Formation Of Oligopeptides Research Articles

Nano-pulsed discharge plasma-induced abiotic oligopeptide formation from diketopiperazine.

Conventional oligopeptide synthesis techniques involve environmentally harmful procedures and materials. In addition, the efficient accumulation of oligopeptides under Hadean Earth environments regarding the origin of life remains still unclear. In these processes, the formation of diketopiperazine is a big issue due to the strong inhibition for further elongation beyond dipeptides. Hydrothermal media enables environmentally friendly oligopeptide synthesis. However, hydrothermal oligopeptide synthesis produces large amounts of diketopiperazine (DKP), due to its thermodynamic stability. DKP inhibits dipeptide elongation and also constitutes an inhibitory pathway in conventional oligopeptide synthesis. Here, we show an efficient pathway for oligopeptide formation using a specially designed experimental setup to run both thermal and non-thermal discharge plasma, generated by nano-pulsed electric discharge with 16-23kV voltage and 300-430 A current within ca. 500ns. DKP (14%) was converted to dipeptides and higher oligopeptides in an aqueous solution containing alanine-DKP at pH 4.5, after 20min of 50 pps thermal plasma irradiation. This is the first study to report efficient oligopeptide synthesis in aqueous medium using nano-pulsed plasma (with thermal plasma being more efficient than non-thermal plasma) via DKP ring-opening. This unexpected finding is implicative to evaluate the pathway how the oligopeptides could have accumulated in the primitive Earth with high-energy plasma sources such as thunder as well as to facilitate the green synthesis of oligopeptides.

Unbinding events of amino acids and peptides from water–pyrite interfaces: A case study of life’s origin on mineral surfaces

Selective binding of aqueous-phase amino acids to mineral surfaces is regarded as a plausible first step in oligopeptide formation on early Earth. To clarify the strength and underlying mechanism of amino acid binding to pyrite surfaces, we measured the unbinding (pull-off) force of ten amino acids and two oligo-peptides from water-pyrite interfaces using atomic force microscopy (AFM). The most probable unbinding force could be described by a linearly increasing function with the size of the amino acid and a characteristic offset. A good correlation was obtained between the most probable unbinding force and the residue volume, surface area and polarizability of samples suggesting at least a partial contribution of van der Waals (vdW) forces, especially the London dispersion force. These results are useful in analysis of adhesion phenomena of amino acids in the given environmental settings such as in this work.

Effects of Lactobacillus helveticus Fermentation on the Ca2+ Release and Antioxidative Properties of Sheep Bone Hydrolysate

Both the calcium and collagen in bone powder are hard to be absorbed by the body. Although enzymatic hydrolysis by protease increased the bio-availability of bone powder, it was a meaningful try to further increase Ca2+ release, oligopeptide formation and antioxidant activity of the sheep bone hydrolysate (SBH) by lactic acid bacteria (LAB) fermentation. Lactobacillus helveticus was selected as the starter for its highest protease-producing ability among 5 tested LAB strains. The content of liberated Ca2+ was measured as the responsive value in the response surface methodology (RSM) for optimizing the fermenting parameters. When SBH (adjusted to pH 6.1) supplemented with 1.0% glucose was inoculated 3.0% L. helveticus and incubated for 29.4 h at 36℃, Ca2+ content in the fermented SBH significantly increased (p<0.01), and so did the degree of hydrolysis and the obtaining rate of oligopeptide. The viable counts of L. helveticus reached to 1.1×1010 CFU/mL. Results of Pearson correlation analysis demonstrated that LAB viable counts, Ca2+ levels, obtaining rates of oligopeptide and the yield of polypeptide were positively correlated with each other (p<0.01). The abilities of SBH to scavenge the free radicals of DPPH, OH and ABTS were also markedly enhanced after fermentation. In conclusion, L. helveticus fermentation can further boost the release of free Ca2+ and oligopeptide, enhance the antioxidant ability of SBH. The L. helveticus fermented SBH can be developed as a novel functional dietary supplement product.

Does the Abiotic Formation of Oligopeptides on TiO₂ Nanoparticles Require Special Catalytic Sites? Apparently Not.

