Native and denatured forms of proteins can be discriminated at edge plane carbon electrodes

In an attempt to develop a label-free electrochemical method for detection of changes in protein structures based on oxidizability of tyrosine and tryptophan residues we tested different types of carbon electrodes. We found that using edge plane pyrolytic graphite electrode (EPGE) we can discriminate between native and denatured forms of human serum albumin (HSA) and of other proteins, such as bovine and chicken serum albumin, aldolase and concanavalin. Treatment of natively unfolded α-synuclein with 8 M urea resulted only in a small change in the tyrosine oxidation peak, in a good agreement with absence of highly ordered structure in this protein. Using square wave voltammetry with EPGE we were able to follow the course of HSA denaturation at different urea concentrations. The electrochemical denaturation curve agreed reasonably well with that based on intrinsic fluorescence of tyrosine and tryptophan. It can be expected that the electrochemical method will be applicable to a large number of proteins and may become useful in biomedicine and proteomics.     

Chronopotentiometric Determination of Redox States of Peptides

Reduced and oxidized forms of peptides were studied by different electrochemical methods at carbon and hanging mercury drop (HMDE) electrodes. Striking differences between the reduced and oxidized peptides were obtained by constant current chronopotentiometric stripping analysis (CPSA) at HMDE. Peptides yielded electrocatalytic peak H at highly negative potentials (ca. ?1.75 V). Reduced peptides adsorbed at positively charged HMDE produced substantially higher peak H than the oxidized forms. Voltammetry reflected the peptide redox state less efficiently. Different orientation of reduced and oxidized molecules at the positively charged electrode and very fast potential changes in CPSA were probably responsible for the observed effects.     

Catalysis of Hydrogen Evolution by Polylysine,Polyarginine and Polyhistidine at Mercury Electrodes

Protein catalyzed hydrogen evolution reaction at mercury‐containing electrodes controlled by constant‐current chronopotentiometric stripping (CPS) is representing a new tool useful in protein research. The resulting CPS peak H is sensitive to changes in the protein structure and its amino acid composition. Besides CPS, cyclic voltammetry appears to be useful for study of poly(amino acids) as an intermediate model system between peptides and macromolecular proteins. Here we show that similarly as arginine in polyarginine and lysine in polylysine also histidine residues in polyhistidine contribute to the catalysis of hydrogen evolution under the given conditions. Peak potentials of individual poly(amino acids) are different and depend on the type of amino acid residues.     

Proteins and peptides voltammetry: Trends,potential, and limitations

Numerous biological processes are connected with the efficient electron transfer reactions in proteins and peptides. In this review, we discuss briefly the relevance and current challenges associated with the voltammetric analysis of peptides and proteins with and without a metal redox center. Special attention is paid to the integration of electrochemical methods with new nanomaterials which offers amplification of multiplexing capabilities for simultaneous and very sensitive examination of various proteins. After critically discussing the most interesting approaches in the proteins/peptides voltammetric analysis reported so far, for the single or multiplexed examination of such biomolecules with demonstrated applicability in the real-sample analysis, existing challenges still need to be addressed and future directions in this field will be pointed out.     

Sortase-Mediated Transpeptidation for Site-Specific Modification of Peptides,Glycopeptides, and Proteins

Sortases are a family of transpeptidases found in gram-positive bacteria responsible for covalent anchoring of cell surface proteins to bacterial cell walls. It has been discovered that sortase A (SrtA) of Staphylococcus aureus origin is rather promiscuous and can accept various molecules as substrates. As a result, SrtA has been widely used to ligate peptides and proteins with a variety of nucleophiles, and the ligation products are useful for research in chemical biology, proteomics, biomedicine, etc. This review summarizes the recent applications of SrtA with special emphasis on SrtA-catalyzed ligation of carbohydrates with peptides and proteins.     

Biotinylation of Peptides/Proteins Using Biocytin Hydrazide

Biocytin hydrazide is widely used to biotinylate the carbohydrate moieties of glycoproteins. In this study, however, biocytin hydrazide was found to be able to directly biotinylate peptides and proteins. This phenomenon may cause false identification of non‐glycopeptides/non‐glycoproteins as glycopeptides/glycoproteins. Here, we report a systematic investigation of the reaction of peptides/proteins with biocytin hydrazide. Matrix‐assisted laser desorption/ionization time‐of‐flight mass spectrometry is used to analyze the biotinylation reaction between peptides/proteins and biocytin hydrazide. Peptides/proteins were reacted with biocytin hydrazide in diverse solvent systems with different biocytin hydrazide concentrations for up to 96 h at temperatures ranging from 4 °C to 65 °C. Singly biotinylated or multiply biotinylated peptides/proteins are observed. The efficiency of the biotinylation reaction increases with higher temperature, higher biocytin hydrazide concentration, or longer reaction time. The influence of buffer pH on the biotinylation reaction of peptides/proteins is less pronounced. The biotinylation efficiency is optimum at neutral pH. Data suggests that the peptides are biotinylated as efficiently as proteins. The observation that peptides/proteins condense only with biocytin hydrazide, 2‐iminobiotin hydrazide, adipic dihydrazide and phenyl hydrazine but not with biocytin HCl and 2‐iminobiotin, indicates that the biotinylation reaction of peptides/proteins occurs with the hydrazide moiety but not with biotin moiety of the biotinylated reagent. The postsource decay data of biotinylated P₁₄R indicates that biocytin hydrazide condenses with the guanidino group of arginine's side chain of P₁₄R, indicating that besides N‐terminal and lysine residue of peptides/proteins, arginine residue is capable of reacting with biocytin hydrazide.     

