Chemical Modification Of Amino Acids Research Articles

Increased Amino Acid Absorption Mediated by Lacticaseibacillus rhamnosus IDCC 3201 in High-Protein Diet-Fed Mice.

The use of dietary protein products has increased with interests in health promotion, and demand for sports supplements. Among various protein sources, milk protein is one of the most widely employed, given its economic and nutritional advantages. However, recent studies have revealed that milk protein undergoes fecal excretion without complete hydrolysis in the intestines. To increase protein digestibility, heating and drying were implemented; however, these methods reduce protein quality by causing denaturation, aggregation, and chemical modification of amino acids. In the present study, we observed that Lacticaseibacillus rhamnosus IDCC 3201 actively secretes proteases that hydrolyze milk proteins. Furthermore, we showed that co-administration of milk proteins and L. rhamnosus IDCC 3201 increased the digestibility and plasma concentrations of amino acids in a high-protein diet mouse model. Thus, food supplementation of L. rhamnosus IDCC 3201 can be an alternative strategy to increase the digestibility of proteins.

A Fluorogenic Assay: Analysis of Chemical Modification of Lysine and Arginine to Control Proteolytic Activity of Trypsin

The chemical modification of amino acids plays an important role in the modulation of proteins or peptides and has useful applications in the activation and stabilization of enzymes, chemical biology, shotgun proteomics, and the production of peptide-based drugs. Although chemoselective modification of amino acids such as lysine and arginine via the insertion of respective chemical moieties as citraconic anhydride and phenyl glyoxal is important for achieving desired application objectives and has been extensively reported, the extent and chemoselectivity of the chemical modification of specific amino acids using specific chemical agents (blocking or modifying agents) has yet to be sufficiently clarified owing to a lack of suitable assay methodologies. In this study, we examined the utility of a fluorogenic assay method, based on a fluorogenic tripeptide substrate (FP-AA1-AA2-AA3) and the proteolytic enzyme trypsin, in determinations of the extent and chemoselectivity of the chemical modification of lysine or arginine. As substrates, we used two fluorogenic tripeptide probes, MeRho-Lys-Gly-Leu(Ac) (lysine-specific substrate) and MeRho-Arg-Gly-Leu(Ac) (arginine-specific substrate), which were designed, synthesized, and evaluated for chemoselective modification of specific amino acids (lysine and arginine) using the fluorogenic assay. The results are summarized in terms of half-maximal inhibitory concentrations (IC50) for the extent of modification and ratios of IC50 values (IC50arginine/IC50lysine and IC50lysine/IC50arginine) as a measure of the chemoselectivity of chemical modification for amino acids lysine and arginine. This novel fluorogenic assay was found to be rapid, precise, and reproducible for determinations of the extent and chemoselectivity of chemical modification.

SFB 1309: Collaborating to Understand the Chemical Biology of Epigenetic Modifications

The discovery of DNA has been one of the most important findings of the last century, yet there is still much more to uncover about the ‘additional chemical layer’ brought about by the chemical modification of amino acids and nucleotide bases. A large collaboration of researchers at institutions across Germany, known as SFB 1309, is led by Professor Thomas Carell at the Ludwig-Maximilians University in Munich. A key focus of SFB 1309 is to elucidate the details of the second layer of information beyond the sequence layer of biochemical molecules called Watson-Crick bases within our DNA.

Myoblast Phosphoproteomics as a Tool to Investigate Global Signaling Events During Myogenesis.

Protein phosphorylation is a universal covalent chemical modification of amino acids involved in a large number of biological processes including cell signaling, metabolism, proliferation, differentiation, survival/death, ageing, and many more. Regulation of protein phosphorylation is essential in myogenesis and indeed, when the enzymatic activity of protein kinases is distrupted in myoblasts, myogenesis is affected. In this chapter we describe a method to profile the phosphoproteome of myoblasts using mass spectrometry. Phosphate groups are labile and easily lost during the processing of samples for mass spectrometry. Thus, effective methods to enrich for phosphopeptides from protein extracts have been developed. Here, we discuss and present in detail two such methods that we routinely employ. These methods are based on a sample enrichment step performed on titanium dioxide matrices followed by label-free tandem mass spectrometry and semi-quantitation.