The oligomerization of non-activated amino acids catalyzed by nanostrucrured mineral oxide surfaces holds promises as a sustainable route for the industrial production of polypeptides. To analyze the influence of the surface type on the catalytic process, we performed, via a mild Chemical Vapor Deposition approach, the oligomerization of Glycine on two samples of TiO2 nanoparticles characterized by different relative amounts of defective surface terminations. Based on infrared spectroscopy and mass spectrometry data, we show herein that the formation of peptide bonds on titania nanoparticles does not require highly energetic surface terminations, but can occur also on the most abundant and thermodynamically most stable {101} facets of nanosized anatase.

Preliminary Oligomerization in a Glycolic Acid-Glycine Mixture: A Free Energy Map.

Glycolic acid and glycine can potentially self-oligomerize or co-oligomerize in solution by forming ester and amide bonds. Using density functional theory with implicit solvent, we have mapped a baseline free energy landscape to compare the relative stabilities of monomers, dimers, and trimers in solution. We find that amide bond formation is favored over ester bond formation both kinetically and thermodynamically, although the differences decrease when zwitterionic species are taken into account. The replacement of ester linkages by amide bonds is favored over lengthening the oligomer, suggesting that one route to oligopeptide formation is utilizing oligoesters as a starting point. We also find that diketopiperazine, the cyclic dimer of glycine, is favored over the linear dimer; however, the linear trimers are favored over their cyclic counterparts. Because glycolic acid and glycine are dominant products from a Strecker synthesis starting from formaldehyde and HCN, this study sheds light on potential pathways to prebiotic formation of oligopeptides via oligoesters.

Characterization of Endogenous Protease and the Changes in Proteolytic Activity ofAcetes vulgarisandMacrobrachium lanchesteriDuringKapiProduction

Characteristics of endogenous proteases of shrimp, Acetes vulgaris (AP) and Macrobrachium lanchesteri (MP) as well as the changes in proteolytic activity during Kapi production were investigated. Maximal activity of AP and MP was found at pH 7, 60C and pH 8, 60C, respectively. Activity of both proteases decreased with increasing NaCl concentration (0–30%). Both extracts were strongly inhibited by N-ethylmaleimide-phenylmethane-sulfonyl fluoride (PMSF) and soybean trypsin inhibitor (SBTI), suggesting that major proteases belonged to serine proteases. This was coincidental with high trypsin activity toward BAPNA and chymotrypsin activity toward BTEE. Proteolytic activity, trypsin and chymotrypsin were detectable throughout Kapi fermentation. The activity was decreased when salting was implemented. Nevertheless, activities increased continuously with increasing fermentation time. During Kapi production, proteins underwent degradation as indicated by the formation of oligopeptides and disappearance of myosin heavy chain and actin. Therefore, both endogenous and microbial proteases were more likely involved in proteolysis of shrimp during Kapi production. Practical Applications Kapi, traditional salted shrimp paste, is usually used as a condiment to enhance the palatability of many Thai foods. Recently, small shrimp Acetes Vulgaris and Macrobrachium lanchesteri have become the new alternative raw materials for Kapi production because of their availability. During fermentation, protein hydrolysis is induced by endogenous proteases in shrimp as well as those produced by halophilic bacteria. Those changes medicated by proteolysis can be associated with the final characteristics of Kapi.

Formation of oligopeptides in high yield under simple programmable conditions.

Many high-yielding reactions for forming peptide bonds have been developed but these are complex, requiring activated amino-acid precursors and heterogeneous supports. Herein we demonstrate the programmable one-pot dehydration–hydration condensation of amino acids forming oligopeptide chains in around 50% yield. A digital recursive reactor system was developed to investigate this process, performing these reactions with control over parameters such as temperature, number of cycles, cycle duration, initial monomer concentration and initial pH. Glycine oligopeptides up to 20 amino acids long were formed with very high monomer-to-oligomer conversion, and the majority of these products comprised three amino acid residues or more. Having established the formation of glycine homo-oligopeptides, we then demonstrated the co-condensation of glycine with eight other amino acids (Ala, Asp, Glu, His, Lys, Pro, Thr and Val), incorporating a range of side-chain functionality.

