Enhanced Proteolytic Activity of Covalently Bound Enzymes in Photopolymerized Sol Gel

Recent Advances in Hybrid Biomimetic Polymer-Based Films: from Assembly to Applications

Biological membranes, in addition to being a cell boundary, can host a variety of proteins that are involved in different biological functions, including selective nutrient transport, signal transduction, inter- and intra-cellular communication, and cell-cell recognition. Due to their extreme complexity, there has been an increasing interest in developing model membrane systems of controlled properties based on combinations of polymers and different biomacromolecules, i.e., polymer-based hybrid films. In this review, we have highlighted recent advances in the development and applications of hybrid biomimetic planar systems based on different polymeric species. We have focused in particular on hybrid films based on (i) polyelectrolytes, (ii) polymer brushes, as well as (iii) tethers and cushions formed from synthetic polymers, and (iv) block copolymers and their combinations with biomacromolecules, such as lipids, proteins, enzymes, biopolymers, and chosen nanoparticles. In this respect, multiple approaches to the synthesis, characterization, and processing of such hybrid films have been presented. The review has further exemplified their bioengineering, biomedical, and environmental applications, in dependence on the composition and properties of the respective hybrids. We believed that this comprehensive review would be of interest to both the specialists in the field of biomimicry as well as persons entering the field.

Systematic Evaluation of Immobilized Trypsin-Based Fast Protein Digestion for Deep and High-Throughput Bottom-Up Proteomics

Immobilized trypsin (IM) has been recognized as an alternative to free trypsin (FT) for accelerating protein digestion 30 years ago. However, some questions of IM still need to be answered. How does the solid matrix of IM influence its preference for protein cleavage and how well can IM perform for deep bottom-up proteomics compared to FT? By analyzing Escherichia coli proteome samples digested with amine or carboxyl functionalized magnetic bead-based IM (IM-N or IM-C) or FT, it is observed that IM-N with the nearly neutral solid matrix, IM-C with the negatively charged solid matrix, and FT have similar cleavage preference considering the microenvironment surrounding the cleavage sites. IM-N (15 min) and FT (12 h) both approach 9000 protein identifications (IDs) from a mouse brain proteome. Compared to FT, IM-N has no bias in the digestion of proteins that are involved in various biological processes, are located in different components of cells, have diverse functions, and are expressed in varying abundance. A high-throughput bottom-up proteomics workflow comprising IM-N-based rapid protein cleavage and fast CZE-MS/MS enables the completion of protein sample preparation, CZE-MS/MS analysis, and data analysis in only 3 h, resulting in 1000 protein IDs from the mouse brain proteome.

Preparation and characterization of a packed bead immobilized trypsin reactor integrated into a PDMS microfluidic chip for rapid protein digestion

This paper demonstrates the design, efficiency and applicability of a simple, inexpensive and high sample throughput microchip immobilized enzymatic reactor (IMER) for rapid protein digestion. The IMER contains conventional silica particles with covalently immobilized trypsin packed inside of a poly(dimethylsiloxane) (PDMS) microchip channel (10mm×1mm×35µm). The microchip consists of 9 different channels, enabling 9 simultaneous protein digestions. Trypsin was covalently immobilized using carbodiimide activation, the ideal trypsin/silica particle ratio (i.e. measured mass ratio before the immobilization reaction) was determined. The amount of immobilized trypsin was 10-15μg trypsin for 1mg silica particle. Migration times of CZE peptide maps showed good repeatability and reproducibility (RSD%=0.02-0.31%). The IMER maintained its activity for 2 months, in this period it was used effectively for rapid proteolysis. Four proteins (myoglobin, lysozyme, hemoglobin and albumin) in a wide size range (15-70kDa) were digested to demonstrate the applicability of the reactor. Their CZE peptide maps were compared to peptide maps obtained from standard in-solution digestion of the four proteins. The number of peptide peaks correlated well with the theoretically expected peptide number in both cases, the peak patterns of the electropherograms were similar, however, digestion with the microchip IMER requires only <10s, while in-solution digestion takes 16h. LC-MS/MS peptide mapping was also carried out, the four proteins were identified with satisfying sequence coverages (29-50%), trypsin autolysis peptides were not detected. The protein content of human serum was digested with the IMER and with in-solution digestion.