Stepwise extraction, chemical modification, GC–MS separation, and determination of amino acids in human plasma#

AbstractA method for isolation of enriched fractions of amino acids from human plasma followed by derivatization, gas chromatography separation and mass spectrometry identification is described. The method involves a stepwise extraction of plasma constituents with the use of two solvents: (a) extraction with methanol yields a concentrate of polyols, urea, carbohydrates and most long‐chain saturated and unsaturated aliphatic acids, and (b) further solubilization with water produces mainly a concentrate of amino acids. Chemical modification of amino acids with methyl chloroformate/methanol gives rise to methyl esters of methoxycarbonyl derivatives. The derivatization products are stable and quite suitable for gas chromatography with mass spectrometry analysis. The electron ionization mass spectra of the derivatization products reveal specific fragmentation patterns applicable for structure elucidation. The efficiency of the method is demonstrated by gas chromatography with mass spectrometry identification of 19 amino acids as their methyl esters of methoxycarbonyl derivatives in Standard Reference Material 1950 Metabolites in Frozen Human Plasma.

Chemically Modified Silk Proteins

Silks are of central importance as smart natural biomaterials and are attracting increasing attention for their biomimetic potential due to their sophisticated molecular structure, self‐assembly mechanism, impressive mechanical properties, biocompatibility, and biodegradability. The versatility of silk proteins (SP) allows the chemical modification of silk‐based materials with diverse morphologies under harsh conditions. The chemical modification of amino acids within SP enables the expanded generation of new biomaterials and the extension of their potential functional applications. The authors review the current chemical modification strategies and routes for the functionalization of SP.

ActiveDriverDB: human disease mutations and genome variation in post-translational modification sites of proteins.

Interpretation of genetic variation is needed for deciphering genotype-phenotype associations, mechanisms of inherited disease, and cancer driver mutations. Millions of single nucleotide variants (SNVs) in human genomes are known and thousands are associated with disease. An estimated 21% of disease-associated amino acid substitutions corresponding to missense SNVs are located in protein sites of post-translational modifications (PTMs), chemical modifications of amino acids that extend protein function. ActiveDriverDB is a comprehensive human proteo-genomics database that annotates disease mutations and population variants through the lens of PTMs. We integrated >385,000 published PTM sites with ∼3.6 million substitutions from The Cancer Genome Atlas (TCGA), the ClinVar database of disease genes, and human genome sequencing projects. The database includes site-specific interaction networks of proteins, upstream enzymes such as kinases, and drugs targeting these enzymes. We also predicted network-rewiring impact of mutations by analyzing gains and losses of kinase-bound sequence motifs. ActiveDriverDB provides detailed visualization, filtering, browsing and searching options for studying PTM-associated mutations. Users can upload mutation datasets interactively and use our application programming interface in pipelines. Integrative analysis of mutations and PTMs may help decipher molecular mechanisms of phenotypes and disease, as exemplified by case studies of TP53, BRCA2 and VHL. The open-source database is available at https://www.ActiveDriverDB.org.

PROTEASE INHIBITOR FROM WHITE CRANBERRY BEANS (PHASEOLUS VULGARIS): ISOLATION, PURIFICATION AND CHARACTERIZATION

Objective: The main objective of the study was isolation, purification and characterization of protein protease inhibitor from the seeds of Phaseolus vulgaris and analysis of its antimicrobial potential.Methods: The protease inhibitor was extracted by homogenizing seeds of Phaseolus vulgaris in 0.1 M phosphate buffer (pH-7.0). The crude extract of the inhibitor was purified by using ammonium sulphate precipitation followed by DEAE Cellulose ion exchange chromatography. The protease inhibitor was characterized to determine its optimum pH and pH stability, optimum temperature and temperature stability, stability in the presence of chemical modifiers, thermal stabilizers, metal ions, detergents, oxidising and reducing agents. The antimicrobial potential of the inhibitor against various bacterial species was confirmed using agar well diffusion method.Results: The extracted protease inhibitor was purified to homogeneity with a 1.4 fold increase in the specific activity and 56 % purification yield. Inhibitor was optimally active at pH 7.0 and a temperature of 50 °C as well as showed considerable stability over pH ranging from 4.0-11.0 and up to a temperature of 70 °C for 4 h duration. The inhibitor was substantially active and stable in the presence of surfactants 1 % (v/v) Tween 20, 4 % (v/v) of oxidizing agents such as dimethyl sulphoxide (DMSO) and hydrogen peroxide (H2O2), 0.8 % (v/v) of reducing agents β-mercaptoethanol and Sodium thioglycolate. Metal ions Mg++, Ca++and Zn++enhanced the activity of inhibitor while CaCl2, glycine and glycerol promoted thermal stability of the inhibitor. Chemical modification of amino acids at the active site by diethyl pyrocarbonate (DEPC) and phenyl methyl sulphonyl fluoride (PMSF) led to decrease in the inhibitory activity. The stoichiometry of trysin-protease inhibitor interaction was 1:2 while 216 μg of the inhibitor effected 50 % inhibition. The inhibitor displayed antimicrobial activity against Aeromonas hydrophilla, Citrobacter freundii and Acinetobacter baumanii.Conclusion: The experimental results confirmed the anti proteolytic action of protease inhibitor extracted from P. vulgaris as well as its promising antimicrobial properties. Thus isolated protease inhibitor has significant industrial and therapeutic potential.

