Racemization studies in peptide synthesis through the separation of protected epimeric peptides by reversed-phase high performance liquid chromatography.

Separation of protected epimeric peptides, Z-Gly-Xaa-Xbb-OMe (where Xaa and Xbb = chiral amino acid residues), by reversed-phase HPLC was utilized for studying racemization in peptide synthesis. Thus, the following factors which might affect the extent of racemization during the coupling by the carbodiimide method were investigated: the combination of amino acid residues to be coupled, coexisting tertiary amine salts, and the relative configuration of the amino acid residues. The following points were revealed: the combination of bulky residues at the coupling site results in extensive racemization in a polar solvent such as DMF, the amine hydrochlorides cause less racemization than the p-toluene-sulfonates in DMF, and the influence of relative configuration differs depending on the solvent and the individuality of the amino components. Furthermore, the racemization-suppressing effect of some additives in the carbodiimide method was reevaluated by employing the same procedure.     

Racemization of Individual Aspartate Residues in Human Myelin Basic Protein

Human myelin basic protein (MBP), a long-lived brain protein, undergoes gradual racemization of its amino acids, primarily aspartic acid and serine. Purified protein was treated at neutral pH with trypsin to yield peptides that were separated by HPLC using a C18 column. Twenty-nine peptides were isolated and analyzed for amino acid composition and aspartate racemization. Each aspartate and asparagine in the protein was racemized to a different extent, ranging from 2.2 to 17.1% D isomer. When the racemization was examined in terms of the beta-structure model of MBP, a correlation was observed in which six aspartate/asparagine residues assumed to be associated with myelin membrane lipids showed little racemization (2.2-4.9% D isomer), whereas five other aspartate residues were more highly racemized (9.9-17.1% D isomer). Although the observed aspartate racemization may be related to steric hindrance by neighboring residues and/or the protein secondary structure, interaction of aspartates with membrane lipids may also be a major factor. The data are compatible with a model in which each MBP molecule interacts with adjacent cytoplasmic layers of myelin membrane through a beta-sheet on one surface and loops and helices on the other surface, thereby stabilizing the myelin multilamellar structure.     

Racemization of alpha-melanotropin

Racemization of the amino acid residues of alpha-melanotropin was measured after exposure of the peptide to alkali for various lengths of time. Rates of racemization were then compared to the rate of transformation by alkali of alpha-melanotropin into a hormone with prolonged melanotropic activity. When in vitro prolongation became maximal, serine, methionine, histidine, phenylalanine and arginine were racemized 50-70%, glutamic acid, tyrosine and tryptophan 30-40% and lysine, proline and valine 10% or less. Racemization of a particular amino acid residue in alpha-melanotropin could not be associated with induction of prolongation of activity. Rather, partial racemization at multiple sites in the molecule seems almost as effective as extensive or total racemization of a single residue in producing a hormone with prolonged biological effects.     

Isolation of R-(−)-3-Hydroxy-β-ionone from Burley Tobacco

The tritium-hydrogen exchange method was used to determine the total racemization of amino acid residues of four proteins (ribonuclease A, lysozyme, soybean protein and casein) during their exposure to an alkali. Tritium was incorporated with first order kinetics into these proteins during their incubation in 0.2 n NaOH at 40°C. The tritium-hydrogen exchange increased as the temperature and the alkali concentration increased. In contrast, pepsin digestibility decreased extensively in the initial stage of the treatment. This phenomenon was verified by the subsite theory of protease, that only minor racemization renders the extended range of the peptide chain around the racemized amino acids non-susceptible to pepsin. General precautions against the racemization of food protein treated with alkalis are discussed briefly in terms of the deterioration of nutrients.     

Native chemical ligation in dimethylformamide can be performed chemoselectively without racemization

Native chemical ligation of unprotected peptides in organic solvents has been previously reported as a fast, efficient, and suitable method for coupling of hydrophobic peptides. However, it has not been determined whether the reaction can be carried out without possible side reactions or racemization. Here, we present a study on the chemoselectivity of this method by model reactions designed to test the reactivity of Arg and Lys side chains as well as that of α‐amino groups. A possible racemization of the C‐terminal amino acid of the N‐terminal peptide was also investigated. The results show that ligation in organic solvents can be conducted chemoselectively without side reactions with other nucleophilic groups. Furthermore, no racemization of the C‐terminal amino acid was observed if both educts were added simultaneously. Thus, native chemical ligation can be performed either in aqueous buffer systems or in organic solvents paving the way for the synthesis of larger hydrophobic peptides and/or membrane proteins. Copyright © 2012 European Peptide Society and John Wiley & Sons, Ltd.     

