Monolith-based immobilized enzyme reactors: Recent developments and applications for proteome analysis

A systematic evaluation of sample preparation and 2-D gel electrophoresis protocol for mosquito proteomic profiling

-Mosquito act as the carrier insect to transfer pathogens into hosts for various vector-borne diseases.To identify the pathogenesis causing determinant, comprehensive knowledge of the protein expression in different tissues and physiological conditions is very important. The most widely used technique is 2-D gel electrophoresis to study the protein expression in mosquitoes. 2-D gel electrophoresis is the multistep process to resolve intact protein with similar molecular weight. It is also useful to separate post-translational modified protein, which are not distinguished through shotgun proteomic analysis. Here, we optimized the protocol for 2-D gel electrophoresis that can effectively resolve the protein in mosquitoes and some other insects, to target immunogenic protein to fight against the vector borne disease. The optimized 2-D protocol helps to resolve complex proteomic data which is very difficult to analyze in mosquitoes.The updated protocol improved the protein solubility, resolution and visualization that help in comparative analysis of protein expression.

A review on the immobilization of pepsin: A Lys-poor enzyme that is unstable at alkaline pH values

Pepsin is a protease used in many different applications, and in many instances, it is utilized in an immobilized form to prevent contamination of the reaction product. This enzyme has two peculiarities that make its immobilization complex. The first one is related to the poor presence of primary amino groups on its surface (just one Lys and the terminal amino group). The second one is its poor stability at alkaline pH values. Both features make the immobilization of this enzyme to be considered a complicated goal, as most of the immobilization protocols utilize primary amino groups for immobilization. This review presents some of the attempts to get immobilized pepsin biocatalyst and their applications. The high density of anionic groups (Asp and Glu) make the anion exchange of the enzyme simpler, but this makes many of the strategies utilized to immobilize the enzyme (e.g., amino-glutaraldehyde supports) more related to a mixed ion exchange/hydrophobic adsorption than to real covalent immobilization. Finally, we propose some possibilities that can permit not only the covalent immobilization of this enzyme, but also their stabilization via multipoint covalent attachment.

Development of a multidimensional online method for the characterization and quantification of monoclonal antibodies using immobilized flow-through enzyme reactors

Complete characterization and quantification of monoclonal antibodies often rely on enzymatic digestion with trypsin. In order to accelerate and automate this frequently performed sample preparation step, immobilized enzyme reactors (IMER) compatible with standard HPLC systems were used. This allows an automated online approach in all analytical laboratories. We were able to demonstrate that the required digestion time for the model monoclonal antibody rituximab could be reduced to 20 min. Nevertheless, a previous denaturation of the protein is required, which also needs 20 min. Recoveries were determined at various concentrations and were 100% ± 1% at 100 ng on column, 96% ± 7% at 250 ng on column and 98% ± 2% at 450 ng on column. Despite these good recoveries, complete digestion was not achieved, resulting in a poorer limit of quantification. This is 50 ng on column under optimized IMER conditions, whereas an offline digest on the same system achieved 0.3 ng on column. Furthermore, our work revealed that TRIS buffers, when used with an IMER system, led to alteration of the peptides and induced modifications in the peptides. Therefore, the addition of TRIS should be avoided when working at elevated temperatures of about 60 °C. Nevertheless, our results have shown that the recovery is not significantly influenced whether TRIS is used or not (recovery: 96 ± 7% with TRIS vs. 100 ± 9% without TRIS).

Flow-through enzymatic reactors using polymer monoliths: From motivation to application

The application of monolithic materials as carriers for enzymes has rapidly expanded to the realization of flow-through analysis and bioconversion processes. This expansion is partly attributed to the absence from diffusion limitation in many monoliths-based enzyme reactors. Particularly, the relatively ease of introducing functional groups renders polymer monoliths attractive as enzyme carriers. After summarizing the motivation to develop enzymatic reactors using polymer monoliths, this review reports the most recent applications of such reactors. Besides, the present review focuses on the crucial characteristics of polymer monoliths affecting the immobilization of enzymes and the processing parameters dictating the performance of the resulting enzymatic reactors. This review is intended to provide a guideline for designing and applying flow-through enzymatic reactors using polymer monoliths.

Microfluidic immobilized enzyme reactors for continuous biocatalysis

This review investigates strategies for employing μ-IMERs for continuous biocatalysis via a top-down approach.

