Efficient Tryptic Proteolysis Accelerated by Laser Radiation for Peptide Mapping in Proteome Analysis

Nanoproteases: Alternatives to Natural Protease for Biotechnological Applications

Some nanomaterials with intrinsic protease-like activity have the advantages of good stability, biosafety, low price, large-scale preparation and unique property of nanomaterials, which are promising alternatives for natural proteases in various applications. An especial term, "nanoprotease", has been coined to stress the intrinsic proteolytic property of these nanomaterials. As a new generation of artificial proteases, they have become a burgeoning field, attracting many researchers to design and synthesize high performance nanoproteases. In this review, we summarize recent progress on all types of nanoproteases with regard of their activity, mechanism and application and introduce a new and effective strategy for engineering high-performance nanoproteases. In addition, we discuss the challenges and opportunities of nanoprotease research in the future.

Metal Organic Framework Cubosomes

We demonstrate a general strategy for the synthesis of ordered bicontinuous-structured metal organic frameworks (MOFs) by using polymer cubosomes (PCs) with a double primitive structure (Im 3 ‾ ${\bar{3}}$ m symmetry) as the template. The filling of MOF precursors in the open channel of PCs, followed by their coordination and removal of the template, generates MOF cubosomes with a single primitive topology (Pm 3 ‾ ${\bar{3}}$ m) and average mesopore diameters of 60-65 nm. Mechanism study reveals that the formation of ZIF-8 cubosomes undergoes a new MOF growth process, which involves the formation of individual MOF seeds in the template, their growth and eventual fusion into the cubosomes. Their growth kinetics follows the Avrami equation with an Avrami exponent of n=3 and a growth rate of k=1.33×10^-4 , indicating their fast 3D heterogeneous growth mode. Serving as a bioreactor, the ZIF-8 cubosomes show high loading of trypsin enzyme, leading to a high catalytic activity in the proteolysis of bovine serum albumin.

Synthesis and Characterization of Hypercoordinated Silicon Anions: Catching Intermediates of Lewis Base Catalysis

Anionic hypercoordinated silicates with weak donors were proposed as key intermediates in numerous silicon‐based reactions. However, their short‐lived nature rendered even spectroscopic observations highly challenging. Here, we characterize hypercoordinated silicon anions, including the first bromido‐, iodido‐, formato‐, acetato‐, triflato‐ and sulfato‐silicates. This is enabled by a new, donor‐free polymeric form of Lewis superacidic bis(perchlorocatecholato)silane 1. Spectroscopic, structural, and computational insights allow a reassessment of Gutmann's empirical rules for the role of silicon hypercoordination in synthesis and catalysis. The electronic perturbations of 1 exerted on the bound anions indicate pronounced substrate activation.

Peptide and protein assays using customizable bio-affinity arrays combined with ambient ionization mass spectrometry

High-throughput identification and quantification of protein/peptide biomarkers from biofluids in a label-free manner is achieved by interfacing bio-affinity arrays (BAAs) with nano-electrospray desorption electrospray ionization mass spectrometry (nano-DESI-MS). A wide spectrum of proteins and peptides ranging from phosphopeptides to cis-diol biomolecules as well as thrombin can be rapidly extracted via arbitrarily predefined affinity interactions including coordination chemistry, covalent bonding, and biological recognition. An integrated MS platform allows continuous interrogation. Profiling and quantitation of dysregulated phosphopeptides from small-volume (∼5 μL) serum samples has been successfully demonstrated. As a front-end device adapted to any mass spectrometer, this MS platform might hold much promise in protein/peptide analysis in point-of-care (POC) diagnostics and clinical applications.

Customizable bio-affinity arrays were interfaced with ambient ionization mass spectrometry for high-throughput assays of protein/peptide biomarkers in biofluids.