Age-dependent accumulation of protein residues which can be hydrolyzed to D-aspartic acid in human erythrocytes

We have measured the rate of accumulation of amino acid residues in human erythrocyte membrane and cytosolic proteins which give D-aspartic acid upon acid hydrolysis. These residues would include D-aspartic acid, D-asparagine, as well as the beta-transpeptidation product, D-isoaspartic acid. Measurements made using age (density) fractionated cells indicate that racemization at these residues occurs on membrane proteins with a t1% (the time required to convert 1% to the D configuration) of about 38.6 days. Fractionation of membrane components revealed a faster rate of racemization for intrinsic proteins than for extrinsic proteins. On the other hand, significant age-dependent racemization was not detected for cytosolic proteins, and the calculated t1% value for these proteins is at least 4 times larger. These results suggest that in the 120-day life span of an erythrocyte, significant racemization of membrane (but not cytosolic) proteins can occur. We have also determined that the rates of accumulation of these residues for erythrocyte membrane and cytosolic proteins incubated in vitro are similar to those observed in vivo. These observations are discussed in terms of the possible cellular metabolism of racemized proteins.     

Functional prediction: identification of protein orthologs and paralogs

Orthologs typically retain the same function in the course of evolution. Using beta-decarboxylating dehydrogenase family as a model, we demonstrate that orthologs can be confidently identified. The strategy is based on our recent findings that substitutions of only a few amino acid residues in these enzymes are sufficient to exchange substrate and coenzyme specificities. Hence, the few major specificity determinants can serve as reliable markers for determining orthologous or paralogous relationships. The power of this approach has been demonstrated by correcting similarity-based functional misassignment and discovering new genes and related pathways, and should be broadly applicable to other enzyme families.     

Limiting racemization and aspartimide formation in microwave-enhanced Fmoc solid phase peptide synthesis.

Microwave energy represents an efficient manner to accelerate both the deprotection and coupling reactions in 9-fluorenylmethyloxycarbonyl (Fmoc) solid phase peptide synthesis (SPPS). Typical SPPS side reactions including racemization and aspartimide formation can occur with microwave energy but can easily be controlled by routine use of optimized methods. Cysteine, histidine, and aspartic acid were susceptible to racemization during microwave SPPS of a model 20mer peptide containing all 20 natural amino acids. Lowering the microwave coupling temperature from 80 degrees C to 50 degrees C limited racemization of histidine and cysteine. Additionally, coupling of both histidine and cysteine can be performed conventionally while the rest of the peptide is synthesized using microwave without any deleterious effect, as racemization during the coupling reaction was limited to the activated ester state of the amino acids up to 80 degrees C. Use of the hindered amine, collidine, in the coupling reaction also minimized formation of D-cysteine. Aspartimide formation and subsequent racemization of aspartic acid was reduced by the addition of HOBt to the deprotection solution and/or use of piperazine in place of piperidine.     

Selectivity in vitamin B-6 model reactions: Selective α or β deuteration of amino acids under transamination or racemization conditions

Al(III)-catalyzed reactions of vitamin B-6 (pyridoxal)-amino acid schiff bases have been studied in ²H₂O. By using excess of the amino acid and varying conditions, amino acids selectively deuterated in the α-position, the β-position, or in both α- and β-positions are isolated. Reaction conditions are those of model systems in which amino acids are known to be reversibly transaminated and racemized by pyridoxal and Al(III). The racemization reaction leads to α-deuteration of the amino acid while transamination followed by its reverse leads to both α- and β-deuteration. The two reactions are viewed as passing through a common dihydropyridine intermediate. The Al(III) serves as an interesting model for the enzyme in that it not only catalyzes transamination and racemization but also can be made to select which of these reactions predominates. This selective catalysis of these reactions is attributed to strong and different pH dependence of the reactivity of various sites of the dihydropyridine intermediate for vitamin B-6 catalysis when incorporated in an Al(III) complex. The biochemical importance of this selectivity and the practical extension of the method of deuteration to other amino acids is discussed.     

