Chemical Modification Of Proteins Research Articles

Inactivation of Indispensable Bacterial Proteins by Early Proteins of Bacteriophages:Implication in Antibacterial Drug Discovery

Bacteriophages utilize host bacterial cellular machineries for their own reproduction and completion of life cycles. The early proteins that phage synthesize immediately after the entry of their genomes into bacterial cells participate in inhibiting host macromolecular biosynthesis, initiating phage-specific replication and synthesizing late proteins. Inhibition of synthesis of host macromolecules that eventually leads to cell death is generally performed by the physical and/or chemical modification of indispensable host proteins by early proteins. Interestingly, most modified bacterial proteins were shown to take part actively in phage-specific transcription and replication. Research on phages in last nine decades has demonstrated such lethal early proteins that interact with or chemically modify indispensable host proteins. Among the host proteins inhibited by lethal phage proteins, several are not inhibited by any chemical inhibitor available today. Under the context of widespread dissemination of antibiotic-resistant strains of pathogenic bacteria in recent years, the information of lethal phage proteins and cognate host proteins could be extremely invaluable as they may lead to the identification of novel antibacterial compounds. In this review, we summarize the current knowledge about some early phage proteins, their cognate host proteins and their mechanism of action and also describe how the above interacting proteins had been exploited in antibacterial drug discovery.

Modification of Soy Protein Plastic with Functional Monomer with Reactive Extrusion

Chemical modification of soy protein with monomers such as maleic anhydride, glycidyl methacrylate and styrene was accomplished using reactive extrusion technology. Thermal and mechanical properties of the modified soy protein plastics were characterized with differential scanning calorimetry (DSC), a dynamic mechanical analyzer (DMA) and a United Testing System load frame. It was found that the denaturation temperature and the glass transition temperature of soy protein plastic changed. In addition, the tensile properties of modified soy protein plastic improved. Attenuated total reflection Fourier transform infrared (ATR-FTIR) and X-ray photoelectron spectroscopy (XPS) were used to characterize the structure of modified soy proteins. A suggestion of the interaction between soy protein and functional group in functional polymers is given. Through the in-situ interaction between the polymer and soy protein plastic, the mechanical properties of the soy protein plastic can be adjusted and controlled.

Physiology and pharmacology of alcohol: the imidazobenzodiazepine alcohol antagonist site on subtypes of GABAA receptors as an opportunity for drug development?

Alcohol (ethanol, EtOH) has pleiotropic actions and induces a number of acute and long-term effects due to direct actions on alcohol targets, and effects of alcohol metabolites and metabolism. Many detrimental health consequences are due to EtOH metabolism and metabolites, in particular acetaldehyde, whose high reactivity leads to nonspecific chemical modifications of proteins and nucleic acids. Like acetaldehyde, alcohol has been widely considered a nonspecific drug, despite rather persuasive evidence implicating inhibitory GABA(A) receptors (GABA(A)Rs) in acute alcohol actions, for example, a GABA(A)R ligand, the imidazobenzodiazepine Ro15-4513 antagonizes many low-to-moderate dose alcohol actions in mammals. It was therefore rather surprising that abundant types of synaptic GABA(A)Rs are generally not responsive to relevant low concentrations of EtOH. In contrast, delta-subunit-containing GABA(A)Rs and extrasynaptic tonic GABA currents mediated by these receptors are sensitive to alcohol concentrations that are reached in blood and tissues during low-to-moderate alcohol consumption. We recently showed that low-dose alcohol enhancement on highly alcohol-sensitive GABA(A)R subtypes is antagonized by Ro15-4513 in an apparently competitive manner, providing a molecular explanation for behavioural Ro15-4513 alcohol antagonism. The identification of a Ro15-4513/EtOH binding site on unique GABA(A)R subtypes opens the possibility to characterize this alcohol site(s) and screen for compounds that modulate the function of EtOH/Ro15-4513-sensitive GABA(A)Rs. The utility of such drugs might range from novel alcohol antagonists that might be useful in the emergency room, to drugs for the treatment of alcoholism, as well as alcohol-mimetic drugs to harness acute positive effects of alcohol.