Limited proteolysis in porous membrane reactors containing immobilized trypsin

Trypsin-containing membranes effect limited digestion to identify facile digestion sites in protein structures.

Silane-coated magnetic nanoparticles with surface thiol functions for conjugation with gold nanostars

Small (d∼ 8 nm) magnetite nanoparticles, Fe3O4NP, are prepared and coated with mercaptopropyl trimethoxysilane (MPTS) to form Fe3O4NP@MPTS. In the coating step controlled MPTS/Fe3O4NP molar ratios are used, ranging from 1 to 7.8 × 10(4). The total quantity of MPTS per Fe3O4NP is determined by SEM-EDS analysis and the average number of free, reactive -SH groups per Fe3O4NP is calculated by a colorimetric method. At very low molar ratios MPTS forms a submonolayer on the Fe3O4NP surface with all -SH free to react, while on increasing the MPTS/Fe3O4NP molar ratio the (CH3O)3Si- groups of MPTS polymerize, forming a progressively thicker shell, in which only a small fraction of the -SH groups, positioned on the shell surface, is available for further reaction. The MPTS shell reduces the magnetic interactions occurring between the magnetite cores, lowering the occurrence and strength of collective magnetic states, with Fe3O4NP@MPTS showing the typical behaviour expected for a sample with a mono-modal size distribution of superparamagnetic nanoparticles. Interaction of Fe3O4NP@MPTS with gold nanostars (GNS) was tested, using both Fe3O4NP@MPTS with a MPTS submonolayer and with increasing shell thickness. Provided that a good balance is used between the number of available -SH and the overall size of Fe3O4NP@MPTS, the free thiols of such nanoparticles bind GNS decorating their surface, as shown by UV-Vis spectroscopy and TEM imaging.

Protein Analysis by Ambient Ionization Mass Spectrometry Using Trypsin-Immobilized Organosiloxane Polymer Surfaces

In the growing field of proteomic research, rapid and simple protein analysis is a crucial component of protein identification. We report the use of immobilized trypsin on hybrid organic-inorganic organosiloxane (T-OSX) polymers for the on-surface, in situ digestion of four model proteins: melittin, cytochrome c, myoglobin, and bovine serum albumin. Tryptic digestion products were sampled, detected, and identified using desorption electrospray ionization mass spectrometry (DESI-MS) and nanoDESI-MS. These novel, reusable T-OSX arrays on glass slides allow for protein digestion in methanol:water solvents (1:1, v/v) and analysis directly from the same polymer surface without the need for sample preparation, high temperature, and pH conditions typically required for in-solution trypsin digestions. Digestion reactions were conducted with 2 μL protein sample droplets (0.35 mM) at incubation temperatures of 4, 25, 37, and 65 °C and digestion reaction times between 2 and 24 h. Sequence coverages were dependent on the hydrophobicity of the OSX polymer support and varied by temperature and digestion time. Under the best conditions, the sequence coverages, determined by DESI-MS, were 100% for melittin, 100% for cytochrome c, 90% for myoglobin, and 65% for bovine serum albumin.