Sortase-Mediated Transpeptidation for Site-Specific Modification of Peptides, Glycopeptides, and Proteins

Sortases are a family of transpeptidases found in Gram-positive bacteria responsible for covalent anchoring of cell surface proteins to bacterial cell walls. It has been discovered that sortase A (SrtA) of Staphylococcus aureus origin is rather promiscuous and can accept various molecules as substrates. As a result, SrtA has been widely used to ligate peptides and proteins with a variety of nucleophiles, and the ligation products are useful for research in chemical biology, proteomics, biomedicine, etc. This review summarizes the recent applications of SrtA with special emphasis on SrtA-catalyzed ligation of carbohydrates with peptides and proteins.     

Chronopotentiometric Analysis of Proteins at Charged Electrode Surfaces

Protein properties and functions are strongly dependent on the structure and amino acid content. In this work, catalytic hydrogen evolution reaction (CHER) of five proteins (human serum albumin, lysozyme, β‐synuclein, H2 A and H3 histones) were studied using constant current chronopotentiometric stripping (CPS) with the aim to find out the association between protein content and its electrochemical response. We have shown that the height and potential of CPS peak H in dependence on accumulation potential differed for the studied proteins, while the CPS peak area was almost the same for all of them. CV and CPS peaks H of Cys‐containing proteins appeared at less negative potentials in comparison to proteins without Cys, suggesting easier CHER. Acidic and basic proteins not containing Cys can be also recognized due to their different CPS response after their adsorption at the positive and negative charged interface.     

Engineered Histidine-Rich Peptides Enhance Endosomal Escape for Antibody-Targeted Intracellular Delivery of Functional Proteins

Currently, the clinical application of protein/peptide therapeutics is mainly limited to the modulation of diseases in extracellular spaces. Intracellular targets are hardly accessed, owing largely to the endosomal entrapment of internalized proteins/peptides. Here, we report a strategy to design and construct peptides that enable endosome-to-cytosol delivery based on an extension of the “histidine switch” principle. By substituting the Arg/Lys residues in cationic cell-penetrating peptides (CPPs) with histidine, we obtained peptides with pH-dependent membrane-perturbation activity. These peptides do not randomly penetrate cells like CPPs, but imitate the endosomal escape of CPPs following cellular uptake. Working with one such 16-residue peptide (hsLMWP) with high endosomal escape capacity, we engineered modular fusion proteins and achieved antibody-targeted delivery of diverse protein cargoes—including the pro-apoptotic protein BID (BH3-interacting domain death agonist) and Cre recombinase—into the cytosol of multiple cancer cell types. After extensive in vitro testing, an in vivo analysis with xenograft mice ultimately demonstrated that a trastuzumab-hsLMWP-BID fusion conferred strong anti-tumor efficacy without apparent side effects. Notably, our fusion protein features a modular design, allowing flexible applications for any antibody/cargo combination of choice. Therefore, the potential applications extend throughout life science and biomedicine, including gene editing, cancer treatment, and immunotherapy.     

Self‐Assembly of Proteins: Towards Supramolecular Materials

The study of protein self‐assembly has attracted great interest over the decades, due to the important role that proteins play in life. In contrast to the major achievements that have been made in the fields of DNA origami, RNA, and synthetic peptides, methods for the design of self‐assembling proteins have progressed more slowly. This Concept article provides a brief overview of studies on native protein and artificial scaffold assemblies and highlights advances in designing self‐assembling proteins. The discussions are focused on design strategies for self‐assembling proteins, including protein fusion, chemical conjugation, supramolecular, and computational‐aided de novo design.     

