off-line reference analytics.

Development and Testing of a 4-Columns Periodic Counter-Current Chromatography System Based on Membrane Adsorbers

Continuous chromatography can surmount the disadvantages of batch chromatography like low productivities and extensive usage of consumables. In this work, a 4-column continuous chromatographic system based on the principle of periodic counter-current chromatography (PCCC) was developed and tested with a model protein mixture of BSA and lysozyme. The PCCC system was specially designed for membrane adsorbers as an alternative to conventional columns to facilitate the use of disposable process units and to further increase the productivity due to higher convective mass transport in the membrane adsorber. Membrane adsorber Sartobind® Q was used to continuously purify BSA from the protein mixture. The usage of PCCC led to an increased capacity utilization (here 20%) and higher space–time-yields, and thus to a remarkable productivity increase and cost savings.

Performance Comparison of a Laterally-Fed Membrane Chromatography (LFMC) Device with a Commercial Resin Packed Column.

The use of conventional membrane adsorbers such as radial flow devices is largely restricted to flow-through applications, such as virus and endotoxin removal, as they fail to give acceptable resolution in bind-and-elute separations. Laterally-fed membrane chromatography or LFMC devices have been specifically developed to combine high-speed with high-resolution. In this study, an LFMC device containing a stack of strong cation exchange membranes was compared with an equivalent resin packed column. Preliminary characterization experiments showed that the LFMC device had a significantly greater number of theoretical plates per metre than the column. These devices were used to separate a ternary model protein mixture consisting of ovalbumin, conalbumin and lysozyme. The resolution obtained with the LFMC device was better than that obtained with the column. For instance, the LFMC device could resolve lysozyme dimer from lysozyme monomer, which was not possible using the column. In addition, the LFMC device could be operated at lower pressure and at significantly higher flow rates. The devices were then compared based on an application case study, i.e., preparative separation of monoclonal antibody charge variants. The LFMC device gave significantly better separation of these variants than the column.

Grafting polymerization of glycidyl methacrylate onto capillary-channeled polymer (C-CP) fibers as a ligand binding platform: Applications in immobilized metal-ion affinity chromatography (IMAC) protein separations

Immobilized metal-ion affinity chromatography (IMAC) is a valuable method for preparative and analytical-scale protein separations. Nylon 6 capillary-channeled polymer (C-CP) fibers were grafted with glycidyl methacrylate (GMA) as a monomer with ceric ammonium nitrate (in dilute nitric acid) used as the initiator. The polymerization reaction occurs rapidly (15 min) in a residential microwave. Iminodiacetic acid (IDA) is then attached to the grafted GMA polymers by reacting with the reactive terminal epoxide groups. Different parameters regarding the grafting time, initiator concentration and conversion time were investigated to find the optimal conditions for the entire modification process. The resulting nylon-IDA fibers were characterized by attenuated total reflection-Fourier transform infrared spectroscopy (ATR-FTIR) and scanning electron microscopy (SEM). The resulting carboxyl density and copper binding capacity were determined to be 612 ± 21 μmol g−1 and 375 ± 12 μmol g−1, respectively. When charged with Cu2+ ions and packed in a column format, the nylon-IDA fibers can be applied as an IMAC stationary phase for the separation of histidine rich proteins. The performance of this novel phase was evaluated through the separation of a mixture of model proteins (cytochrome C, α-chymotrypsinogen A and lysozyme) and a recombinant histidine-tagged protein (his-tagged ubiquitin). Despite multi-step modifications, columns of the modified fibers still maintain the anticipated high levels of throughput and efficiency, with binding capacities of 6.89 ± 0.56 mg lysozyme g−1 fiber and 6.32 ± 0.12 mg His-tagged ubiquitin g−1 fiber.

Depletion of High-Molecular-Mass Proteins for the Identification of Small Proteins and Short Open Reading Frame Encoded Peptides in Cellular Proteomes.

