Size-selective proteolysis on mesoporous silica-based trypsin nanoreactor for low-MW proteome analysis

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.

Post-Synthetic Surface Modification of Metal-Organic Frameworks and Their Potential Applications

Metal-organic frameworks (MOFs) are porous hybrid materials with countless potential applications. Most of these rely on their porous structure, tunable composition, and the possibility of incorporating and expanding their functions. Although functionalization of the inner surface of MOF crystals has received considerable attention in recent years, methods to functionalize selectively the outer crystal surface of MOFs are developed to a lesser extent, despite their importance. This article summarizes different types of post-synthetic modifications and possible applications of modified materials such as: catalysis, adsorption, drug delivery, mixed matrix membranes, and stabilization of porous liquids.

Mesoporous Silica as Sorbents and Enzymatic Nanoreactors for Microbial Membrane Proteomics

The membrane proteins of microbes are at the forefront of host and parasite interactions. Having a general view of the functions of microbial membrane proteins is vital for many biomedical studies on microbiota. Nevertheless, due to the strong hydrophobicity and low concentration of membrane proteins, it is hard to efficiently enrich and digest the proteins for mass spectrometry analysis. Herein, we design an enzymatic nanoreactor for the digestion of membrane proteins using methylated well-ordered hexagonal mesoporous silica (Met-SBA-15). The material can efficiently extract hydrophobic membrane proteins and host the proteolysis in nanopores. The performance of the enzymatic nanoreactor is first demonstrated using standard hydrophobic proteins and then validated using membrane proteins extracted from Escherichia coli (E. coli) or a mixed bacterial sample of eight strains. Using the nanoreactor, 431 membrane proteins are identified from E. coli, accounting for 38.5% of all membrane proteins of the species, which is much more than that by the widely used in-solution digestion protocol. From the mixed bacterial sample of eight strains, 1395 membrane proteins are identified using the nanoreactor. On the contrary, the traditional in-solution proteolysis workflow only leads to the identification of 477 membrane proteins, demonstrating that the Met-SBA-15 can be offered as an excellent tool for microbial membrane proteome research and is expected to be used in human microbiota studies, e.g. host-microbe interactions.

New insights into the structure-performance relationships of mesoporous materials in analytical science

Mesoporous materials are ideal carriers for guest molecules and they have been widely used in analytical science. The unique mesoporous structure provides special properties including large specific surface area, tunable pore size, and excellent pore connectivity. The structural properties of mesoporous materials have been largely made use of to improve the performance of analytical methods. For instance, the large specific surface area of mesoporous materials can provide abundant active sites and increase the probability of contact between analytes and active sites to produce stronger signals, thus leading to the improvement of detection sensitivity. The connections between analytical performances and the structural properties of mesoporous materials have not been discussed previously. Understanding the "structure-performance relationship" is highly important for the development of analytical methods with excellent performance based on mesoporous materials. In this review, we discuss the structural properties of mesoporous materials that can be optimized to improve the analytical performance. The discussion is divided into five sections according to the analytical performances: (i) selectivity-related structural properties, (ii) sensitivity-related structural properties, (iii) response time-related structural properties, (iv) stability-related structural properties, and (v) recovery time-related structural properties.

Specific enrichment combined with highly efficient solid-phase tagging for the sensitive detection of heparin based on boronic acid-functionalized mesoporous silica nanospheres

A combined specific enrichment and highly efficient solid-phase tagging approach is presented for heparin detection using boronic acid-functionalized mesoporous silica nanospheres as extraction sorbents and nanoscale reactors. It exhibits a faster reaction time (only 6 min), higher tagging-product purity and lower applicable sample concentration compared with liquid-phase tagging.

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.

Fast solid-phase extraction of N-linked glycopeptides by amine-functionalized mesoporous silica nanoparticles

For the first time, mesoporous material has been introduced into N-glycoproteome extraction based on a reductive amination reaction, which greatly enhanced the enrichment efficiency and deglycosylation efficiency.