Challenges and Advances in the Fabrication of Monolithic Bioseparation Materials and their Applications in Proteomics Research

High-performance liquid chromatography integrated with tandem mass spectrometry (HPLC-MS/MS) has become a powerful technique for proteomics research. Its performance heavily depends on the separation efficiency of HPLC, which in turn depends on the chromatographic material. As the "heart" of the HPLC system, the chromatographic material is required to achieve excellent column efficiency and fast analysis. Monolithic materials, fabricated as continuous supports with interconnected skeletal structure and flow-through pores, are regarded as an alternative to particle-packed columns. Such materials are featured with easy preparation, fast mass transfer, high porosity, low back pressure, and miniaturization, and are next-generation separation materials for high-throughput proteins and peptides analysis. Herein, the recent progress regarding the fabrication of various monolithic materials is reviewed. Special emphasis is placed on studies of the fabrication of monolithic capillary columns and their applications in separation of biomolecules by capillary liquid chromatography (cLC). The applications of monolithic materials in the digestion, enrichment, and separation of phosphopeptides and glycopeptides from biological samples are also considered. Finally, advances in comprehensive 2D HPLC separations using monolithic columns are also shown.

Development of an integrated chromatographic system for ω-transaminase-IMER characterization useful for flow-chemistry applications

An integrated chromatographic system was developed to rapidly investigate the biocatalytic properties of ω-transaminases useful for the synthesis of chiral amines. ATA-117, an (R)-selective ω-transaminase was selected as a proof of concept. The enzyme was purified and covalently immobilized on an epoxy monolithic silica support to create an immobilized enzyme reactor (IMER). Reactor efficiency was evaluated in the conversion of a model substrate. The IMER was coupled through a switching valve to an achiral analytical column for separation and quantitation of the transamination products. The best conditions of the transaminase-catalyzed bioconversion were optimized by a design of experiments (DoE) approach. The production of (R)-1-(4-methoxyphenyl)propan-2-amine and (R)-1-methyl-3-phenylpropylamine, intermediates for the synthesis of the bronchodilator formoterol and the antihypertensive dilevalol respectively, was achieved in the presence of different amino donors. The enantiomeric excess (ee) was determined off-line by developing a derivatization procedure using Nα-(2,4-dinitro-5-fluorophenyl)-L-alaninamide reagent. The most satisfactory conversion yields were 60% for (R)-1-(4-methoxyphenyl)propan-2-amine and 29% for (R)-1-methyl-3-phenylpropylamine, using isopropylamine as amino donor. The enantiomeric excess of the reactions were 84%_R and 99%_R, respectively.

Development of a parallel microbore hollow fiber enzyme reactor platform for online 18O-labeling: Application to lectin-specific lung cancer N-glycoproteome

We introduce a simple online ¹⁸O-labeling protocol for protein samples that uses a parallelizing microbore hollow fiber enzyme reactor (mHFER) as an alternative tool for online proteolytic digestion. Online ¹⁸O-labeling is performed by separately attaching two mHFERs in parallel to a 10-port switching valve with a high-pressure syringe pump and two syringes containing ¹⁶O- or ¹⁸O-water. ¹⁶O-/¹⁸O-labeled peptides are formed in this manner and simultaneously analyzed online using nanoflow liquid chromatography-tandem mass spectrometry (nLC-MS/MS) without any residual trypsin activity. The usefulness of a parallel mHFER platform (P-mHFER) in ¹⁸O-labeling was tested using both cytochrome C and alpha-1-acid-glycoprotein to verify the incorporation level of two ¹⁸O atoms into tryptic peptides and to provide a quantitative assessment with varied mixing ratios. Additionally, our ¹⁸O-labeling approach was used to study the serum N-glycoproteome from lung cancer patients and controls to evaluate the applicability of lectin-based quantitative N-glycoproteomics. We successfully quantified 76 peptides (from 62 N-glycoproteins). Nineteen of these peptides from lung cancer serum were up-/down-regulated at least 2.5-fold compared to controls. As a result, the P-mHFER-based online ¹⁸O-labeling platform presented here can be a simple and reproducible way to allow quantitative proteomic analysis of diverse proteome samples.

Polyethylenimine: a very useful ionic polymer in the design of immobilized enzyme biocatalysts

This review discusses the possible roles of polyethylenimine (PEI) in the design of improved immobilized biocatalysts from diverse perspectives.

Monoliths in capillary electrochromatography and capillary liquid chromatography in conjunction with mass spectrometry

Here, we have reviewed separation studies utilizing monolithic capillary columns for separation of compounds preceding MS analysis. The review is divided in two parts according to the used separation method, namely CEC and capillary LC (cLC). Based on our overview, monolithic CEC-MS technique have been more focused on the syntheses of highly specialized and selective separation phase materials for fast and efficient separation of specific types of analytes. In contrast, monolithic cLC-MS is more widely used and is often employed, for instance, in the analysis of oligonucleotides, metabolites, and peptides and proteins in proteomic studies. While poly(styrene-divinylbenzene)-based and silica-based monolithic capillaries found their place in proteomic analyses, the other laboratory-synthesized monoliths still wait for their wider utilization in routine analyses. The development of new monolithic materials will most likely continue due to the demand of more efficient and rapid separation of increasingly complex samples.