A rational approach to the synthesis of phosphonamidate peptides

Summary A rational approach to the synthesis of phosphonamidate pseudopeptides is described. This strategy can be easily applied to the preparation of peptides containing phosphonic acid residues at various positions, as well as sidechain-functionalized amino acid residues. The reaction conditions are compatible with the severe lability of the P-N bond, and the absence of racemization is demonstrated by³¹P NMR analysis. This approach is suitable for application in solid-phase synthesis of biologically active phosphonopeptides.     

Functional Constraints of Alcohol Dehydrogenase (ADH) of Tephritidae and Relationships with Other Dipteran Species

Alcohol dehydrogenase is considered a very important enzyme in insect metabolism because it is involved (in its homodimeric form) in the catalysis of the reversible conversion of various alcohols in larval feeding sites to their corresponding aldehydes and ketones, thus contributing to detoxification and metabolic purposes. Using 14 amino acid ADH sequences recently determined in our laboratory, we constructed a three-dimensional (3D) model of olive fruit fly Bactrocera oleae ADH1 and ADH2, based on the known homologous Drosophila lebanonensis ADH structure, and the amino acid residues that have been proposed as being responsible for catalysis were located on it. Moreover, in a comparative study of the ADH sequences, the residues occupying characteristic positions in the ADH of species of the Bactrocera and Ceratitis genera (called genus-specific) as well as residues appearing only in ADH1 or ADH2 (called isozymic-specific) were defined and localized on the 3D model. All regions important for catalytic activity, such as those forming the substrate- and coenzyme-binding sites, are highly conserved in all tephritid species examined. Genus-specific amino acids are located on the outside of the protein, on loops and regions predicted to be antigenic. The higher percentage of genus-specific amino acid variation seems to be centered in the NAD adenine-binding site, located near the surface of the protein molecule. Nine of 12 isozymic-specific positions are lined along an arc on the surface of the protein, thus linking the two monomer bases of the dimer via the C-terminal interacting loops. Furthermore, the distribution of isozymic- and genus-specific amino acids on the monomer–monomer interface may have some evolutionary significance. Most amino acids predicted to be antigenic are positioned in peripheral regions of nonfunctional importance, but surprisingly, an additional antigenic region is contained within the (highly conserved in tephritids) C-terminal tail.     

Radiolysis,racemization, and the origin of optical activity

An investigation has been undertaken to determine whether ionizing radiation might engender racemization (radioracemization) of optically active amino acids, along with their well-known radiolysis. We have exposed a number of solid and dissolved optically active amino acids to the ionizing radiation from a 3000-Ci ⁶⁰Co γ-ray source for periods of time which would engender substantial, but not total radiolysis. γ-Ray doses which caused 55–68% radiolysis of solid amino acids typically engendered 2–5% racemization. Aqueous solutions of the sodium salts of amino acids which underwent 53–66% radiolysis typically showed 5–11% racemization. The corresponding hydrochloride salts in aqueous solution, however, underwent little or no racemization. In aqueous solution both percentage degradation and percentage racemization were approximately proportional to γ-ray dosage within the range employed (1–36 × 10⁶ rads). Mechanisms for the radioracemization of amino acids in the solid state and as dissolved sodium salts are proposed, and the absence of racemization for dissolved hydrochloride salts is rationalized. Implications of these observations with regard to the origin of optical activity by the Vester-Ulbricht β-decay mechanism are discussed, as are their implications regarding the use of diagenetic racemization rates of ancient amino acid samples as criteria for geochronological and geothermometric calculations.     

Serine racemases from barley, Hordeum vulgare L., and other plant species represent a distinct eukaryotic group: gene cloning and recombinant protein characterization

Several d-amino acids have been identified in plants. However, the biosynthetic pathway to them is unclear. In this study, we cloned and sequenced a cDNA encoding a serine racemase from barley which contained an open reading frame encoding 337 amino acid residues. The deduced amino acid sequence showed significant identity to plant and mammalian serine racemases and contained conserved pyridoxal 5-phosphate (PLP)-binding lysine and PLP-interacting amino acid residues. The purified gene product catalyzed not only racemization of serine but also dehydration of serine to pyruvate. The enzyme requires PLP and divalent cations such as Ca(2+), Mg(2+), or Mn(2+), but not ATP, whereas mammalian serine racemase activity is increased by ATP. In addition to the results regarding the effect of ATP on enzyme activity and the phylogenetic analysis of eukaryotic serine racemases, the antiserum against Arabidopsis serine racemase did not form a precipitate with barley and rice serine racemases. This suggests that plant serine racemases represent a distinct group in the eukaryotic serine racemase family and can be clustered into monocot and dicot types.     

