Pronase E-Based Generation of Fluorescent Peptide Fragments: Tracking Intracellular Peptide Fate in Single Cells

Organophosphate esters inhibit enzymatic proteolysis through non-covalent interactions

Enzymatic proteolysis is the key process to produce bioavailable nitrogen in natural terrestrial and aquatic ecosystems for microorganisms and plants. However, little is known on how protein degradation is influenced by organic contaminants. As we known, the overuse of organophosphate esters (OPEs) has caused serious pollution in soil, water, and sediment. Thereby we studied the effect of OPEs on the proteolysis of protein GB1 in aqueous system at neutral pH, and explored the underlying molecular mechanism. Colorimetric ninhydrin methods and SDS-PAGE results revealed that OPEs inhibited the enzymatic hydrolysis of protein GB1. Based on fluorescence quenching experiments, the binding constant (LogKA) were found in order: 6.16 (dibutyl phosphate) > 5.11 (diethyl phosphate) > 1.78 (tributyl phosphate) > 0.876 (triethyl phosphate), proving the interactions between OPEs and protein GB1. Further spectroscopic experiments and molecular docking simulations showed that OPEs could entered the pocket structure of GB1 and induced secondary structural changes and protein folding through non-covalent interactions dominated by hydrogen bonding and van der Waals forces. In addition, organophosphate diesters (di-OPEs) and long-chain OPEs had stronger affinity to GB1, due to the more negative and denser electrostatic surface potential distributions. The deformation of proteins hindered the contact between their active sites and enzymes, leading to the inhibition of GB1 hydrolysis. This study deepened our understanding of the effect of OPEs on protein transformation and degradation, which could further influence the ecological functions and nutrient cycling.

Cystine-cored diphenylalanine appended peptide-based self-assembled fluorescent nanostructures direct redox-responsive drug delivery

Fabrication of stimuli-responsive superstructure capable of delivering chemotherapeutics directly to the cancer cell by sparing healthy cells is crucial. Herein, we developed redox-responsive hollow spherical assemblies through self-assembly of disulfide-linked cysteine-diphenylalanine (SN). These fluorescent hollow spheres display intrinsic green fluorescence, are proteolytically stable and biocompatible, and allow for real-time monitoring of their intracellular entry. The disulfide bond facilitates selective degradation in the presence of high glutathione (GSH) concentrations, prevalent in cancer cells. We achieved efficient encapsulation (68.72%) of the anticancer drug doxorubicin (Dox) and demonstrated GSH-dependent, redox-responsive drug release within cancerous cells. SN-Dox exhibited a 20-fold lower effective concentration (2.5 μM) for compromising breast cancer cell viability compared to non-malignant cells (50 μM). The ability of SN-Dox to initiate DNA damage signaling and trigger apoptosis was comparable to that of the unencapsulated drug. Our findings highlight the potential of SN for creating site-specific drug delivery vehicles for sustained therapeutic release.

Functionalized Fluorescent Nanostructures Generated from Self-Assembly of a Cationic Tripeptide Direct Cell-Selective Chemotherapeutic Drug Delivery

Nanodrug delivery systems (NDDs) capable of conveying chemotherapeutics directly into malignant cells without harming healthy ones are of significant interest in the field of cancer therapy. However, the development of nanostructures with the requisite biocompatibility, inherent optical properties, cellular penetration ability, encapsulation capability, and target selectivity has remained elusive. In an effort to develop cell-selective NDDs, we have synthesized a cationic tripeptide Boc-Arg-Trp-Phe-OMe (PA1), which self-assembles into well-ordered spheres in 100% aqueous medium. The inherent fluorescence properties of the peptide PA1 were shifted from the ultraviolet to the visible region by the self-assembly. These fluorescent nanostructures are proteolytically stable, photostable, and biocompatible, with characteristic blue fluorescence signals that permit us to monitor their intracellular entry in real time. We also demonstrate that these tripeptide spherical structures (TPSS) have the capacity to entrap the chemotherapeutic drug doxorubicin (Dox), shuttle the encapsulated drug within cancerous cells, and initiate the DNA damage signaling cascade, which culminates in apoptosis. Next, we functionalized the TPSS with an epithelial-cell-specific epithelial cell adhesion molecule aptamer. Aptamer-conjugated PA1 (PA1-Apt) facilitated efficient Dox delivery into the breast cancer epithelial cell line MCF7, resulting in cell death. However, cells of the human cardiomyocyte cell line AC16 were resistant to the cell killing actions of PA1-Apt. Together, these data demonstrate that not only can the self-assembly of cationic tripeptides like PA1 be exploited for efficient drug encapsulation and delivery but their unique chemistry also allows for functional modifications, which can improve the selectivity of these versatile NDDs.