Caesalpinia bonduc serine proteinase inhibitor CbTI–2: Exploring the conformational features and antimalarial activity

Seeds of tropical legumes posses a repertoire of proteinase inhibitors (PI) and the current study highlights some structural/functional features of a strong serine PI from the seeds of Caesalpinia bonduc (CbTI–2). Following purification, N-terminal sequence of CbTI–2 revealed over 40% similarity with a few serine PIs of Caesalpinioideae subfamily. Upon exposure to metal ions and ionic/non ionic surfactants, CbTI–2 showed immense variation in the levels of antitryptic activity. Exposure of CbTI–2 to 1,4-Dithiothreitol, Guanidinium HCl, H2O2 and Dimethyl sulfoxide led to a steady loss of inhibitory activity. Chemical modification of amino acids suggested an arginine as the active site residue. Circular Dichroism spectrum of native CbTI–2 revealed an unordered state. Secondary structure composition of CbTI–2 following exposure to extreme conditions (heat, acidic/alkaline environment, Guanidine hydrochloride and DTT) showed considerable perturbations that caused severe loss of antiproteolytic activity. DLS studies yielded a hydrodynamic radius of ∼2.2nm for CbTI–2 and also reconfirmed 1:1 stoichiometry for the trypsin-CbTI–2 complex. Initial studies indicated CbTI–2 to be a potent antiplasmodial agent by being highly toxic towards growth, schizont rupture process and erythrocytic invasion of Plasmodium falciparum.

The role of intra-domain disulfide bonds in heat-induced irreversible denaturation of camelid single domain VHH antibodies.

Camelid-derived single domain VHH antibodies are highly heat resistant, and the mechanism of heat-induced VHH denaturation predominantly relies on the chemical modification of amino acids. Although chemical modification of disulfide bonds has been recognized as a cause for heat-induced denaturation of many proteins, there have been no mutagenesis studies, in which the number of disulfide bonds was controlled. In this article, we examined a series of mutants of two different VHHs with single, double or no disulfide bonds, and scrutinized the effects of these disulfide bond modifications on VHH denaturation. With the exception of one mutant, the heat resistance of VHHs decreased when the number of disulfide bonds increased. The effect of disulfide bonds on heat denaturation was more striking if the VHH had a second disulfide bond, suggesting that the contribution of disulfide shuffling is significant in proteins with multiple disulfide bonds. Furthermore, our results directly indicate that removal of a disulfide bond can indeed increase the heat resistance of a protein, irrespective of the negative impact on equilibrium thermodynamic stability.

ChemInform Abstract: Peptidomimetics via Modifications of Amino Acids and Peptide Bonds

AbstractReview: 258 refs.

Chemical modification of amino acids by atmospheric-pressure cold plasma in aqueous solution

Plasma medicine is an attractive new research area, but the principles of plasma modification of biomolecules in aqueous solution remain elusive. In this study, we investigated the chemical effects of atmospheric-pressure cold plasma on 20 naturally occurring amino acids in aqueous solution. High-resolution mass spectrometry revealed that chemical modifications of 14 amino acids were observed after plasma treatment: (i) hydroxylation and nitration of aromatic rings in tyrosine, phenylalanine and tryptophan; (ii) sulfonation and disulfide linkage formation of thiol groups in cysteine; (iii) sulfoxidation of methionine and (iv) amidation and ring-opening of five-membered rings in histidine and proline. A competitive reaction experiment using 20 amino acids demonstrated that sulfur-containing and aromatic amino acids were preferentially decreased by the plasma treatment. These data provide fundamental information for elucidating the mechanism of protein inactivation for biomedical plasma applications.