Electroanalytical Application of Carbon Based Electrodes to the Pharmaceuticals

Abstract

Carbon and its derivatives, as the high performance material, occupy a special place in electrochemistry due to its ‐in many ways‐ extreme properties. Recent trends and advances in the electrochemistry of carbon‐based electrodes are reviewed. The varieties of carbon‐based electrodes, their basic physicochemical properties and some characteristics are surveyed. Special attention is paid to the possibilities of carbon‐based electrodes in electroanalytical investigation in pharmaceutical dosage forms and biological samples using modern electrochemical techniques. This review includes a summary of the rules that must be considered for drug analysis from its dosage forms and biological samples using carbon‐based electrodes. The present review is the first comprehensive report on the heterogeneous and homogeneous carbon electrodes, and an addition to many excellent reviews on carbon electrodes in the literature. This review summarizes some of the recent developments and applications of carbon‐based electrodes for drug compounds in their dosage forms and in biological samples in the period from 1996 till 2006. Also some further selected designs (screen‐printed; carbon nanotubes, etc.) and applications have been discussed.     

A Single Atom Change Facilitates the Membrane Transport of Green Fluorescent Proteins in Mammalian Cells

Direct delivery of proteins into mammalian cells is a challenging problem in biological and biomedical applications. The most common strategies for the delivery of proteins into the cells include the use of cell‐penetrating peptides or supercharged proteins. Herein, we show for the first time that a single atom change, hydrogen to halogen, at one of the tyrosine residues can increase the cellular entry of ～28 kDa green fluorescent protein (GFP) in mammalian cells. The protein uptake is facilitated by a receptor‐mediated endocytosis and the cargo can be released effectively into cytosol by co‐treatment with the endosomolytic peptide ppTG21.     

On the Adsorption and Reduction of the Herbicide Picloram on Mercury and Carbon Electrodes

At concentrations higher than 2?10^?4 M , and below pH 3, the cyclic voltammograms of picloram (=4‐amino‐3,5,6‐trichloropyridine‐2‐carboxylic acid) on Hg electrodes show two prepeak systems (named I and II attending to the proximity to the main reductions peak), which can be attributed to the weak adsorption of reactant and the strong adsorption of the product at the electrode surface. The system II is due to the uncharged form of picloram, and system I to the picloram protonated at the pyridine N‐atom. Small amounts of the surfactant Triton X‐100 (=α‐[4‐(1,1,3,3‐tetramethylbutyl)phenyl]‐ω‐hydroxypoly(oxyethane‐1,2‐diyl)) cause the disappearance of system I, the shift of system II, and also affect the intensities and widths of anodic and cathodic peaks but not the charge passed in each peak. Thus, the adsorption process responsible for the appearance of system I is inhibited by the presence of Triton; by contrast, the process corresponding to system II is only modified by the surfactant, becoming an electrochemical process occurring at the potentials corresponding to system II, which is more reversible than that observed in the absence of Triton. The addition of Triton permitted the analysis of the main reduction process. Convolution voltammetry of the main reduction peak is consistent with the loss of a Cl‐atom in equilibrium which occurs after a reversible electron transfer and is followed by the reductions of both species present in the equilibrium (Scheme 2). This is also the reduction mechanism on a glassy carbon electrode but the electron transfer on the carbon electrode increases with respect to the mercury electrodes; in addition, the loss of the Cl‐atom does not take place on the electrode surface. From the recording of differential capacity–potential curves, it was concluded that picloram is adsorbed on the carbon electrode; but this adsorption is too weak to induce the appearance of prepeak systems.     

Evaluation of peptide fractionation strategies used in proteome analysis

Peptide fractionation is extremely important for the comprehensive analysis of complex protein mixtures. Although a few comparisons of the relative separation efficiencies of 2‐D methodologies using complex biological samples have appeared, a systematic evaluation was conducted in this study. Four different fractionation methods, namely strong‐cation exchange, hydrophilic interaction chromatography, alkaline‐RP and solution isoelectric focusing, which can be used prior to LC‐MS/MS analysis, were compared. Strong‐cation exchange × RPLC was used after desalting the sample; significantly more proteins were identified, compared with the nondesalted sample (1990 and 1375). We also found that the use of a combination of analytical methods resulted in a dramatic increase in the number of unique peptides that could be identified, compared with only a small increase in protein levels. The increased number of distinct peptides that can be identified is especially beneficial, not only for unequivocally identifying proteins but also for proteomic studies involving posttranslational modifications and peptide‐based quantification approaches using stable isotope labeling. The identification and quantification of more peptides per protein provide valuable information that improves both the quantification of, and confidence of protein identification.     

Electrochemical characterisation of macroporous electrodes: Recent advances and hidden pitfalls

Investigating the intrinsic kinetics of macroporous electrodes by means of cyclic voltammetry (CV) and electrochemical impedance spectroscopy (EIS) is an exceptionally challenging task with a multitude of hidden pitfalls. The classical analysis (e.g. the Randles–?ev?ík or the Nicholson methods) cannot be used for macroporous electrodes as these can only be applied to electrodes which exhibit mass transport controlled by planar semi-infinite diffusion and that have spatially uniform redox activity. Unfortunately, a number of recent articles incorrectly interprete data by applying classical analysis to macroporous electrodes. To address this, the CV and EIS analysis methods, which can be used for macroporous electrodes are reviewed and discussed.     