Behavior of Amino Acids when Volatilized in the Presence of Silica Gel and Pulverized Basaltic Lava

To evaluate the types of amino acid thermal transformations caused by silicate materials, we studied the volatilization products of Aib, L-Ala, L-Val and L-Leu under temperatures of up to 270 °C in the presence of silica gel as a model catalyst and pulverized basaltic lava samples. It was found that silica gel catalyzes nearly quantitative condensation of amino acids, where piperazinediones are the major products, whereas lava samples have much lower catalytic efficiency. In addition bicyclic and tricyclic amidines and several products of their subsequent thermal decomposition have been identified using the coupled technique of GC-FTIR-MS and HPLC-PB-MS, with auxiliary computer simulation of IR spectra and NMR spectroscopy. The decomposition is due to dehydrogenation, elimination of the alkyl substituents and dehydration as well as cleavage of the bicyclic ring system. The imidazole ring appears to be more resistant to thermal decomposition as compared to the pyperazine moiety, giving rise to the formation of different substituted imidazolones. The amidines were found to hydrolyze under treatment with concentrated HCl, releasing the starting amino acids and thus behaving as amino acid anhydrides. The thermal transformations cause significant racemization of amino acid residues. Based on our observations, the formation of amidine-type products is suggested to be rather common in the high-temperature experiments on amino acid condensation.     

Molecular and biochemical characterization of a serine racemase from Arabidopsis thaliana

A cDNA encoding a homolog of mammalian serine racemase, a unique enzyme in eukaryotes, was isolated from Arabidopsis thaliana and expressed in Escherichia coli cells. The gene product, of which the amino acid residues for binding pyridoxal 5'-phosphate (PLP) are conserved in this as well as mammalian serine racemases, catalyzes not only serine racemization but also dehydration of serine to pyruvate. The enzyme is a homodimer and requires PLP and divalent cations, Ca2+, Mg2+, Mn2+, Fe2+, or Ni2+, at alkaline pH for both activities. The racemization process is highly specific toward L-serine, whereas L-alanine, L-arginine, and L-glutamine were poor substrates. The Vmax/Km values for racemase activity of L- and D-serine are 2.0 and 1.4 nmol/mg/min/mM, respectively, and those values for L- and D-serine on dehydratase activity are 13 and 5.3 nmol/mg/min/mM, i.e. consistent with the theory of racemization reaction and the specificity of dehydration toward L-serine. Hybridization analysis showed that the serine racemase gene was expressed in various organs of A. thaliana.     

Racemization in the synthesis of polytripeptide models of a collagen.

Racemization in the synthesis of tripeptide intermediates and their polymers was investigated, using L -amino acid oxidase. Stepwise investigation of peptide intermediates showed no racemization during peptide coupling steps or deprotection of benzyl esters by hydrogenolysis. Saponification of one of the methyl esters produced some racemization. Preparation of active esters from N-protected tripeptide acids containing optically active C-terminal amino acid, with one exception, produced racemization. The fractionated polymers were found to contain less racemized amino acids than the crude products or starting monomeric tripeptides, indicating that the racemized sequences gave rise to lower molecular-weight oligomers. The sequences investigated were -Pro-Pro-Ala-, -Ala-Pro-Pro-, -Val-Pro-Pro-, -Pro-Pro-Leu-, -Pro-Gly-Leu-, -Pro-Gly-Phe-, -Pro-Gly-Val-, -Gly-Val-Pro-, -Phe-Pro-Gly-, -Leu-Pro-Gly-, and Ile-Pro-Gly-.     

Effect of copper(II) chloride on suppression of racemization in peptide synthesis by the carbodiimide method.