Oxidative stress: Lipid peroxidation products as predictors in disease progression

Oxidative stress is implicated in the pathogenesis of numerous disease processes, including diabetes mellitus, atherosclerosis, ischemia reperfusion injury, rheumatoid arthritis, neurodegenerative diseases as well as in the aging process. Chemical modification of amino acids in protein during lipid peroxidation (LPO) results in the formation of lipoxidation products, which may serve as indicators of oxidative stress in vivo. The various types of aldehydes such as 4-hydroxynonenal, malondialdehyde, acrolein and others produced during LPO may serve as potent oxidative stress biomarkers. Their activation in different signaling cascades lead to apoptosis, differentiation, proliferation, etc., Increased amount of these aldehydes in aging or with metabolic complications or in other diseases indicate their pathophysiological significance. Thus, LPO products or other oxidative stress biomarkers may open the way for the development of early detection, prevention, and therapeutic strategies for stress associated human diseases. Now-a-days, antioxidant supplementation has become an increasingly popular practice to restore the redox homeostatic condition of the cell. Disease specific, target directed, bioavailable antioxidants may be beneficial for sustenance of the quality-of-life in future days.

Peptidomimetics via modifications of amino acids and peptide bonds

Peptidomimetics represent an important field in chemistry, pharmacology and material science as they circumvent the limitations of traditional peptides used in therapy. Self-structural organizations such as turns, helices, sheets and loops can be accessed by chemical modifications of amino acids or peptides. In-depth structural and conformational analysis and structure-activity relationships (SAR) offer a way to establish peptidomimetic libraries. Herein, we review recent developments in peptidomimetics that are formed via heteroatom replacement within the native amino acid backbone. Each sub-section describes structural features, utility and preparative methods.

Novel Extracellular PHB Depolymerase from Streptomyces ascomycinicus: PHB Copolymers Degradation in Acidic Conditions

The ascomycin-producer strain Streptomyces ascomycinicus has been proven to be an extracellular poly(R)-3-hydroxybutyrate (PHB) degrader. The fkbU gene, encoding a PHB depolymerase (PhaZSa), has been cloned in E. coli and Rhodococcus sp. T104 strains for gene expression. Gram-positive host Rhodococcus sp. T104 was able to produce and secrete to the extracellular medium an active protein form. PhaZSa was purified by two hydrophobic interaction chromatographic steps, and afterwards was biochemically as well as structurally characterized. The enzyme was found to be a monomer with a molecular mass of 48.4 kDa, and displayed highest activity at 45°C and pH 6, thus being the first PHB depolymerase from a gram-positive bacterium presenting an acidic pH optimum. The PHB depolymerase activity of PhaZSa was increased in the presence of divalent cations due to non-essential activation, and also in the presence of methyl-β-cyclodextrin and PEG 3350. Protein structure was analyzed, revealing a globular shape with an alpha-beta hydrolase fold. The amino acids comprising the catalytic triad, Ser131-Asp209-His269, were identified by multiple sequence alignment, chemical modification of amino acids and site-directed mutagenesis. These structural results supported the proposal of a three-dimensional model for this depolymerase. PhaZSa was able to degrade PHB, but also demonstrated its ability to degrade films made of PHB, PHBV copolymers and a blend of PHB and starch (7∶3 proportion wt/wt). The features shown by PhaZSa make it an interesting candidate for industrial applications involving PHB degradation.

N-ε-fructosyllysine and N-ε-carboxymethyllysine, but not lysinoalanine, are available for absorption after simulated gastrointestinal digestion

Food processing leads to a variety of chemical modifications of amino acids in food proteins. Recent studies have shown that some modified amino acids resulting from glycation reactions can pass the intestinal barrier when they are bound in dipeptides. In this study, we investigated as to what extent modified amino acids are released from post-translationally modified casein during simulated gastrointestinal digestion. Casein was enriched with N-ε-fructoselysine, N-ε-carboxymethyllysine, and lysinoalanine, in different degrees of modification. The casein samples were subjected to a two-step proteolysis procedure, simulating gastrointestinal digestion. The digestibility of modified casein as measured by analytical size-exclusion chromatography (SEC) decreased with increasing degree of modification especially after enrichment of fructoselysine and lysinoalanine. Semi-preparative SEC of digested casein samples revealed that fructoselysine and carboxymethyllysine are released bound in peptides smaller than 1,000 Da, which is comparable to native amino acids. The glycation compounds should, therefore, be available for absorption. Lysinoalanine as a crosslinking amino acid, however, is mostly released into longer peptides of at least 30-40 amino acids which should strongly impair its absorption availability.