A new sample preparation method for the absolute quantitation of a target proteome using 18O labeling combined with multiple reaction monitoring mass spectrometry

A new sample preparation method for target proteome absolute quantitation using ¹⁸O labeling-MRM MS.

Nanostructured porous Si optical biosensors: effect of thermal oxidation on their performance and properties

The influence of thermal oxidation conditions on the performance of porous Si optical biosensors used for label-free and real-time monitoring of enzymatic activity is studied. We compare three oxidation temperatures (400, 600, and 800 °C) and their effect on the enzyme immobilization efficiency and the intrinsic stability of the resulting oxidized porous Si (PSiO2), Fabry-Pérot thin films. Importantly, we show that the thermal oxidation profoundly affects the biosensing performance in terms of greater optical sensitivity, by monitoring the catalytic activity of horseradish peroxidase and trypsin-immobilized PSiO2. Despite the significant decrease in porous volume and specific surface area (confirmed by nitrogen gas adsorption-desorption studies) with elevating the oxidation temperature, higher content and surface coverage of the immobilized enzymes is attained. This in turn leads to greater optical stability and sensitivity of PSiO2 nanostructures. Specifically, films produced at 800 °C exhibit stable optical readout in aqueous buffers combined with superior biosensing performance. Thus, by proper control of the oxide layer formation, we can eliminate the aging effect, thus achieving efficient immobilization of different biomolecules, optical signal stability, and sensitivity.

Influence of surface-imprinted nanoparticles on trypsin activity

Here, the modulation of enzyme activity is presented by protein-imprinted nanoparticles produced using a solid-phase approach. Using trypsin as target, binding of the nanoparticles to the enzyme results in its inhibition or in stabilization, depending on the orientation of the immobilized enzyme used during imprinting.

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.

Applications of nanomaterials in mass spectrometry analysis

Mass spectrometry (MS) based analyses have received intense research interest in a series of rapidly developing disciplines. Although current MS techniques have enjoyed great successes, several key challenges still remain in practical applications, especially for the detection of biomolecules in biological systems. The use of nanomaterials in MS based analysis provides a promising approach due to their unique physical and chemical properties. In this review, nanomaterials with different compositions and nanostructures employed in MS applications are summarised and classified by their functions. Such an integrated and wide reaching review will provide a comprehensive handbook to researchers with various backgrounds working in this exciting interdisciplinary area.

Multiplex acute leukemia cytosensing using multifunctional hybrid electrochemical nanoprobes at a hierarchically nanoarchitectured electrode interface

We have developed a robust, nanobiotechnology-based electrochemical cytosensing approach with high sensitivity, selectivity, and reproducibility toward the simultaneous multiplex detection and classification of both acute myeloid leukemia and acute lymphocytic leukemia cells. The construction of the electrochemical cytosensor involves the hierarchical assembly of dual aptamer-functionalized, multilayered graphene-Au nanoparticle electrode interface and the utilization of hybrid electrochemical nanoprobes co-functionalized with redox tags, horseradish peroxidase, and cell-targeting nucleic acid aptamers. The hybrid nanoprobes are multifunctional, capable of specifically targeting the cells of interest, amplifying the electrochemical signals, and generating distinguishable signals for multiplex cytosensing. The as-assembled electrode interface not only greatly facilitates the interfacial electron transfer process due to its high conductivity and surface area but also exhibits excellent biocompatibility and specificity for cell recognition and adhesion. A superstructured sandwich-type sensor geometry is adopted for electrochemical cytosensing, with the cells of interest sandwiched between the nanoprobes and the electrode interface. Such an electrochemical sensing strategy allows for ultrasensitive, multiplex acute leukemia cytosensing with a detection limit as low as ~350 cells per mL and a wide linear response range from 5 × 10(2) to 1 × 10(7) cells per mL for HL-60 and CEM cells, with minimal cross-reactivity and interference from non-targeting cells. This electrochemical cytosensing approach holds great promise as a new point-of-care diagnostic tool for early detection and classification of human acute leukemia and may be readily expanded to multiplex cytosensing of other cancer cells.