Peptide mapping of proteins by capillary electromigration methods

This review article provides a wide overview of important developments and applications of capillary electromigration methods in the area of peptide mapping of proteins in the period 1997-mid-2022, including review articles on this topic. It deals with all major aspects of peptide mapping by capillary electromigration methods: i) precleavage sample preparation involving purification, preconcentration, denaturation, reduction and alkylation of protein(s) to be analyzed, ii) generation of peptide fragments by off-line or on-line enzymatic and/or chemical cleavage of protein(s), iii) postcleavage preparation of the generated peptide mixture for capillary electromigration separation, iv) separation of the complex peptide mixtures by one-, two- and multidimensional capillary electromigration methods coupled with mass spectrometry detection, and v) a large application of peptide mapping for variable purposes, such as qualitative analysis of monoclonal antibodies and other protein biopharmaceuticals, monitoring of posttranslational modifications, determination of primary structure and investigation of function of proteins in biochemical and clinical research, characterization of proteins of variable origin as well as for protein and peptide identification in proteomic and peptidomic studies.

Recent Advances in Trace Bioanalysis by Capillary Electrophoresis

Recently, single cell analysis is becoming more and more important to elucidate cellular heterogeneity. Except for nucleic acid that can be amplified by PCR, the required technical level for single cell analysis is extremely high and the appropriate design of sample preparation and a sensitive analytical system is necessary. Capillary/microchip electrophoresis (CE/MCE) can separate biomolecules in nL-scale solution with high resolution, and it is highly compatible with trace samples like a single cell. Coupled with highly sensitive detectors such as laser-induced fluorescence and nano-electrospray ionization-mass spectrometry, zmol level analytes can be detected. For further enhancing sensitivity, online sample preconcentration techniques can be employed. By integrating these high-sensitive techniques, single cell analysis of metabolites, proteins, and lipids have been achieved. This review paper highlights successful research on CE/MCE-based trace bioanalysis in recent 10 years. Firstly, an overview of basic knowledge on CE/MCE including sensitivity enhancement techniques is provided. Applications to trace bioanalysis are then introduced with discussion on current issues and future prospects.

Selection and optimization of enzyme reporters for chemical cytometry

Chemical cytometry, sensitive analytical measurements of single cells, reveals inherent heterogeneity of cells within a population which is masked or averaged out when using bulk analysis techniques. A particular challenge of chemical cytometry is the development of a suitable reporter or probe for the desired measurement. These reporters must be sufficiently specific for measuring the desired process; possess a lifetime long enough to accomplish the measurement; and have the ability to be loaded into single cells. This chapter details our approach to rationally design and improve peptide substrates as reporters of enzyme activity utilizing chemical cytometry. This method details the iterative approach used to design, characterize, and identify a peptidase-resistant peptide reporter which acts as a kinase substrate within intact cells. Small-scale, rationally designed peptide libraries are generated to rapidly and economically screen candidate reporter peptides for substrate suitability and peptidase resistance. Also detailed are strategies to characterize and validate the designed reporters by determining kinetic parameters, intracellular substrate specificity, resistance to degradation by intracellular peptidases, and behavior within lysates and intact cells.

Single Cell Proteomics for Molecular Targets in Lung Cancer: High-Dimensional Data Acquisition and Analysis

In the proteomic and genomic era, lung cancer researchers are increasingly under challenge with traditional protein analyzing tools. High output, multiplexed analytical procedures are in demand for disclosing the post-translational modification, molecular interactions and signaling pathways of proteins precisely, specifically, dynamically and systematically, as well as for identifying novel proteins and their functions. This could be better realized by single-cell proteomic methods than conventional proteomic methods. Using single-cell proteomic tools including flow cytometry, mass cytometry, microfluidics and chip technologies, chemical cytometry, single-cell western blotting, the quantity and functions of proteins are analyzed simultaneously. Aside from deciphering disease mechanisms, single-cell proteomic techniques facilitate the identification and screening of biomarkers, molecular targets and promising compounds as well. This review summarized single-cell proteomic tools and their use in lung cancer.