Organic-inorganic hybrid nanoflowers: types, characteristics, and future prospects

Organic-inorganic hybrid nanoflowers, a newly developed class of flower-like hybrid nanoparticles, have received much attention due to their simple synthesis, high efficiency, and enzyme stabilizing ability. This article covers, in detail, the types, structural features, mechanism of formation, and bio-related applications of hybrid nanoflowers. The five major types of hybrid nanoflowers are discussed, i.e., copper-protein, calcium-protein, and manganese-protein hybrid nanoflowers, copper-DNA hybrid nanoflowers, and capsular hybrid nanoflowers. The structural features of these nanoflowers, such as size, shape, and protein ratio generally determine their applications. Thus, the specific characteristics of hybrid nanoflowers are summarized in this review. The interfacial mechanism of nanoflower formation is examined in three steps: first, combination of metal ion and organic matter; second, formation of petals; third, growth of nanoflowers. The explanations provided herein can be utilized in the development of innovative approaches for the synthesis of hybrid nanoflowers for prospective development of a plethora of hybrid nanoflowers. The future prospects of hybrid nanoflowers in the biotechnology industry, medicine, sensing, and catalysis are also discussed.

Nanostructures for peroxidases

Peroxidases are enzymes catalyzing redox reactions that cleave peroxides. Their active redox centers have heme, cysteine thiols, selenium, manganese, and other chemical moieties. Peroxidases and their mimetic systems have several technological and biomedical applications such as environment protection, energy production, bioremediation, sensors and immunoassays design, and drug delivery devices. The combination of peroxidases or systems with peroxidase-like activity with nanostructures such as nanoparticles, nanotubes, thin films, liposomes, micelles, nanoflowers, nanorods and others is often an efficient strategy to improve catalytic activity, targeting, and reusability.

Self-assembled enzyme-inorganic hybrid nanoflowers and their application to enzyme purification

We report a novel method to synthesize organic-inorganic nanoflowers for crude soybean peroxidase (SBP) purification. A hierarchical flower-like spherical structure with hundreds of nanopetals was self-assembled by using crude SBP as the organic component and Cu3(PO4)2·3H2O as the inorganic component. The structure of the hybrid nanoflowers was confirmed by Fourier-transform infrared spectroscopy, X-ray diffraction, and energy-dispersive X-ray spectroscopy, and the enzymatic activity of SBP embedded in the hybrid nanoflowers was evaluated using guaiacol as substrate. Compared with free crude SBP in solution, SBP embedded in hybrid nanoflowers exhibited enhanced enzymatic activity (∼446%). The hybrid nanoflowers also exhibited excellent reusability and reproducibility during cycle analysis. These results demonstrate that synthesis of hybrid nanoflowers is an effective enzyme purification strategy.

Functional microgels assisted tryptic digestion and quantification of cytochrome c through internal standard mass spectrometry

Quantitation of cytochrome c (Cyt c) in cell lysates through surface-assisted laser desorption/ionization mass spectrometry (SALDI-MS) using gold nanoparticles (Au NPs) as the matrix and GR-10 peptide as an internal standard has been demonstrated. To shorten digestion time, temperature sensitive microgels containing trypsin (TR) and Au NPs have been employed. As-prepared functional microgels (TR/Au NPs/MGs) allow digestion of Cyt c within 15 s under microwave irradiation. The internal standard SALDI-MS approach provides linearity (R(2) = 0.98) of MS signal ratio (I 1168.6/I 1067.6) of the tryptic digested peptide (m/z 1168.6) to GR-10 peptide (m/z 1067.6) against the concentration of Cyt c ranging from 25 to 200 nM, with a limit of detection (at a signal-to-noise ratio of 3) of 10 nM. This approach has been validated by the analysis of the lysates of HeLa cells, with an average concentration of 13.7 ± 3.5 μM for cytoplasmic Cyt c. Increased concentrations of Cyt c in the HeLa cells treated with etoposide (a commercial drug) or carbon dots (potential drug) have been revealed through this simple, sensitive, and rapid SALDI-MS approach, supporting the drugs induced Cyt c-mediated apoptosis of the cells. This study has shown that this internal standard SALDI-MS approach holds great potential for cell study.