Homogeneous surface oxidation of organosilicates by controlled combustion of adsorbed fuels: a facile method for low-temperature processing

We have developed a method for the oxidation of organosilicate materials at temperatures considerably lower than those typically required for uncatalyzed oxidation. The process utilizes a combustible fuel delivered to the surface in an oxidizing environment to locally oxidize materials with carbon-silicon bonds. It also provides a level of control that cannot be achieved through standard high-energy top-to-bottom oxidative procedures such as UV-ozone and O2 plasmas. While the latter processes attack the outer interface, local oxidation can be achieved using our process by manipulating the distribution of the combustible fuel. We use this technique to generate oxidized porous organosilicate films with either a sharp oxidation front or uniform oxidation where the relative carbon content can be controlled through the film thickness depending on processing conditions. Further, we show that this process can also be used to seal bulk interconnected microporosity in films (<1 nm) without substantially changing the refractive index of the material. For both the nominally dense and porous films, the surface oxidation is accompanied by an increase in the Young's modulus and the oxidized films can be readily functionalized using standard silane chemistry to provide a variety of chemical functionalities.

Photoluminescent enzymatic sensor based on nanoporous anodic alumina

Herein, we present a smart enzymatic sensor based on nanoporous anodic alumina (NAA) and its photoluminescence (PL) in the UV-visible range. The as-produced structure of NAA is functionalized and activated in order to perform the enzyme immobilization in a controlled manner. The whole process is monitored through the PL spectrum and each stage is characterized by an exclusive barcode, which is associated with the PL oscillations. This characteristic property allows us to calculate the change in the effective optical thickness that takes place after each stage. This makes it possible to accurately detect and quantify the immobilized enzyme within the NAA structure. Finally, the NAA geometry (i.e., the pore length and its diameter) is optimized to improve the enzyme immobilization and its detection inside the pores. This enzymatic sensor can give quick and accurate measurements of enzyme levels, what is crucial in clinical enzymology to prevent and detect diseases at their primary stage.

Periodic mesoporous organosilica as a multifunctional nanodevice for large-scale characterization of membrane proteins

A versatile protocol has been developed for large-scale characterization of hydrophobic membrane proteins based on the periodic mesoporous organosilica (PMO) acting as both an extractor for hydrophobic substrate capture and a nanoreactor for efficient in situ digestion. With introduction of organic groups in the pore frameworks and the presence of hydrophilic silanol groups on the surface, PMO can be well-dispersed into not only an organic solution to concentrate the dissolved membrane proteins but also an aqueous solution containing enzymes for sequential rapid proteolysis in the nanopores. The unique amphiphilic property of PMO ensures a facile switch in different solutions to realize the processes of substrate dissolution, enrichment, and digestion effectively. Furthermore, this novel PMO-assisted protocol has been successfully applied for identification of complex membrane proteins extracted from mouse liver as proof of general applicability.

In mesopore protein digestion: a new forthcoming strategy in proteomics

The conventional protocols for in solution or in gel protein digestion require many steps and long reaction times. The use of trypsin immobilized onto solid supports has recently captured the attention of many research groups, because these systems can speed-up protein digestion significantly. The utilization of new materials such as mesoporous silica as supports, in which enzyme and substrate are dramatically concentrated and confined in the nanospace, offers new opportunities to reduce the complexity of proteomics workflows. An overview of the procedures for in situ proteolysis of single proteins or complex protein mixtures is reported, with a special focus on porous materials used as catalysts. The challenging efforts for designing such systems aimed at mimicking the biochemistry of living cells are reviewed. Potentials, limitations and challenges of this branch of enzyme catalysis, which we indicate as in mesopore digestion, are discussed, in relation to its suitability for high-speed and high-throughput proteomics.