Copper(II) chloride was found to be an extremely efficient racemization-suppressing additive in the DCC method as compared with the hitherto known ones, by employing the model coupling Z-Gly-L-Val-OH + H-L-Val-OMe in DMF. Although some other copper salts also had a profound effect, copper(II) chloride was the best from the viewpoint of both racemization suppression and coupling efficiency. The effectiveness of copper(II) chloride was further confirmed by employing the EDC-mediated couplings of Z-Gly-containing dipeptides with amino acid esters or dipeptide esters, and those of Z-L-Ala (or L-Val)-L-Val-OH with amino acid esters or dipeptide esters. In almost all the cases studied, no detectable amount (less than 0.1%) of epimer was observed by the HPLC analysis in the presence of copper(II) chloride. This was also the case even with an extremely stringent coupling system Z-L-Pro-L-Val-OH + H-L-Pro-OMe. With reference to the mechanism of racemization suppression, it was found that copper(II) chloride has a strong ability to suppress the racemization of the 5(4H)-oxazolone, which may be formed from an activated carboxyl component during the coupling.     

A systematic study of the amino acid compositions and D/L ratios in fossil bones from two french neanderthalian sites

The reaction of racemization in which the L amino acids are reversibly converted into the corresponding D amino acids, proceeds in geological environment at such a slow rate that it may be used as a geochronometer. However, in fossils several parameters may affect the rate of racemization, i.e. moisture, surface, pH buffer and metal cations. This work consists of a systematic study of total amino acid content in fossil bones from two neanderthalian sites. The amino acid distributions of all specimens were determined and compared to that of fresh bone. The D/L amino acid were quantified and expressed in terms of age as a function of the temperature. The results led us to consider the «La Roquette» site older than «Les Canalettes» site.     

Kinetic study of racemization of aspartyl residues in recombinant human alphaA-crystallin

Asp58 and Asp151 in human lens alphaA-crystallin invert and isomerize to d-beta-aspartyl residues with age. Here, we report that the racemization rate constants (k) of Asp58 and Asp151 residues in human recombinant alphaA-crystallin at 37 degrees C are 3.72 +/- 0.8 x 10(-4) and 10.7 +/- 0.7 x 10(-4)/day, respectively. The activation energy of racemization of Asp58 and Asp151 in the protein was 27.0 +/- 0.5 kcal/mol and 21.0 +/- 0.5 kcal/mol, respectively. The time required for the D/L ratio of Asp58 and Asp151 to approximate to 1.0 (D/L ratio of Asp = 0.99) at 37 degrees C was estimated as 20.9 +/- 3.7 and 6.80 +/- 0.4 years, respectively. Thus, Asp151 is more susceptible to racemization than Asp58, consistent with data from short model peptides. However, the racemization rates of both Asp58 and Asp151 residues in the protein were twice as rapid as in model peptides. These results indicate that the racemization of Asp residues in alphaA-crystallin may be influenced not only by the primary structure but also by the higher order structure around Asp residues in the protein.     

Effects of N-Terminal Deletion Mutation on Rabbit Muscle Lactate Dehydrogenase

Deletion mutants of rabbit muscle lactate dehydrogenase (LDH) were constructed using polymerase chain reaction (PCR) to study the roles of N-terminal residues. The coding sequences of the first 5 (LD5) and 10 (LD10) amino acids of the N-terminus were deleted and the gene was inserted into the prokaryotic expression vector pET21b. The mutant enzymes were expressed in E. coli BL21/DE3 and were purified. Then their characteristics and stabilities were studied. The results showed LDH was completely inactivated when the first 10 N-terminal amino acid residues were removed, but the mutant (LD10) could have partially restored activity in the presence of structure-making ions. The removal of the first 5 and 10 N-terminal amino acid residues did not affect the aggregation state of the enzyme, that is, LD5 and LD10 were still tetramers. The stabilities of recombinant wild-type LDH (RW-LD), LD5, and LD10 were compared by incubating them at low pH, elevated temperature, and high GuHCl. The results showed that the N-terminal deletion mutants were more sensitive to denaturing environments; they were easily inactivated and unfolded. Their instability increased and their ability to refold decreased with the increased number of amino acid residues removed from the N-terminus of LDH. These results confirm that the N-terminus of LDH plays a crucial role in stabilizing the structure and in maintaining the function of the enzyme.