A Novel Combined Microstrip Resonator/Nanospray Ionization Source for Microwave-Assisted Trypsin Digestion of Proteins

Enzymatic digestion of proteins is a critical step in bottom-up and middle-down proteomics. Here, we demonstrate a method for decreasing the time required for proteolytic digestion of proteins from multiple hours to minutes by using an in-line microstrip cavity for programmed microwave heating. When a nanospray emitter tip, containing a digestion sample, is exposed to a region of highly focused microwave field, the rate of proteolytic digestion is enhanced and the time required for digestion greatly decreased. The design is advantageous for mass spectrometry because the solution-based digestion can then be directly sprayed from a nanoelectrospray tip emitter, decreasing sample transfer loss and allowing the system to be used in a flow-through proteolytic workflow. Microwave-assisted digestion using this method is evaluated against standard overnight digestion protocols using a variety of proteins, evaluating sequence coverage and observed peptide location, digestion rate, and overall efficacy. The influence of applied microwave power is investigated, and enzymatic kinetic parameters are evaluated to estimate temperature within the microreactor. Finally, the modulation of the proteolytic digestion of proteins based upon the modulation of applied microwave power is demonstrated on a time scale of seconds in a flow-through system.

A novel protocol for enzymatic digestion based on covalent binding by protein immobilization

The process of protein digestion is a critical step for successful protein identification in proteomic analysis. Many efforts have been dedicated to enhancing the digestion efficiency for sufficient digestion. Among these approaches, protein complete denaturation with denaturants is a common process for better digestion. However, the removal of denaturants was tedious or would cause protein loss and other problems. In this work, a feasible digestion approach, immobilized protein digestion (IPD), based on covalent binding has been developed. Proteins can be completely denatured and immobilized on the surface of functional materials by covalent binding to form a monolayer. Subsequently, varieties of denaturants or contaminants would be removed thoroughly by washing. To achieve fast immobilization and high digestion efficiency, different functional materials and denaturants were selected. Compared with traditional in-solution digestion, the method achieved a prominent increase in identified peptides numbers and sequence coverage of proteins. Data analysis also showed that covalent binding could evidently decrease enzymatic missed cleavage for various protein sequences. Furthermore, possible peptide losses due to covalent binding were also investigated. Also, it has been proved to be efficient for complex biological sample digestion. Graphical abstract Workflow of the IPD method, including protein denaturation, immobilization, digestion, and identification.

Laser-assisted proteolysis for accelerating and enhancing protein N-termini analysis

RATIONALE

Targeted analysis of protein N-termini contributes to elucidating the starting sites and post-translational modifications of mature protein N-termini. Tryptic digestion is important in protein N-termini analysis, as well as in conventional bottom-up proteomics strategies. It is essential to explore a new proteolysis method for the enhancement of protein N-termini analysis.

METHODS

Laser-assisted proteolysis was compared with conventional overnight proteolysis. Four standard proteins were studied as models and analyzed by matrix-assisted laser desorption/ionization time-of-flight mass spectrometry. 100 pg of synthesized peptide was used as internal standard for comparison of N-terminus intensity. Laser-assisted proteolysis was demonstrated to accelerate and enhance N-termini analysis. A complex mouse liver proteome sample was used to validate the effect of laser-assisted proteolysis.

RESULTS

According to online database search, the number of matched peptides of four model proteins and the sequence coverage were comparable between the two proteolysis methods. Laser exposure time (40 s) could enhance the release of the N-terminus in model proteins. The number of identified N-termini in mouse liver was improved by 28.3% in the laser-assisted digest, compared to the conventional overnight digest. The time cost for digestion was shortened from overnight to 40 s.

CONCLUSIONS

Laser-assisted proteolysis was demonstrated to accelerate proteolysis and enhance N-termini analysis. If laser-assisted proteolysis was integrated into protein N-termini targeted methods, the performance of those methods should be improved. Copyright © 2016 John Wiley & Sons, Ltd.

Ultrasensitive Proteome Profiling for 100 Living Cells by Direct Cell Injection, Online Digestion and Nano-LC-MS/MS Analysis

Single-cell proteome analysis has always been an exciting goal because it provides crucial information about cellular heterogeneity and dynamic change. Here we presented an integrated proteome analysis device (iPAD) for 100 living cells (iPAD-100) that might be suitable for single-cell analysis. Once cells were cultured, the iPAD-100 could be applied to inject 100 living cells, to transform the living cells into peptides, and to produce protein identification results with total automation. Due to the major obstacle for detection limit of mass spectrometry, we applied the iPAD-100 to analyze the proteome of 100 cells. In total, 813 proteins were identified in a DLD-cell proteome by three duplicate runs. Gene Ontology analysis revealed that proteins from different cellular compartments were well-represented, including membrane proteins. The iPAD-100 greatly simplified the sampling process, reduced sample loss, and prevented contamination. As a result, proteins whose copy numbers were lower than 1000 were identified from 100-cell samples with the iPAD-100, showing that a detection limit of 200 zmol was achieved. With increased sensitivity of mass spectrometry, the iPAD-100 may be able to reveal bountiful proteome information from a single cell in the near future.