Preparation of high efficiency and low carry-over immobilized enzymatic reactor with methacrylic acid-silica hybrid monolith as matrix for on-line protein digestion

In this work, a novel kind of organic-silica hybrid monolith based immobilized enzymatic reactor (IMER) was developed. The monolithic support was prepared by a single step "one-pot" strategy via the polycondensation of tetramethoxysilane and vinyltrimethoxysilane and in situ copolymerization of methacrylic acid and vinyl group on the precondensed siloxanes with ammonium persulfate as the thermal initiator. Subsequently, the monolith was activated by N-(3-dimethylaminopropyl) - N'-ethylcarbodiimide (EDC) and N-hydroxysuccinimide (NHS), followed by the modification of branched polyethylenimine (PEI) to improve the hydrophilicity. Finally, after activated by EDC and NHS, trypsin was covalently immobilized onto the monolithic support. The performance of such a microreactor was evaluated by the in sequence digestion of bovine serum albumin (BSA) and myoglobin, followed by MALDI-TOF-MS analysis. Compared to those obtained by traditional in-solution digestion, not only higher sequence coverages for BSA (74±1.4% vs. 59.5±2.7%, n=6) and myoglobin (93±3% vs. 81±4.5%, n=6) were obtained, but also the digestion time was shortened from 24h to 2.5 min, demonstrating the high digestion efficiency of such an IMER. The carry-over of these two proteins on the IMER was investigated, and peptides from BSA could not be found in mass spectrum of myoglobin digests, attributed to the good hydrophilicity of our developed monolithic support. Moreover, the dynamic concentration range for protein digestion was proved to be four orders of magnitude, and the IMER could endure at least 7-day consecutive usage. Furthermore, such an IMER was coupled with nano-RPLC-ESI/MS/MS for the analysis of extracted proteins from Escherichia coli. Compared to formerly reported silica hybrid monolith based IMER and the traditional in-solution counterpart, by our developed IMER, although the identified protein number was similar, the identified distinct peptide number was improved by 7% and 25% respectively, beneficial to improve the reliability of protein identification. The IMER was further online integrated with two-dimensional nano-HPLC-MS/MS system for the analysis of protein extracts from hepatocellular carcinoma (HCC) cells with low metastasis rate, and more than 3000 protein groups were identified, with only 46 proteins identified from the residues of the IMER. All these results demonstrated that such a hybrid monolith based IMER would be of great promise in the high throughput and high confidence proteome analysis.

Facile synthesis of enzyme-inorganic hybrid nanoflowers and its application as a colorimetric platform for visual detection of hydrogen peroxide and phenol

This study reports a facile approach for the synthesis of horseradish peroxidise (HRP)-inorganic hybrid nanoflowers by self-assembly of HRP and copper phosphate (Cu3(PO4)2·3H2O) in aqueous solution. Several reaction parameters that affect the formation of the hybrid nanoflowers were investigated and a hierarchical flowerlike spherical structure with hundreds of nanopetals was obtained under the optimum synthetic conditions. The enzymatic activity of HRP embedded in hybrid naonflowers was evaluated based on the principle of HRP catalyzing the oxidation of o-phenylenediamine (OPD) in the presence of hydrogen peroxide (H2O2). The results showed that 506% enhancement of enzymatic activity in the hybrid nanoflowers could be achieved compared with the free HRP in solution. Taking advantages of the structural feature with catalytic property, a nanoflower-based colorimetric platform was newly designed and applied for fast and sensitive visual detection of H2O2 and phenol. The limits of detection (LODs) for H2O2 and phenol were as low as 0.5 μM and 1.0 μM by the naked-eye visualization, which meet the requirements of detection of both analytes in clinical diagnosis and environmental water. The proposed method has been successfully applied to the analysis of low-level H2O2 in spiked human serum and phenol in sewage, respectively. The recoveries for all the determinations were higher than 92.6%. In addition, the hybrid nanoflowers exhibited excellent reusability and reproducibility in cycle analysis. These primary results demonstrate that the hybrid nanoflowers have a great potential for applications in biomedical and environmental chemistry.