Kinetic Analysis of Enzymes Immobilized in Porous Film Arrays

Measuring the catalytic activity of immobilized enzymes underpins development of biosensing, bioprocessing, and analytical chemistry tools. To expand the range of approaches available for measuring enzymatic activity, we report on a technique to probe activity of enzymes immobilized in porous materials in the absence of confounding mass transport artifacts. We measured reaction kinetics of calf intestinal alkaline phosphatase (CIAP) immobilized in benzophenone-modified polyacrylamide (BPMA-PAAm) gel films housed in an array of fluidically isolated chambers. To ensure kinetics measurements are not confounded by mass transport limitations, we employed Weisz's modulus (Φ), which compares observed enzyme-catalyzed reaction rates to characteristic substrate diffusion times. We characterized activity of CIAP immobilized in BPMA-PAAm gels in a reaction-limited regime (Φ ≪ 0.15 for all measurements), allowing us to isolate the effect of immobilization on enzymatic activity. Immobilization of CIAP in BPMA-PAAm gels produced a ∼2× loss in apparent enzyme-substrate affinity (Km) and ∼200× decrease in intrinsic catalytic activity (kcat) relative to in-solution measurements. As estimating Km and kcat requires multiple steps of data manipulation, we developed a computational approach (bootstrapping) to propagate uncertainty in calibration data through all data manipulation steps. Numerical simulation revealed that calibration error is only negligible when the normalized root-mean-squared error (NRMSE) in the calibration falls below 0.05%. Importantly, bootstrapping is independent of the mathematical model, and thus generalizable beyond enzyme kinetics studies. Furthermore, the measurement tool presented can be readily adapted to study other porous immobilization supports, facilitating rational design (immobilization method, geometry, enzyme loading) of immobilized-enzyme devices.

Recent developments in capillary and microchip electroseparations of peptides (2015-mid 2017)

The review brings a comprehensive overview of recent developments and applications of high performance capillary and microchip electroseparation methods (zone electrophoresis, isotachophoresis, isoelectric focusing, affinity electrophoresis, electrokinetic chromatography, and electrochromatography) to analysis, microscale isolation, purification, and physicochemical and biochemical characterization of peptides in the years 2015, 2016, and ca. up to the middle of 2017. Advances in the investigation of electromigration properties of peptides and in the methodology of their analysis (sample preseparation, preconcentration and derivatization, adsorption suppression and EOF control, and detection) are described. New developments in particular CE and CEC methods are presented and several types of their applications to peptide analysis are reported: qualitative and quantitative analysis, determination in complex (bio)matrices, monitoring of chemical and enzymatical reactions and physical changes, amino acid, sequence and chiral analysis, and peptide mapping of proteins. Some micropreparative peptide separations are shown and capabilities of CE and CEC methods to provide important physicochemical characteristics of peptides are demonstrated.

Single Cell Chemical Cytometry of Akt Activity in Rheumatoid Arthritis and Normal Fibroblast-like Synoviocytes in Response to Tumor Necrosis Factor α

The etiology of rheumatoid arthritis (RA) is poorly understood, and 30% of patients are unresponsive to established treatments targeting tumor necrosis factor α (TNFα). Akt kinase is implicated in TNFα signaling and may act as a barometer of patient responses to biologic therapies. Fluorescent peptide sensors and chemical cytometry were employed to directly measure Akt activity as well as proteolytic activity in individual fibroblast-like synoviocytes (FLS) from RA and normal subjects. The specificity of the peptide reporter was evaluated and shown to be a valid measure of Akt activity in single cells. The effect of TNFα treatment on Akt activity was highly heterogeneous between normal and RA subjects, which was not observable in bulk analyses. In 2 RA subjects, a bimodal distribution of Akt activity was observed, primarily due to a subpopulation (21.7%: RA Subject 5; 23.8%: RA Subject 6) of cells in which >60% of the reporter was phosphorylated. These subjects also possessed statistically elevated proteolytic cleavage of the reporter relative to normal subjects, suggesting heterogeneity in Akt and protease activity that may play a role in the RA-affected joint. We expect that chemical cytometry studies pairing peptide reporters with capillary electrophoresis will provide valuable data regarding aberrant kinase activity from small samples of clinical interest.