Microfluidic Superheating for Peptide Sequence Elucidation

Herein, we introduce microfluidic superheating as a new method for peptide fragmentation prior to mass spectrometric analysis. The superheating conditions were found to be stable up to 240 °C for more than 30 min without elevated pressure or boiling of the aqueous sample. As proof of principle, we exposed the peptides ACTH1-10 and OVA257-264 to various superheating conditions, causing different degrees of decomposition. Optimized superheating conditions resulted in the entire peptide ladder sequence of the y-ions, allowing the amino acid sequence to be deduced from a single-stage mass spectrum. Thus, obtaining information in the same quality as from tandem mass spectrometry can be achieved by a single superheating step.

Construction of a high-performance magnetic enzyme nanosystem for rapid tryptic digestion

A magnetic enzyme nanosystem have been designed and constructed by a polydopamine (PDA)-modification strategy. The magnetic enzyme nanosystem has well defined core-shell structure and a relatively high saturation magnetization (Ms) value of 48.3 emu g(-1). The magnetic enzyme system can realize rapid, efficient and reusable tryptic digestion of proteins by taking advantage of its magnetic core and biofunctional shell. Various standard proteins (e.g. cytochrome C (Cyt-C), myoglobin (MYO) and bovine serum albumin (BSA)) have been used to evaluate the effectiveness of the magnetic enzyme nanosystem. The results show that the magnetic enzyme nanosystem can digest the proteins in 30 minutes, and the results are comparable to conventional 12 hours in-solution digestion. Furthermore, the magnetic enzyme nanosystem is also effective in the digestion of low-concentration proteins, even at as low as 5 ng μL(-1) substrate concentration. Importantly, the system can be reused several times, and has excellent stability for storage. Therefore, this work will be highly beneficial for the rapid digestion and identification of proteins in future proteomics.

Highly sensitive thrombin detection by matrix assisted laser desorption ionization-time of flight mass spectrometry with aptamer functionalized core-shell Fe₃O₄@C@Au magnetic microspheres

Here, we describe a sensitive and specific method for thrombin detection with aptamer functionalized core-shell Fe(3)O(4)@C@Au magnetic microspheres (Au-MMPs). Firstly, Au-MMPs were synthesized through surface adsorption of gold nanoparticles onto PDDA functionalized Fe(3)O(4)@C magnetic microspheres. Then, the as-synthesized Au-MMPs were developed as new substrate for immobilization of thrombin binding aptamer (TBA) through easy formation of Au-S bond. After that, the prepared aptamer functionalized Au-MMPs (TBA@Au-MMPs) were used as effective magnetic absorbent to extract trace level of thrombin from dilute solutions. Finally, enriched thrombin was digested by trypsin and analyzed by matrix assisted laser desorption ionization-time of flight (MALDI-TOF) mass spectrometry. Taking advantage of the efficient affinity extraction ability of our TBA@Au-MMPs and the sensitive mass readout of MALDI-TOF, highly sensitive detection of thrombin was achieved. The limit of detection was as low as 18 fmol, corresponding to 0.36 nM thrombin in 50 μL original solution. Linear relation was observed within a concentration range from 0.5 nM to 10nM with linear correlation R(2)=0.998. Other proteins including human serum albumin (HSA), Ig G, transferrin, oval albumin (OVA) and fetal calf serum did not interfere with thrombin detection. This simple method holds great potential for analyzing, sensing, purification and preconcentration of proteins in biological fluids.

Highly efficient proteolysis accelerated by electromagnetic waves for Peptide mapping

Proteomics will contribute greatly to the understanding of gene functions in the post-genomic era. In proteome research, protein digestion is a key procedure prior to mass spectrometry identification. During the past decade, a variety of electromagnetic waves have been employed to accelerate proteolysis. This review focuses on the recent advances and the key strategies of these novel proteolysis approaches for digesting and identifying proteins. The subjects covered include microwave-accelerated protein digestion, infrared-assisted proteolysis, ultraviolet-enhanced protein digestion, laser-assisted proteolysis, and future prospects. It is expected that these novel proteolysis strategies accelerated by various electromagnetic waves will become powerful tools in proteome research and will find wide applications in high throughput protein digestion and identification.