Uncovering immobilized trypsin digestion features from large-scale proteome data generated by high-resolution mass spectrometry

Immobilized trypsin produces very fast protein digestion, which is attractive for application to high throughput bottom-up proteomics. While there is a rich literature on the preparation of immobilized trypsin, there are very few studies that investigate its application to complex proteomic samples. In this work, we compared solution-phase trypsin with trypsin immobilized on magnetic microspheres for digestion of two complex proteomes, Escherichia coli and the MCF7 cell line. The digests were separated by HPLC, and detected with a Q-Exactive mass spectrometer, which generated high resolution and high quality parent- and fragment-ion mass spectra. The data were analyzed using MaxQuant. We make several conclusions about the features of immobilized trypsin digestion of complex proteomes. First, both immobilized and solution-phase trypsin generate peptides that sample the same protein pool. Second, immobilized trypsin can digest complex proteomes two orders of magnitude faster than solution-phase trypsin while retaining similar numbers of protein identifications and proteome depth. Digestion using immobilized trypsin for 5-min produces a similar number of missed cleavages as solution-based trypsin digestion for 4-h; digestion using immobilized trypsin for 20-min produces a similar number of missed cleavages as solution-based trypsin digestion for 12-h. Third, immobilized trypsin produces quantitatively reproducible digestion of complex proteomes. Finally, there is small but measurable loss of peptide due to non-specific adsorption to the immobilization matrix. This adsorption generates a bias against detection of basic peptides.

Facile synthesis of enzyme–inorganic hybrid nanoflowers and their application as an immobilized trypsin reactor for highly efficient protein digestion

Hybrid nanoflowers were synthesized by a novel approach. The nanoflowers exhibited an enhanced enzymatic activity and can be used as an immobilized enzyme reactor (IMER) for highly efficient protein digestion.

A new nanobiocatalytic system based on allosteric effect with dramatically enhanced enzymatic performance

We report a rational design of CaHPO(4)-α-amylase hybrid nanobiocatalytic system based on allosteric effect and an explanation of the increase in catalytic activity when certain enzymes are immobilized in specific nanomaterials. Employing a calcification approach in aqueous solutions, we acquired such new nanobiocatalytic systems with three different morphologies, i.e., nanoflowers, nanoplates, and parallel hexahedrons. Through studying enzymatic performance of these systems and free α-amylase with/without Ca(2+), we demonstrated how two factors, allosteric regulation and morphology of the as-synthesized nanostructures, predominantly influence enzymatic activity. Benefiting from both the allosteric modulation and its hierarchical structure, CaHPO(4)-α-amylase hybrid nanoflowers exhibited dramatically enhanced enzymatic activity. As a bonus, the new system we devised was found to enjoy higher stability and durability than free α-amylase plus Ca(2+).

Recent advances in preparation and application of hybrid organic-silica monolithic capillary columns

Hybrid organic-silica monolithic columns, regarded as a second generation of silica-based monoliths, have received much interest due to their unique properties over the pure silica-based monoliths. This review mainly focuses on development in the fields of preparation of hybrid monolithic columns in a capillary and their application for CEC and capillary liquid chromatography separation, as well as for sample pretreatment of solid-phase microextraction and immobilized enzyme reactor since July 2010. The preparation approaches are comprehensively summarized with three routes: (i) general sol-gel process using trialkoxysilanes and tetraalkoxysilanes as coprecursors; (ii) "one-pot" process of alkoxysilanes and organic monomers concomitantly proceeding sol-gel chemistry and free radical polymerization; and (iii) other polymerization approaches of organic monomers containing silanes. The modification of hybrid monoliths containing reactive groups to acquire the desired surface functionality is also described.