The identification of small proteins and peptides (below ca. 100-150 amino acids) in complex biological samples is hampered by the dominance of higher-molecular-weight proteins. On the contrary, the increasing knowledge about alternative or short open reading frames creates a need for methods that allow the existence of the corresponding gene products to be proven in proteomics experiments. We present an acetonitrile-based precipitation methodology that depletes the majority of proteins above ca. 15 kDa. Parameters such as depletion mixture composition, pH, and temperature were optimized using a model protein mixture, and the method was evaluated in comparison with the established differential solubility method. The approach was applied to the analysis of the low-molecular-weight proteome of the archaea Methanosarcina mazei by means of LC-MS. The data clearly show a beneficial effect from a reduction of complexity, especially in terms of the quality of MS/MS-based identification of small proteins. This fast, detergent-free method allowed for, with minimal sample manipulation, the successful identification of several not yet identified short open reading frame encoded peptides in M. mazei.

Heart-cut nano-LC-CZE-MS for the characterization of proteins on the intact level.

Multidimensional separation techniques play an increasingly important role in separation science, especially for the analysis of complex samples such as proteins. The combination of reversed-phase liquid chromatography in the nanoscale and CZE is especially beneficial due to their nearly orthogonal separation mechanism and well-suited geometries/dimensions. Here, a heart-cut nano-LC-CZE-MS setup was developed utilizing for the first time a mechanical 4-port valve as LC-CE interface. A model protein mixture containing four different protein species was first separated by nano LC followed by a heart-cut transfer of individual LC peaks and subsequent CZE-MS analysis. In the CZE dimension, various glycoforms of one protein species were separated. Improved separation capabilities were achieved compared to the 1D methods, which was exemplarily shown for ribonuclease B and its different glycosylated forms. LODs in the lower μg/mL range were determined, which are considerably lower compared to traditional CZE-MS. In addition, this study represents the first application of an LC-CE-MS system for intact protein analysis. The nano-LC-CZE-MS system is expected to be applicable to various other analytical challenges.

Ligand-protein target screening from cell matrices using reactive desorption electrospray ionization-mass spectrometry via a native-denatured exchange approach.

Native mass spectrometry has been recognized as a powerful tool for probing interactions between small molecules, such as drugs and natural products, and target proteins. However, the presence of heterogeneous proteins and metabolites in real biological systems can alter the conformations of target proteins or compete with candidate ligands, thus necessitating a method for measuring binding stoichiometries in matrices aside from the extensively used pure/recombinant protein systems. Furthermore, some small molecule-protein interactions have a transient and low-affinity nature and thus can be mis-assigned as nonspecific binding complexes that are often formed during the native ESI process. A native-denatured exchange (NDX) approach was recently developed using a reactive desorption electrospray ionization-mass spectrometer (DESI-MS) setup to screen specific interacting partners. The method works by gradually increasing the composition of denaturing solvents contained in the DESI spray and thus conferring a switch from a native to denatured ionization environment. This change impairs three-dimensional structures of target proteins and disrupts specific ligand-protein interactions, leading to decreased holo/apo ratios. In contrast, ligand-protein complexes exhibiting different trends are assigned as nonspecific interactions. Herein, we applied the NDX approach to probe specific ligand-protein interactions in biological matrices. We first used mixtures of model ligands and proteins to examine the use of reactive DESI-MS in recognizing ligand-target binding in mixtures. Subsequently, we used the NDX approach to analyze binding affinity curves of ligands to target proteins spiked in cell lysates with the aid of size exclusion chromatography and demonstrated its use in probing specific ligand-protein interactions from cell matrices.

Resolving protein mixtures using microfluidic diffusional sizing combined with synchrotron radiation circular dichroism.

Circular dichroism spectroscopy has become a powerful tool to characterise proteins and other biomolecules. For heterogeneous samples such as those present for interacting proteins, typically only average spectroscopic features can be resolved. Here we overcome this limitation by using free-flow microfluidic size separation in-line with synchrotron radiation circular dichroism to resolve the secondary structure of each component of a model protein mixture containing monomers and fibrils. To enable this objective, we have integrated far-UV compatible measurement chambers into PDMS-based microfluidic devices. Two architectures are proposed so as to accommodate for a wide range of concentrations. The approach, which can be used in combination with other bulk measurement techniques, paves the way to the study of complex mixtures such as the ones associated with protein misfolding and aggregation diseases including Alzheimer's and Parkinson's diseases.