10.1007/s11828-008-1003-2

In modern science proteomic analysis is inseparable from other fields of systemic biology. Possessing huge resources quantitative proteomics operates colossal information on molecular mechanisms of life. Advances in proteomics help researchers to solve complex problems of cell signaling, posttranslational modification, structure and funciotnal homology of proteins, molecular diagnostics etc. More than 40 various methods have been developed in proteomics for quantitative analysis of proteins. Although each method is unique and has certain advantages and disadvantages all these use various isotope labels (tags). In this review we will consider the most popular and effective methods employing both chemical modifications of proteins and also metabolic and enzymatic methods of isotope labeling.

Succination of Proteins by Fumarate

S-(2-succinyl)cysteine (2SC) is a chemical modification of proteins formed by a Michael addition reaction between the Krebs cycle intermediate, fumarate, and thiol groups in protein--a process known as succination of protein. Succination causes irreversible inactivation of glyceraldehyde-3-phosphate dehydrogenase (GAPDH) in vitro. GAPDH was immunoprecipitated from muscle of diabetic rats, then analyzed by ultra-performance liquid chromatography-electrospray ionization-mass spectroscopy. Succination of GAPDH was increased in muscle of diabetic rats, and the extent of succination correlated strongly with the decrease in specific activity of the enzyme. We propose that 2SC is a biomarker of mitochondrial and oxidative stress in diabetes and that succination of GAPDH and other thiol proteins may provide the chemical link between glucotoxicity and the pathogenesis of diabetic complications.

Important role of peroxynitrite‐nitric oxide interaction for S‐, N‐ and C‐nitrosation reactions

Biological nitrosations belong to a set of redox based chemical posttranslational modifications of proteins that are involved in cellular regulation. Peroxynitrite is a central player in redox signaling and is expected to play a role in nitrosation. In earlier work we and others have suggested that nitrosation is mediated by intermediates that arise by cellular fluxes of nitric oxide and superoxide but the nature of such intermediates remained elusive. In the present study we have investigated model systems for cellular nitrosation using phenol, diaminonaphthaline and isocitrate dehydrogenase as substrates for C‐, N‐, and S‐nitrosation. The thermal aerobic decay of Sin‐1 into equal amounts of NO and superoxide was used and NONOate was added as a NO source which lead to a nitrosation maximum at a NO:superoxide ratio of 3:1. When Cu, Zn‐SOD was present during the decay of Sin‐1 a gradual shift to NO formation was indicated by use of an NO‐sensitive electrode and a SOD dependent maximum of nitrosations was obtained also in this system. Qualitatively similar results were obtained when the SOD mimetic osmium tetroxide was used. We conclude from the various systems investigated that biological nitrosations can arise from fluxes of NO and superoxide at ratios of about 3:1. It is too early to speculate on the mechanism involved but the systems presented seem to be valid models to elucidate biological nitrosation reactions.

Characterization of IgG1 Immunoglobulins and Peptide−Fc Fusion Proteins by Limited Proteolysis in Conjunction with LC−MS

A combinatory approach for the characterization of post-translational and chemical modifications in high molecular weight therapeutic proteins like antibodies and peptide-Fc fusion proteins (MW > or = 50 000 Da) is presented. In this approach, well-established techniques such as limited proteolysis, reversed-phase (RP) high-performance liquid chromatography (HPLC), and in-line mass spectrometry (MS) were combined for the characterization of a monoclonal IgG1 antibody and three different peptide-Fc fusion proteins. The one commonality of these molecules is the presence of a similarly accessible lysine residue either located in the flexible hinge region of the antibody or in the flexible linker of the peptide-Fc fusion proteins. Applying limited proteolysis using endoproteinase Lys-C resulted in the predominant cleavage C-terminal of this lysine residue. The created fragments, two identical Fab domain fragments and one Fc domain fragment derived from the IgG1 antibody and one Fc domain fragment and each of the three individual peptide moieties generated from the peptide-Fc fusion proteins, were readily accessible for complete separation by RP-HPLC and detailed characterization by in-line MS analysis. This approach facilitated rapid detection of a variety of chemical modifications such as methionine oxidation, disulfide bond scrambling, and reduction as well as the characterization of various carbohydrate chains. We found limited proteolysis followed by RP-HPLC-MS to be less time-consuming for sample preparation, analysis, and data interpretation than traditional peptide mapping procedures. At the same time, the reduced sample complexity provided superior chromatographic and mass spectral resolution than the analysis of the corresponding intact molecules or a large number of enzymatically generated fragments.