Limited proteolysis via millisecond digestions in protease-modified membranes

Sequential adsorption of poly(styrene sulfonate) (PSS) and proteases in porous nylon yields enzymatic membrane reactors for limited protein digestion. Although a high local enzyme density (~30 mg/cm(3)) and small pore diameters in the membrane lead to digestion in <1 s, the low membrane thickness (170 μm) affords control over residence times at the millisecond level to limit digestion. Apomyoglobin digestion demonstrates that peptide lengths increase as the residence time in the membrane decreases. Moreover, electron transfer dissociation (ETD) tandem mass spectrometry (MS/MS) on a large myoglobin proteolytic peptide (8 kDa) provides a resolution of 1-2 amino acids. Under denaturing conditions, limited membrane digestion of bovine serum albumin (BSA) and subsequent ESI-Orbitrap MS analysis reveal large peptides (3-10 kDa) that increase the sequence coverage from 53% (2 s digestion) to 82% (0.05 s digestion). With this approach, we also performed membrane-based limited proteolysis of a large Arabidopsis GTPase, Root Hair Defective 3 (RHD3) and showed suitable probing for labile regions near the C-terminus to suggest what protein reconstruction might make RHD3 more suitable for crystallization.

Protein-inorganic hybrid nanoflowers

Flower-shaped inorganic nanocrystals have been used for applications in catalysis and analytical science, but so far there have been no reports of 'nanoflowers' made of organic components. Here, we report a method for creating hybrid organic-inorganic nanoflowers using copper (II) ions as the inorganic component and various proteins as the organic component. The protein molecules form complexes with the copper ions, and these complexes become nucleation sites for primary crystals of copper phosphate. Interaction between the protein and copper ions then leads to the growth of micrometre-sized particles that have nanoscale features and that are shaped like flower petals. When an enzyme is used as the protein component of the hybrid nanoflower, it exhibits enhanced enzymatic activity and stability compared with the free enzyme. This is attributed to the high surface area and confinement of the enzymes in the nanoflowers.

High efficiency and quantitatively reproducible protein digestion by trypsin-immobilized magnetic microspheres

Aldehyde- and NHS-activated magnetic microspheres were used to immobilize trypsin (CHO-trypsin and NHS-trypsin), and their performance for protein digestion was evaluated by reversed phase liquid chromatography-electrospray ionization-tandem mass spectrometry using an LTQ Orbitrap Velos instrument. NHS-trypsin provided greater sequence coverage and identified more peptides for the digestion of bovine serum albumin. A 1-min digestion at room temperature using the immobilized trypsin also identified more peptides (96±6 vs. 48±1) and produced higher sequence coverage (90±2% vs. 75±2%) than traditional free trypsin digestion for 12h at 37 °C. Analysis of 15 nM (0.001 mg/mL) BSA digested by NHS-trypsin in 1 min at room temperature consistently yielded one detected peptide; 150 nM BSA generated 22 peptides. Peptide intensity and protein spectral count were used to evaluate the run-to-run digestion reproducibility of NHS-trypsin with a three-protein-mixture. Three high intensity peptides for each protein generated intensity ratios from 0.70 to 1.09 and spectral count ratios from 0.78 to 1.18. Finally, RAW 264.7 cell lysates were digested by NHS-trypsin for 10 min and 30 min at room temperature, 604 and 697 protein groups, respectively, were identified by RPLC-ESI-MS/MS, with a peptide false discovery rate of less than 1%. Digestion by solution phase trypsin for 12h at 37 °C resulted in identification of 878 protein groups.