Solid‐State NMR of PEGylated Proteins

PEGylated proteins are widely used in biomedicine but, in spite of their importance, no atomic‐level information is available since they are generally resistant to structural characterization approaches. PEGylated proteins are shown here to yield highly resolved solid‐state NMR spectra, which allows assessment of the structural integrity of proteins when PEGylated for therapeutic or diagnostic use.     

Direct Determination of Bacterial Cell Viability Using Carbon Nanotubes Modified Screen‐printed Electrodes

For the early detection of bacterial infection, there is a need for rapid, sensitive, and label‐free assays. Thus, in this study, nanostrucured microbial electrochemical platform is designed to monitor the viability and cell growth of S. aureus. Using multi‐walled carbon nanotube modified screen‐printed electrodes (MWCNTs/SPE), the cyclic voltammetric measurements showed only one irreversible oxidation peak at 600 mV vs Ag/AgCl that accounts for the viable and metabolically active bacterial cells. The assay was optimized and the secreted metabolites, in the extracellular matrix, were directly detected. The peak current showed a positive correlation with viable cell numbers ranging from OD_{600 nm} of 0.1 to 1.1, indicating that the activity of live cells can be quantified. Consequently, responses of viable and non‐viable cells of S. aureus to the effects of antibiotic and respiratory chain inhibitors were determined. Thus, the proposed nanostructure‐based bacterial sensor provides a reasonable and reliable way for real‐time monitoring of live‐dead cell functions, and antibacterial profiling.     

BSA‐Polysaccharide Interactions at Negatively Charged Electrode Surface. Effects of Current Density.

Constant current chronopotentiometric stripping (CPS) peak H due to catalytic hydrogen evolution reaction on Hg‐containing electrodes appeared useful in the analysis of protein complexes with single‐stranded and double‐stranded DNA as well as with peptides. In dependence on stripping current (I_str), structural transition of the protein alone or in complexes can be followed as a result of the protein exposure to electric field effects. For the first time we show here that the CPS analysis can be used for the study of the interaction of BSA with a polysaccharide namely sodium alginate (SA). BSA‐SA complex formation was accompanied by the shift of the structural transition of BSA to lower ‐I_str intensities. Another polysaccharide dextran did not alter I_str‐dependent structural transition of BSA. BSA‐SA complex can be disturbed by an electric field effect or high ionic strength confirming the electrostatic nature of BSA‐SA interaction.     

Proteomics as an Emergent Tool for Identification of Stress-Induced Proteins in Control and Genetically Modified Wheat Lines

Proteomic methods have been used to identify stress-induced proteins that may have a special role in food science. A new challenge for proteomics has recently been recognised pointing out differences in food protein analysis relevant for nutrition. In this study application of proteomics for traceability of the effect of environmental changes on wheat proteins are addressed. The proteomic analysis involves excision of proteins of interest from two-dimensional (2D) gels, followed by reduction and digestion using trypsin in situ in the spot. The peptides are then analysed using MALDI (matrix assisted laser desorption/ionisation) mass spectrometry and identified by protein databases. The protein set of drought stressed wide-rage herbicide resistant transgenic spring wheat lines: 'T-117', 'T-106-3/a' and 'T-128' and of drought stressed non-transgenic (parent) spring wheat line: 'CY-45' was studied by 2-DE. The drought affected protein expression mostly for the low molecular weight, putative stress-induced proteins were observed in the molecular weight range 15–27 kDa at pH 6,5–7,5. The differentially expressed proteins of albumin and globulin fractions were digested from the gel and digested by trypsin. Number of inhibitor-like proteins were most dominant in the stressed transgenic lines: alpha-amylase/ trypsin inhibitor CM1 precursor, alpha-amylase inhibitor, endogenous alpha-amylase/subtilisin inhibitor (WASI) and a 27 K protein, suggesting that the examined transgenic lines were the sensitive to drought stress.

     

Charge‐Induced Unzipping of Isolated Proteins to a Defined Secondary Structure

Here we present a combined experimental and theoretical study on the secondary structure of isolated proteins as a function of charge state. In infrared spectra of the proteins ubiquitin and cytochrome c, amide I (C=O stretch) and amide II (N–H bend) bands can be found at positions that are typical for condensed‐phase proteins. For high charge states a new band appears, substantially red‐shifted from the amide II band observed at lower charge states. The observations are interpreted in terms of Coulomb‐driven transitions in secondary structures from mostly helical to extended C₅‐type hydrogen‐bonded structures. Support for this interpretation comes from simple energy considerations as well as from quantum chemical calculations on model peptides. This transition in secondary structure is most likely universal for isolated proteins that occur in mass spectrometric experiments.