Efficient Site-Specific Labeling of Proteins via Cysteines

Methods for chemical modifications of proteins have been crucial for the advancement of proteomics. In particular, site-specific covalent labeling of proteins with fluorophores and other moieties has permitted the development of a multitude of assays for proteome analysis. A common approach for such a modification is solvent-accessible cysteine labeling using thiol-reactive dyes. Cysteine is very attractive for site-specific conjugation due to its relative rarity throughout the proteome and the ease of its introduction into a specific site along the protein's amino acid chain. This is achieved by site-directed mutagenesis, most often without perturbing the protein's function. Bottlenecks in this reaction, however, include the maintenance of reactive thiol groups without oxidation before the reaction, and the effective removal of unreacted molecules prior to fluorescence studies. Here, we describe an efficient, specific, and rapid procedure for cysteine labeling starting from well-reduced proteins in the solid state. The efficacy and specificity of the improved procedure are estimated using a variety of single-cysteine proteins and thiol-reactive dyes. Based on UV/vis absorbance spectra, coupling efficiencies are typically in the range 70-90%, and specificities are better than approximately 95%. The labeled proteins are evaluated using fluorescence assays, proving that the covalent modification does not alter their function. In addition to maleimide-based conjugation, this improved procedure may be used for other thiol-reactive conjugations such as haloacetyl, alkyl halide, and disulfide interchange derivatives. This facile and rapid procedure is well suited for high throughput proteome analysis.

Metalloproteins: metal binding predicted on the basis of the amino acid sequence

A protein sequence is often insufficient for knowledge of the chemical formula and the properties of the mature molecule that perform its function. Post-translational modifications are very common and most of them cannot be predicted on the basis of the protein sequence alone. A very common chemical modification of proteins that is not directly encoded by a single gene is the complexation with metal cations. Here it is shown that the uptake of metal ions (calcium, cobalt, copper, iron, magnesium, manganese, nickel or zinc) by proteins can be predicted on the basis of the amino acid composition, by using a mixture of several simplified amino acid alphabets and by employing machine learning methods, with 70–90% accuracy, depending on the type of metal. Not only is it possible to predict if a protein requires a certain metal ion but it is also possible to discriminate amongst various metal species. These results are likely to be useful in structural proteomics, by improving the experiment success rate, and in comparative genomics, where it is interesting to compare metal-ion contents in different organisms. It is particularly important that these predictions can be made when homology-based annotations are impossible.

Covalent modification of stathmin by CCNU determined by FTMS analysis of modified proteins and tryptic peptides

Chemical modification of proteins is often carried out to generate protein-small molecule conjugates for various applications. The high resolution and mass accuracy of a Fourier transform mass spectrometer is particularly useful for assessing the extent or sites of covalent modifications. As protein-small molecule reactions often produce products with variable numbers of the compound incorporated at different sites, a direct mass analysis of the reaction products at times yields mass spectra hard to interpret. Chromatographic separation at protein level could reduce the complexity of a sample, thus allowing more accurate mass spectrometric analysis. In this report, we demonstrate the utility of reversed-phase protein chromatography and FT-ICR mass spectrometry in analyzing CCNU (lomustine, 1-(2-chloroethyl)-3-cyclohexyl-1-nitroso-urea, MW: 233.7 Da) modification of stathmin. With this combined approach, we determined the stoichiometry as well as sites of CCNU incorporation into the protein, demonstrating differential reactivity of several lysyl residues to CCNU alkylation.