Horseradish peroxidase: Modulation of properties by chemical modification of protein and heme

Horseradish peroxidase (HRP) is one of the most studied enzymes of the plant peroxidase superfamily. HRP is also widely used in different bioanalytical applications and diagnostic kits. The methods of genetic engineering and protein design are now widely used to study the catalytic mechanism and to improve properties of the enzyme. Here we review the results of another approach to HRP modification-through the chemical modification of amino acids or prosthetic group of the enzyme. Computer models of HRPs with modified hemes are in good agreement with the experimental data.

TbMP42 is a structure-sensitive ribonuclease that likely follows a metal ion catalysis mechanism.

RNA editing in African trypanosomes is characterized by a uridylate-specific insertion and/or deletion reaction that generates functional mitochondrial transcripts. The process is catalyzed by a multi-enzyme complex, the editosome, which consists of approximately 20 proteins. While for some of the polypeptides a contribution to the editing reaction can be deduced from their domain structure, the involvement of other proteins remains elusive. TbMP42, is a component of the editosome that is characterized by two C2H2-type zinc-finger domains and a putative oligosaccharide/oligonucleotide-binding fold. Recombinant TbMP42 has been shown to possess endo/exoribonuclease activity in vitro; however, the protein lacks canonical nuclease motifs. Using a set of synthetic gRNA/pre-mRNA substrate RNAs, we demonstrate that TbMP42 acts as a topology-dependent ribonuclease that is sensitive to base stacking. We further show that the chelation of Zn2+ cations is inhibitory to the enzyme activity and that the chemical modification of amino acids known to coordinate Zn2+ inactivates rTbMP42. Together, the data are suggestive of a Zn2+-dependent metal ion catalysis mechanism for the ribonucleolytic activity of rTbMP42.

EndoS from Streptococcus pyogenes is hydrolyzed by the cysteine proteinase SpeB and requires glutamic acid 235 and tryptophans for IgG glycan-hydrolyzing activity

BackgroundThe endoglycosidase EndoS and the cysteine proteinase SpeB from the human pathogen Streptococcus pyogenes are functionally related in that they both hydrolyze IgG leading to impairment of opsonizing antibodies and thus enhance bacterial survival in human blood. In this study, we further investigated the relationship between EndoS and SpeB by examining their in vitro temporal production and stability and activity of EndoS. Furthermore, theoretical structure modeling of EndoS combined with site-directed mutagenesis and chemical blocking of amino acids was used to identify amino acids required for the IgG glycan-hydrolyzing activity of EndoS.ResultsWe could show that during growth in vitro S. pyogenes secretes the IgG glycan-hydrolyzing endoglycosidase EndoS prior to the cysteine proteinase SpeB. Upon maturation SpeB hydrolyzes EndoS that then loses its IgG glycan-hydrolyzing activity. Sequence analysis and structural homology modeling of EndoS provided a basis for further analysis of the prerequisites for IgG glycan-hydrolysis. Site-directed mutagenesis and chemical modification of amino acids revealed that glutamic acid 235 is an essential catalytic residue, and that tryptophan residues, but not the abundant lysine or the single cysteine residues, are important for EndoS activity.ConclusionWe present novel information about the amino acid requirements for IgG glycan-hydrolyzing activity of the immunomodulating enzyme EndoS. Furthermore, we show that the cysteine proteinase SpeB processes/degrades EndoS and thus emphasize the importance of the SpeB as a degrading/processing enzyme of proteins from the bacterium itself.

Effects of post-translational modifications on prion protein aggregation and the propagation of scrapie-like characteristics in vitro

Prion diseases, or transmissible spongiform encephalopathies (TSEs) are typically characterised by CNS accumulation of PrP Sc, an aberrant conformer of a normal cellular protein PrP C. It is thought PrP Sc is itself infectious and the causative agent of such diseases. To date, no chemical modifications of PrP Sc, or a sub-population thereof, have been reported. In this study we have investigated whether chemical modification of amino acids within PrP might cause this protein to exhibit aberrant properties and whether these properties can be propagated onto unmodified prion protein. Of particular interest were post-translational modifications resulting from physiological conditions shown to be associated with TSE disease. Here we report that in vitro exposure of recombinant PrP to conditions that imitate the end effects of oxidative/nitrative stress in TSE-infected mouse brains cause the protein to adopt many of the physical characteristics of PrP Sc. Most interestingly, these properties could be propagated onto unmodified PrP protein when the modified protein was used as a template. These data suggest that post-translational modifications of PrP might contribute to the initiation and/or propagation of prion protein-associated plaques in vivo during prion disease, thereby high-lighting novel biochemical pathways as possible therapeutic targets for these conditions.