Xylan degradation improved by a combination of monolithic columns bearing immobilized recombinant β-xylosidase from Aspergillus awamori X-100 and Grindamyl H121 β-xylanase

Synergistic action of exo- and endohydrolazes is preferred for effective destruction of biopolymers. The main purpose of the present work was to develop an efficient tool for degradation of xylan. Macroporous lab-made monolithic columns and commercial CIM-Epoxy disk were used to immobilize the recombinant β-xylosidase from Aspergillus awamori and Grindamyl β-xylanase. The efficiency of xylan degradation using the low-loaded β-xylosidase column appeared to be four times higher than for the in-solution process and about six times higher than for the high-loaded bioreactor. Disk bioreactor with the Grindamil β-xylanase operated in a recirculation mode has shown noticeable advantages over the column design. Additionally, a system comprised of two immobilized enzyme reactors (IMERs) was tested to accelerate the biopolymer hydrolysis, yielding total xylan conversion into xylose within 20 min. Fast online monitoring HPLC procedure was developed where an analytical DEAE CIM disk was added to the two-enzyme system in a conjoint mode. A loss of activity of immobilized enzymes did not exceed 7% after 5 months of the bioreactor usage. We can therefore conclude that the bioreactors developed exhibit high efficiency and remarkable long-term stability.

Coupling isotachophoresis with affinity chromatography for rapid and selective purification with high column utilization, part 2: experimental study

We present an experimental study of coupling of isotachophoresis (ITP) and affinity chromatography (AC) to effect rapid, selective purification with high column utilization and high resolution. We provide a detailed protocol for performing ITP-AC and describe the design of a buffer system to perform sequence specific separation of nucleic acids. We describe the synthesis and functionalization of our affinity substrate, poly(glycidyl methacrylate-co-ethylene dimethacrylate) porous polymer monolith (GMA-EDMA PPM). This substrate allows easy immobilization of affinity probes, is nonsieving (even to macromolecules), and exhibits negligible nonspecific binding. We demonstrate ITP-AC with 25 nt, Cy5 labeled DNA target and a DNA probe and study the spatiotemporal dynamics using epifluorescence imaging. We make qualitative and quantitative comparisons between these data and the model presented in the first part of this two-paper series. We vary the target concentration from 1 pg μL(-1) to 100 pg μL(-1) and ITP velocity over the range of 10-50 μm s(-1), and thereby explore over 4 orders of magnitude of scaled target amount. We observe very good agreement between predictions and experimental data for the spatiotemporal behavior of the coupled ITP and affinity process, and for key figures of merit, including scaled capture length and maximum capture efficiency. Lastly, we demonstrate that the resolution of ITP-AC increases linearly with time and purify 25 nt target DNA from 10,000-fold higher abundance background (contaminating) genomic fish sperm DNA. We perform this capture from 200 μL of sample in under 1 mm column length and within <10 min.

Limited proteolysis in proteomics using protease-immobilized microreactors

Proteolysis is the key step for proteomic studies integrated with MS analysis. Compared with the conventional method of in-solution digestion, proteolysis by a protease-immobilized microreactor has a number of advantages for proteomic analysis; i.e., rapid and efficient digestion, elimination of a purification step of the digests prior to MS, and high stability against a chemical or thermal denaturant. This chapter describes the preparation of the protease-immobilized microreactors and proteolysis performance of these microreactors. Immobilization of proteases by the formation of a polymeric membrane consisting solely of protease-proteins on the inner wall of the microchannel is performed. This was realized either by a cross-linking reaction in a laminar flow between lysine residues sufficiently present on the protein surfaces themselves or in the case of acidic proteins by mixing them with poly-lysine prior to the crosslink-reaction. The present procedure is simple and widely useful not only for proteases but also for several other enzymes.

Facile trypsin immobilization in polymeric membranes for rapid, efficient protein digestion

Sequential adsorption of poly(styrene sulfonate) and trypsin in nylon membranes provides a simple, inexpensive method to create stable, microporous reactors for fast protein digestion. The high local trypsin concentration and short radial diffusion distances in membrane pores facilitate proteolysis in residence times of a few seconds, and the minimal pressure drop across the thin membranes allows their use in syringe filters. Membrane digestion and subsequent MS analysis of bovine serum albumin provide 84% sequence coverage, which is higher than the 71% coverage obtained with in-solution digestion for 16 h or the <50% sequence coverages of other methods that employ immobilized trypsin. Moreover, trypsin-modified membranes digest protein in the presence of 0.05 wt % sodium dodecyl sulfate (SDS), whereas in-solution digestion under similar conditions yields no peptide signals in mass spectra even after removal of SDS. These membrane reactors, which can be easily prepared in any laboratory, have a shelf life of several months and continuously digest protein for at least 33 h without significant loss of activity.