Capillary HILIC-MS: A New Tool for Sensitive Top-Down Proteomics.

Recent progress in top-down proteomics has driven the demand for chromatographic methods compatible with mass spectrometry (MS) that can separate intact proteins. Hydrophilic interaction liquid chromatography (HILIC) has recently shown good potential for the characterization of glycoforms of intact proteins. In the present study, we demonstrate that HILIC can separate a wide range of proteins exhibiting orthogonal selectivity with respect to reversed-phase LC (RPLC). However, the application of HILIC to the analysis of low abundance proteins (e.g., in proteomics analysis) is hampered by low volume loadability, hindering down-scaling of the method to column diameters below 2.1 mm. Moreover, HILIC-MS sensitivity is decreased due to ion suppression from the trifluoroacetic acid (TFA) often used as the ion-pair agent to improve the selectivity and efficiency in the analysis of glycoproteins. Here, we introduce a capillary-based HILIC-MS method that overcomes these problems. Our method uses RPLC trap-columns to load and inject the sample, circumventing issues of protein solubility and volume loadability in capillary columns (200 μm ID). The low flow rates and use of a dopant gas in the electrospray interface improve protein-ionization efficiencies and reduce suppression by TFA. Overall, this allows the separation and detection of small protein quantities (down to 5 ng injected on column) as indicated by the analysis of a mixture of model proteins. The potential of the new capillary HILIC-MS is demonstrated by the analysis of a complex cell lysate.

Similarly sized protein separation of charge‐selective ethylene‐vinyl alcohol copolymer membrane by grafting dimethylaminoethyl methacrylate

ABSTRACTSimilarly sized protein separation was investigated using a charge‐selective membrane, which prepared by grafting dimethylaminoethyl methacrylate (DMAEMA) onto ethylene vinyl alcohol copolymer (EVAL) membrane. Bovine serum albumin (BSA) and bovine hemoglobin (BHb) was used as model proteins. P(DMAEMA), the weak cationic polyelectrolyte with ionizable tertiary amine groups, contributed to the charge‐selective separation for BSA and BHb. At pH 6.0, the grafted EVAL membrane surface was positively charged and BSA was negatively charged, while BHb was positively charged. The BSA was adsorbed onto the membrane surface due to electrostatic interaction and the BHb passed through the membrane into the permeate. The charge‐selective behavior resulted in the separation of the similarly sized protein. The maximum separation factors of static adsorption separation for model protein and binary mixture were 32.4 and 37.2, respectively. In the dynamic separation process, the maximum separation factor value was 6.2. © 2018 Wiley Periodicals, Inc. J. Appl. Polym. Sci. 2018, 135, 46374.

Strategy for the separation of concentrated samples by capillary electrophoresis.

The use of concentrated samples is usually avoided during conventional separations since utilization of concentrated samples normally compromises the quality of separation. However, in case of the detection of low-abundance components, highly concentrated samples are necessary, which leads to an extremely high concentration for high-abundant components. This will make the separation difficult due to the serious longitudinal dispersion. Here, we developed a method to separate high concentration of components based on the modified capillary electrophoresis. The mechanism involves concentrated sample stretched into a wider zone in the higher electric field strength; the sample zone is fractionated into thin sections via a cutting effect; these thin sections are then separated. Based on this mechanism, we examined to separate an overloaded mixture of N,N'-diphenylguanidine and N,N'-di(o-tolyl)guanidine. Baseline separation was achieved due to much small longitudinal dispersion. The theoretical plate numbers of peaks were around 3.5×105 m-1 . The practicality of the new approach is demonstrated in the separation of a model protein mixture, containing lysozyme, bovine serum albumin, and ribonuclease A.

New Interface for Purification of Proteins: One-Dimensional TiO2 Nanotubes Decorated by Fe3O4 Nanoparticles.