Cracking the Enigmatic Linker Histone Code

Recently, the existence of a 'histone code' has been proposed to explain the link between the covalent chemical modification of histone proteins and the epigenetic regulation of gene activity. Although the role of the four 'core' histones has been extensively studied, little is known about the involvement of the linker histone, histone H1 and its variants, in this code. For many years, few sites of chemical modification had been mapped in linker histones, but this has changed recently with the use of functional proteomic techniques, principally mass spectrometry, to characterize these modifications. The functionality of many of these sites, however, remains to be determined.

In Vitro and In Vivo Characterization of Full-Length rFVIII Modified with PEG Via Coupling to Primary Amino Groups.

Chemical modification of recombinant therapeutic proteins with PEG has been shown to enhance the biological half-life. Here we assess the effect of PEGylation on FVIII. Full-length rFVIII bulk drug substance from protein-free fermentation (Advate process, Baxter) was conditioned into a buffer suitable for coupling to polyethylene glycol succinimidyl succinate (linear PEG, 5 kDa PEG chain length). PEG was covalently bound by amine coupling preferentially to lysine residues of FVIII at neutral pH. PEG was removed by ion-exchange chromatography and the PEG-FVIII derivative was concentrated by ultra-diafiltration. The conjugates thus obtained retained about 30–40% of the activity of non-modified rFVIII. The specific activity decreased with the amount of PEG linked to the FVIII molecule. In SDS-PAGE and immunoblot studies PEGylated rFVIII showed a band pattern similar to unmodified FVIII with full-length, heavy chain fragments of 180 kDa and 120 kDa and the light chain fragment of 80 kDa. PEGylation also occurred to a high extent in the B domain of FVIII. All bands appeared broadened due to the attachment of polymeric PEG. The maintenance of functionality of FVIII was demonstrated by its potential to be activated and inactivated by thrombin. In the assay PEGylated and unmodified FVIII were incubated with 1 nM thrombin. Sub-samples were drawn at intervals up to 40 minutes and added to a mixture of FIXa, FX, phospholipid vesicles and Ca2+ containing a thrombin inhibitor. After 3 minutes incubation at 37°C the amount of activated FX (FXa) was measured using a FXa-specific chromogenic substrate. Unmodified rFVIII showed a typical picture of an immediate increase in FXa activity and a subsequent decline with no further FXa generation after 15 minutes. PEGylated rFVIII was activated to the same extent as unmodified FVIII but the decay in FXa generation was slower and did not reach the zero level, even 40 minutes after incubation. The formation of the typical thrombin cleavage fragments, with unmodified as well as PEGylated rFVIII, was demonstrated in a Western blot analysis. The slower inactivation by thrombin was also seen there. The pharmacokinetic properties of PEGylated rFVIII compared with rFVIII were investigated in hemophilia A knock-out mice. Both preparations were applied at a dose of 200 IU rFVIII/kg and groups of mice (n=5) were exsanguinated at several time points up to 24 hours. Terminal half-life for PEGylated rFVIII was calculated at 4.9 hours compared with 1.9 hours for unmodified rFVIII in hemophilia A knock-out mice. AUC was approximately doubled. These results indicate that rFVIII can be biochemically modified with PEG whilst at least partly retaining its major functions, but at the same time prolonging its survival in the circulation of hemophilic mice.

