The role of free amino groups of peptides and proteins in the Folin-Lowry and biuret methods

On an equal weight basis polymyxin B and EM 49 which do not contain tyrosine or tryptophan yielded the same colour intensity as proteins in the Folin-Lowry and biuret methods. But, in the absence of reagent C (alkaline copper reagent) polymyxin B and EM 49 yielded no colour in the Folin-Lowry method. Mono-, di- and tri-formyl polymyxins B formed identical amounts of coloured complexes as polymyxin B in the two methods. However, the tetra- and penta-formyl polymyxins B yielded only one-fifth and one-sixth, respectively, of the expected colour in the Folin-Lowry method. Similarly, 40% and 30%, respectively, of the anticipated amount of colour is formed in the biuret method. Formylated and methylated lysozyme and bovine serum albumins form only 70–75% of the expected colour in the Folin-Lowry method. Since formation of colour by reduction of Folin reagent, in the Folin-Lowry method, is at least partly due to complexes of copper, it was inferred that polymyxin B as well as its mono-, di- and tri-formyl derivatives on the one hand and the tetra- and penta-formyl derivatives on the other differ in their ability to complex Cu(II) The former group of compounds was indeed found to complex as many as three Cu(II) ions whereas the tetra- and penta-formyl polymyxins B complexed only one equivalent, under conditions of excess Cu(II). Under conditions of low Cu(II), polymyxin B and all its derivatives complexed only one Cu(II). In proteins, sites other than amino groups which complex Cu(II) probably play a major role in the reduction of the Folin reagent, since methylated lysozyme and bovine serum albumin yield 70–75% of the colour formed by the unmodified proteins in the Folin-Lowry reaction.     

Functional arginine-containing amino acid sequences in peptides and proteins

L-Arginine is a source of nitrogen oxide and plays a great role in a number of other biochemical processes. Functions and prospects for practical application of five groups of arginine-containing amino acid sequences and synthetic polyarginine sequences are considered. The physiological characteristics of well-known arginine-containing peptides, such as RGD containing, kyotorphin, and tuftsin, are described in detail.     

Functional arginine-containing amino acid sequences in peptides and proteins

L-arginine is a source of nitrogen oxide and plays a great role in a number of other biochemical processes. Functions and prospects for practical application of five groups of arginine-containing amino acid sequences and synthetic polyarginine sequences are considered. The physiological characteristics of well-known arginine-containing peptides, such as RGD peptides, kyotorphin, and tuftsin, are described in detail. The English version of the paper: Russian Journal of Bioorganic Chemistry, 2008, vol. 34, no. 2; see also http://www.maik.ru     

Hypochlorite-induced oxidation of amino acids, peptides and proteins

Summary. Activated phagocytes generate the potent oxidant hypochlorite (HOCl) via the release of the enzyme myeloperoxidase and hydrogen peroxide. HOCl is known to react with a number of biological targets including proteins, DNA, lipids and cholesterol. Proteins are likely to be major targets for reaction with HOCl within a cell due to their abundance and high reactivity with HOCl. This review summarizes information on the rate of reaction of HOCl with proteins, the nature of the intermediates formed, the mechanisms involved in protein oxidation and the products of these reactions. The predicted targets for reaction with HOCl from kinetic modeling studies and the consequences of HOCl-induced protein oxidation are also discussed.     

Specific reduction of carboxyl groups in peptides and proteins by diborane

1. The reaction of several peptides and proteins with diborane was studied under different conditions to determine those most suitable for the specific reduction of carboxyl groups. 2. In the reaction of model peptides and the cyclic peptides bacitracin and tyrocidin, reduction at 0 degrees was entirely specific for the carboxyl groups without affecting the peptide bonds. Acid amide residues were not reduced. Some tripeptides showed anomalous results in that the C-terminal residue was quite resistant to reduction. 3. Specific reduction of carboxyl groups was achieved in each of the following proteins: human serum albumin, egg albumin, adult human haemoglobin, sperm-whale apomyoglobin, horse heart cytochrome c and egg-white lysozyme. The C-terminal amino acid was usually reduced. 4. Conditions for specific reduction of all available carboxyl groups are not easily found and may vary from one substance to another. Specific reduction of a limited number of available carboxyl groups may be generally accomplished by reactions at -10 degrees . 5. It is suggested that this chemical modification, which has the advantage of permanence, may be useful in studying the role of carboxyl groups in the conformation of proteins and in the biological properties of peptides and proteins.     