In this work, a high surface area interface, based on anodic one-dimensional (1D) TiO2 nanotubes homogeneously decorated by Fe3O4 nanoparticles (TiO2NTs@Fe3O4NPs) is reported for the first time for an unprecedented purification of His-tagged recombinant proteins. Excellent purification results were achieved from the model protein mixture, as well as from the whole cell lysate (with His-tagged ubiquitin). Compared to a conventional immobilized-metal affinity chromatography (IMAC) system, specific isolation of selected His-tagged proteins on behalf of other proteins was significantly enhanced on TiO2NTs@Fe3O4NPs interface under optimized binding and elution conditions. The combination of specific isolation properties, magnetic features, biocompatibility, and ease of preparation of this material consisting of two basic metal oxides makes it a suitable candidate for future purification of recombinant proteins in biotechnology. The principally new material bears a large potential to open new pathways for discoveries in nanobiotechnology and nanomedicine.

Root cause investigation of deviations in protein chromatography based on mechanistic models and artificial neural networks

In protein chromatography, process variations, such as aging of column or process errors, can result in deviations of the product and impurity levels. Consequently, the process performance described by purity, yield, or production rate may decrease. Based on visual inspection of the UV signal, it is hard to identify the source of the error and almost unfeasible to determine the quantity of deviation. The problem becomes even more pronounced, if multiple root causes of the deviation are interconnected and lead to an observable deviation. In the presented work, a novel method based on the combination of mechanistic chromatography models and the artificial neural networks is suggested to solve this problem. In a case study using a model protein mixture, the determination of deviations in column capacity and elution gradient length was shown. Maximal errors of 1.5% and 4.90% for the prediction of deviation in column capacity and elution gradient length respectively demonstrated the capability of this method for root cause investigation.

Protein separation through preliminary experiments concerning pH and salt concentration by tube radial distribution chromatography based on phase separation multiphase flow using a polytetrafluoroethylene capillary tube

Protein mixtures were separated using tube radial distribution chromatography (TRDC) in a polytetrafluoroethylene (PTFE) capillary (internal diameter=100µm) separation tube. Separation by TRDC is based on the annular flow in phase separation multiphase flow and features an open-tube capillary without the use of specific packing agents or application of high voltages. Preliminary experiments were conducted to examine the effects of pH and salt concentration on the phase diagram of the ternary mixed solvent solution of water–acetonitrile–ethyl acetate (8:2:1 volume ratio) and on the TRDC system using the ternary mixed solvent solution. A model protein mixture containing peroxidase, lysozyme, and bovine serum albumin was analyzed via TRDC with the ternary mixed solvent solution at various pH values, i.e., buffer–acetonitrile–ethyl acetate (8:2:1 volume ratio). Protein was separated on the chromatograms by the TRDC system, where the elution order was determined by the relation between the isoelectric points of protein and the pH values of the solvent solution.

PH-Responsive magnetic nanospheres for the reversibly selective capture and release of glycoproteins

Glycoproteins are related to many biological activities and diseases and their effective capture and release from a complex mixture is of great significance in proteomics and diagnostics. However, to separate and target glycoproteins with high efficiency and selectivity is difficult, due to the interference of nanomaterials and other proteins in complicated samples. In this study, Fe3O4/carboxymethylated chitosan/poly(3-acrylaminophenylboronic acid) (Fe3O4/CMCS/PAAPBA) nanospheres with enhanced properties are prepared by a facile and economical method, and possess excellent morphology, uniform size (∼300 nm), high saturation magnetization (59 emu g-1), and high magnetic content (79%). Due to the introduction of PAAPBA, the Fe3O4/CMCS/PAAPBA nanospheres have been developed as a pH-responsive strategy to reversibly capture and release glycoproteins with high selectivity and recyclability in a pure protein, a model protein mixture and even a biological sample. Additionally, the Fe3O4/CMCS/PAAPBA nanospheres retained high separation efficiency (∼94%) in a pure protein system after being recycled five times, showing the great potential of the boronate functionalized, pH-stimuli-responsive, magnetic nanospheres in the biomedical field.