Redesign of Protein Domains Using One-Bead-One-Compound Combinatorial Chemistry

A novel combinatorial strategy for the redesign of proteins based on the strength and specificity of intra- and interprotein interactions is described. The strategy has been used to redesign the hydrophobic core of the B domain of protein A. Using one-bead-one-compound combinatorial chemistry, 300 analogues of the C-terminal alpha-helix of the B domain, H3x, have been synthesized using a biocompatible resin and the HMFS linker, allowing the screening to occur while the peptides were bound to the resin. The screening was based on the ability of the H3x analogues to interact with the N-terminal helices of the B domain, H1-H2, and retain the native B domain activity, that is binding to IgG. Eight different analogues containing some nonconservative mutations were obtained from the library, the two most frequent of which, H3P1 and H3P2, were studied in detail. CD analysis revealed that the active analogues interact with H1-H2. To validate the redesign strategy the covalent modified domains H1-H2-H3P1 and H1-H2-H3P2 were synthesized and characterized. CD and NMR analysis revealed that they had a unique, stable, and well-defined three-dimensional structure similar to that for the wild-type B domain. This combinatorial strategy allows us to select for redesigned proteins with the desired activity or the desired physicochemical properties provided the right screening test is used. Furthermore, it is rich in potential for the chemical modification of proteins overcoming the drawbacks associated with the total synthesis of large protein domains.

AutoMotif Server for prediction of phosphorylation sites in proteins using support vector machine: 2007 update

We present here the recent update of AutoMotif Server (AMS 2.0) that predicts post-translational modification sites in protein sequences. The support vector machine (SVM) algorithm was trained on data gathered in 2007 from various sets of proteins containing experimentally verified chemical modifications of proteins. Short sequence segments around a modification site were dissected from a parent protein, and represented in the training set as binary or profile vectors. The updated efficiency of the SVM classification for each type of modification and the predictive power of both representations were estimated using leave-one-out tests for model of general phosphorylation and for modifications catalyzed by several specific protein kinases. The accuracy of the method was improved in comparison to the previous version of the service (Plewczynski et al., "AutoMotif server: prediction of single residue post-translational modifications in proteins", Bioinformatics 21: 2525-7, 2005). The precision of the updated version reached over 90% for selected types of phosphorylation and was optimized in trade of lower recall value of the classification model. The AutoMotif Server version 2007 is freely available at http://ams2.bioinfo.pl/ . Additionally, the reference dataset for optimization of prediction of phosphorylation sites, collected from the UniProtKB was also provided and can be accessed at http://ams2.bioinfo.pl/data/ .

Succination of Protein Thiols during Adipocyte Maturation

Although obesity is a risk factor for development of type 2 diabetes and chemical modification of proteins by advanced glycoxidation and lipoxidation end products is implicated in the development of diabetic complications, little is known about the chemical modification of proteins in adipocytes or adipose tissue. In this study we show that S-(2-succinyl)cysteine (2SC), the product of chemical modification of proteins by the Krebs cycle intermediate, fumarate, is significantly increased during maturation of 3T3-L1 fibroblasts to adipocytes. Fumarate concentration increased > or =5-fold during adipogenesis in medium containing 30 mm glucose, producing a > or =10-fold increase in 2SC-proteins in adipocytes compared with undifferentiated fibroblasts grown in the same high glucose medium. The elevated glucose concentration in the medium during adipocyte maturation correlated with the increase in 2SC, whereas the concentration of the advanced glycoxidation and lipoxidation end products, N(epsilon)-(carboxymethyl)lysine and N(epsilon)-(carboxyethyl)lysine, was unchanged under these conditions. Adipocyte proteins were separated by one- and two-dimensional electrophoresis and approximately 60 2SC-proteins were detected using an anti-2SC polyclonal antibody. Several of the prominent and well resolved proteins were identified by matrix-assisted laser desorption ionization time-of-flight/time-of-flight mass spectrometry. These include cytoskeletal proteins, enzymes, heat shock and chaperone proteins, regulatory proteins, and a fatty acid-binding protein. We propose that the increase in fumarate and 2SC is the result of mitochondrial stress in the adipocyte during adipogenesis and that 2SC may be a useful biomarker of mitochondrial stress in obesity, insulin resistance, and diabetes.