The reaction of 2,4,6-trinitrobenzenesulphonic acid with amino acids, peptides and proteins

1. The kinetics of the reaction of 2,4,6-trinitrobenzenesulphonic acid with various amino acids, peptides and proteins were studied by spectrophotometry. 2. The reaction of the α- and -amino groups in simple amino acids was found to be second-order, and the unprotonated amino group was shown to be the reactive species. 3. By allowing for the concentration of unreactive −NH₃⁺ group, intrinsic reactivities for the free amino groups were derived and shown to be correlated with the basicities. 4. The SH group of N-acetylcysteine was found to be more reactive to 2,4,6-trinitrobenzenesulphonic acid than most amino groups. 5. The reactions of insulin, chymotrypsinogen and ribonuclease with 2,4,6-trinitrobenzenesulphonic acid were analysed in terms of three exponential rate curves, each referring to one or more amino groups of the proteins. 6. The reaction of lysozyme with 2,4,6-trinitrobenzenesulphonic acid was found to display an acceleration effect. 7. From the reaction of 2,4,6-trinitrobenzenesulphonic acid with glutamate dehydrogenase at several enzyme concentrations, it was possible to discern two sets of amino groups of different reactivity, and to show that the number of groups in each set was decreased by aggregation of the enzyme.     

Functionalization of peptides and proteins by aldehyde or keto groups

The functionalization of peptides and proteins by aldehyde or keto groups has become the subject of intensive research since the discovery of the inhibition properties of peptide aldehydes and the advent of protein engineering. The first part of this review focuses upon the tremendous efforts devoted to the solid-phase synthesis of peptide aldehydes as protease inhibitors. The second part describes the utility of the aldehyde or keto functionalities for the site-specific modification of peptides or proteins.     

The first peptides: The evolutionary transition between prebiotic amino acids and early proteins

The issues we attempt to tackle here are what the first peptides did look like when they emerged on the primitive earth, and what simple catalytic activities they fulfilled. We conjecture that the early functional peptides were short (3-8 amino acids long), were made of those amino acids, Gly, Ala, Val and Asp, that are abundantly produced in many prebiotic synthesis experiments and observed in meteorites, and that the neutralization of Asp's negative charge is achieved by metal ions. We further assume that some traces of these prebiotic peptides still exist, in the form of active sites in present-day proteins. Searching these proteins for prebiotic peptide candidates led us to identify three main classes of motifs, bound mainly to Mg²⁺ ions: D(F/Y)DGD corresponding to the active site in RNA polymerases, DGD(G/A)D present in some kinds of mutases, and DAKVGDGD in dihydroxyacetone kinase. All three motifs contain a DGD submotif, which is suggested to be the common ancestor of all active peptides. Moreover, all three manipulate phosphate groups, which was probably a very important biological function in the very first stages of life. The statistical significance of our results is supported by the frequency of these motifs in today's proteins, which is three times higher than expected by chance, with a P-value of 3×10⁻². The implications of our findings in the context of the appearance of life and the possibility of an experimental validation are discussed.     

Strong interaction between disulfide derivatives and aromatic groups in peptides and proteins

The intermolecular interaction energy of complexes of dimethyldisulfide with benzene and cyclohexane, respectively, was computed as function of the relative distance and orientation within each pair of molecules. The energy of the most stable orientation of the dimethyldisulfide-cyclohexane complex is ?2.57 kcal/mol, while that of the most stable orientation of the dimethyldisulfide-benzene complex is ?3.33 kcal/mol. The energy difference of ～0.8 kcal/mol is due to favorable specific nonbonded interactions between the sulfur atoms and the atoms of the aromatic ring. Proper parameterization of empirical interatomic energies, used in computations in this laboratory, accounts for these interactions without the need for a $\text{special}$ sulfur-aromatic potential energy function.     

New cyclization reaction at the amino terminus of peptides and proteins

Mild oxidation with periodate of the 1-amino-2-ol moiety of N-terminal seryl or threonyl peptides and proteins leads to a terminal aldehyde function O=CH-CO- which usually may be exploited for bioconjugate formation (e.g., via oximation with an O-alkyl hydroxylamine). We report that, when followed by a prolyl residue, the O=CH-CO- group can undergo a rapid cyclization and dehydration reaction through nucleophilic attack by the amide nitrogen of the third amino acid residue of the chain. We have characterized the resulting heterocycle, which is stable in aqueous acid, by mass spectrometry and NMR. Quantitative oximation can nevertheless be achieved in such cases by performing a one-pot oxidation-oximation without isolation of the intermediate aldehyde, as is demonstrated with cholera toxin B subunit.