Capillary monolithic bioreactor of immobilized snake venom phosphodiesterase for mass spectrometry based oligodeoxynucleotide sequencing

A capillary monolithic bioreactor of snake venom phosphodiesterase (SVP) was constructed to generate different single-nucleotide mass ladders of oligodeoxynucleotides for mass spectrometry (MS)-based sequencing by immobilization. The immobilization of SVP in the porous silica monolith significantly enhances its stability for prolonged and repeated applications. The constructed capillary bioreactor has the advantages of handling (sub)microliter DNA samples and having good permeability. Benefiting from its good permeability, DNA solutions can be directly injected into the sequential digestion bioreactor simply by hand pushing or a low-pressure microinjection pump. Moreover, the immobilization of SVP facilitates the elimination or repression of the metal adducts of oligodeoxynucleotides, improving the analytical performance of MS sequencing. By the application of capillary bioreactor of immobilized SVP, the sequence-specific modification of single-stranded oligodeoxynucleotide induced by a ubiquitous pollutant acrolein (Acr) was identified, demonstrating its promising applications in identification of sequence-specific damage, which may further our understanding of DNA damage caused mutagenesis.

Controlled structure and properties of silicate nanoparticle networks for incorporation of biosystem components

Inorganic nanoparticles are of technological interest in many fields. We created silicate nanoparticle hydrogels that effectively incorporated biomolecules that are unstable and involved in complicated reactions. The size of the silicate nanoparticles strongly affected both the physical characteristics of the resulting hydrogel and the activity of biomolecules incorporated within the hydrogel. We used high-resolution transmission electron microscopy (TEM) to analyze in detail the hydrogel network patterns formed by the silicate nanoparticles. We obtained clear nanostructured images of biomolecule-nanoparticle composite hydrogels. The TEM images also showed that larger silicate nanoparticles (22 nm) formed more loosely associated silicate networks than did smaller silicate nanoparticles (7 nm). The loosely associated networks formed from larger silicate nanoparticles might facilitate substrate diffusion through the network, thus promoting the observed increased activity of the entrapped biomolecules. This doubled the activity of the incorporated biosystems compared with that of biosystems prepared by our own previously reported method. We propose a reaction scheme to explain the formation of the silicate nanoparticle networks. The successful incorporation of biomolecules into the nanoparticle hydrogels, along with the high level of activity exhibited by the biomolecules required for complicated reaction within the gels, demonstrates the nanocomposites' potential for use in medical applications.

Rapid and enhanced proteolytic digestion using electric-field-oriented enzyme reactor

We have created a novel enzyme reactor using electric field-mediated orientation and immobilization of proteolytic enzymes (trypsin/chymotrypsin) on biocompatible PVDF membranes in a continuous flow-through chamber. Using less than 5min, this reactor in various enzyme combinations can produce enhanced rapid digestion for standardized prototypic proteins, hydrophilic proteins and hydrophobic transmembrane proteins when compared to in-solution techniques. With improved digestive efficiency, our reactor improved the overall functional analysis of lipid raft proteomes by identifying more closely functionally linked proteins and elucidated a richer set of biological processes and pathways linked to the proteins than traditional in-solution methods.

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.

Rapid and efficient proteolysis for proteomic analysis by protease-immobilized microreactor

Proteolysis is an important part of protein identification in proteomics analysis. The conventional method of in-solution digestion of proteins is time-consuming and has limited sensitivity. In this study, trypsin- or alpha-chymotrypsin-immobilized microreactors prepared by a microfluidics-based enzyme-immobilization technique were studied for rapid sample preparation in proteomic analysis. The kinetic studies for hydrolysis of substrate by microreactors revealed that immobilized proteases had higher hydrolytic efficiency than those performed by in-solution digestion. The performance of the microreactors was evaluated by digesting cytochrome c and BSA. Protein digestion was achieved within a short period of time (approximately 5 min) at 30 degrees C without any complicated reduction and alkylation procedures. The efficiency of digestion by trypsin-immobilized reactor was evaluated by analyzing the sequence coverage, which was 47 and 12% for cytochrome c and BSA, respectively. These values were higher than those performed by in-solution digestion. Besides, because of higher stability against high concentration of denaturant, the microreactors can be useful for immediate digestion of the denaturated protein. In the present study, we propose a protease-immobilized microreactor digestion method, which can utilize as a proteome technique for biological and clinical research.