Free radical oxidation of proteins and its relationship with functional state of organisms

Most reactive oxygen species (ROS) in living organisms are produced as byproducts of many processes. Being highly active, ROS interact with virtually all cellular components particularly modifying their properties. In this review, detailed analysis of chemical modifications of proteins on their interaction with ROS is given with particular interest in cleavage of polypeptide chains and oxidation of side chains of amino acid residues. Special attention has been paid to identification of products of free radical modification of proteins with a focus on the formation of additional carbonyl groups, which are the most frequently used markers of these processes. Functional consequences of protein modification by ROS depend on the nature of ROS and protein as well as particular conditions of their interaction. The relationship between protein oxidation and functional state of organisms, particularly aging, hyperoxia and hypoxia, and heat shock, as well as with different pathologies has been analyzed. The final part of the article is devoted to possible ways of protecting proteins against oxidation in vivo.

Staples, Tape Measures, and Bungee Cords: A Variety of Bifunctional Reagents for Understanding and Controlling Ion Channels

Chemical modification of proteins with bifunctional reagents has become a widely used technique for analyzing protein structure and dynamics. A new era is emerging, and scientists can now actually control the function of proteins by tethering molecular switches at a desired position. In a new paper, researchers stretch the technique a bit further by using a reactive derivative of a peptide toxin to probe the subunit composition of a voltage-gated K+ channel.

Site-Specific Formation of Maillard, Oxidation, and Condensation Products from Whey Proteins during Reaction with Lactose

Heat treatment of dairy products leads to structural changes of proteins, which can severely decrease the nutritional value [Mauron, J. J. Nutr. Sci. Vitaminol. (Tokyo) 1990, 36 (Suppl. 1), S57-69]. In this study, model solutions of the two main whey proteins, alpha-lactalbumin and beta-lactoglobulin, respectively, were incubated with lactose, and modifications were monitored by matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF-MS). Lactulosyl residues were the most abundant modifications of alpha-lactalbumin and beta-lactoglobulin. Up to four of these adducts were identified on the proteins. Enzymatical digest with endoproteinase AspN prior to mass spectrometric analysis allowed the detection of further modifications and their localization in the amino acid sequence. Most prominent modifications were lactulosyllysine, Nepsilon-carboxymethyllysine, oxidation of lysine to aminoadipic semialdehyde, oxidation of methionine to methionine sulfoxide, cyclization of N-terminal glutamic acid to a pyrrolidone, and oxidation of cysteine or tryptophan. The presence of methionine oxidation was deduced from a control protein that had been oxidized by hydrogen peroxide. These studies establish MALDI-TOF-MS as a reliable tool to monitor chemical modifications of nutritional proteins during food processing.

Proteomic identification of technologically modified proteins in malt by combination of protein fractionation using convective interaction media and matrix-assisted laser desorption/ionization time-of-flight mass spectrometry

A method for the fast separation of proteins and identification of their modifications based on the use of monolithic chromatographic media and mass spectrometric techniques is described. This method has been developed and applied to the analysis of malt proteins and its posttranslational modifications (glycation). Glycation, one of the most common forms of posttranslational modifications (PTM), can be detected in both biological and industrial samples. Our attention was focused on the investigations of possible chemical modifications of water-soluble barley proteins during malting process by combination of anion-exchange chromatography with matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS). The malt extract was directly fractioned by anion-exchange chromatography using short monolithic columns and a linear gradient from 0 to 700 mM NaCl. Sufficient fractionation was obtained for malt sample, which demonstrates the potential of anion-exchange chromatography on this type of column. Proteins in separated fractions were identified by MALDI-TOF/TOF MS. Our proteomic analysis provided the identification of the major proteins present in the malt that were found to be heterogeneously glycated after malting. One of these proteins: nonspecific lipid transfer protein 1 (LTP1) can be used as a marker for characterization of glycation during malting. This protein and its modifications can be easily determined by the developed method.

Short-term memory

Chemical modification of histone proteins can affect the expression of their associated genes. Some immune cells seem to exploit this process to avoid excessive inflammation while fighting invading pathogens.