The Activation of Free Dipeptides Promoted by Strong Activating Agents in Water Does not Yield Diketopiperazines.

The activation of dipeptides was studied in the perspective of the abiotic formation of oligopeptides of significant length as a requirement for secondary structure formation. The formation of piperazin-2,5-diones (DKP), previously considered as a dead end when activating free dipeptides, was shown in this work to be efficiently suppressed when using strong activating agents (e.g., carbodiimides). This behaviour was explained by the fast formation of a 5(4H)-oxazolone intermediate at a rate that exceeds the time scale of the rotation of the peptide bond from the predominant trans-conformation into the cis-isomer required for DKP formation. No DKP was observed when using strong activating agents whereas phosphate mixed anhydrides or moderately activated esters were observed to predominantly yield DKP. The DKP side-reaction no longer constitutes a drawback for the C-terminus elongation of peptides. These results are considered as additional evidence that pathways involving strong activation are required to drive the emergence of living entities rather than close to equilibrium processes.

Facile Route for the Synthesis of Adamantane‐Containing Polypeptides through Polycondensation of Activated Urethane Derivative of α‐Amino Acids

A facile route has been discovered for the synthesis of polypeptides containing adamantane moieties in the side chain, poly(Nδ‐adamantyl‐l‐glutamine) P1 and poly(Nγ‐adamantyl‐l‐asparagine) P2, through polycondensation of an N‐phenoxycarbonyl derivative of the corresponding Nδ‐adamantyl‐l‐glutamine 1 and Nγ‐adamantyl‐l‐asparagine 2, respectively, along with the elimination of phenol and CO2. The urethane derivatives are readily synthesized by the N‐carbamylation of tetrabutylammonium salts of α‐amino acids with diphenyl carbonate. Polycondensation of the urethane derivative proceeds smoothly upon heating to 60 °C in N,N‐dimethylacetamide using n‐butylamine (n‐BuNH2) as an initiator. Size exclusion chromatography, 1H NMR spectra, and matrix‐assisted laser desorption/ionization time‐of flight mass spectrometry analyses reveal that polycondensation of 1 with n‐BuNH2 yields a well‐defined polypeptide in terms of molecular weight and terminal structure. On the other hand, polycondensation of 2 affords poor molecular weight control and leads to the formation of oligopeptides. Furthermore, using amine‐terminated poly(ethylene‐glycol) in place of n‐BuNH2 yields a diblock copolymer composed of polyether and polypeptide segments bearing an adamantane moiety through polycondensation of the urethane derivative. image

Biased versus unbiased randomness in homo-polymers and copolymers of amino acids in the prebiotic world.

The polymerization of amino acids under anhydrous prebiotic conditions was first studied several decades ago. Here we use a stochastic model stressing the relevant role of the polarity of amino acids in the formation of oligopeptides in a prebiotic milieu. Our goal is to outline the predominance of co-polypeptides over homo-polypeptides, resulting not only from the randomness, but also from polarity properties of amino acids. Our results conclude that there was a higher probability of the formation of co-polypeptides than of homo-polymers. Besides, we may hypothesize that the former would have a more ample spectrum of possible chemical functions than homo-polypeptides.

Mineral-Enhanced Hydrothermal Oligopeptide Formation at the Second Time Scale

Accumulation of biopolymers should have been an essential step for the emergence of life on primitive Earth. However, experimental simulations for submarine hydrothermal vent systems in which high-temperature water spouts through minerals within a short time scale have not been attempted. Here, we show that enhancement of hydrothermal oligopeptide elongation by naturally occurring minerals was successfully verified for the first time by using a mineral-mediated hydrothermal flow reactor system (MMHF). MMHF consists of a narrow tubular reactor packed with mineral particles, and the enhancement or inhibitory activities of 10 types of naturally occurring minerals were successfully evaluated for an elongation reaction from (Ala)(4) to (Ala)(5) and higher oligopeptides in the absence of condensation reagents. It was unexpected that calcite and dolomite facilitated the elongation from (Ala)(4) to (Ala)(5) and higher oligopeptides with 28% yield at pH 7, while tourmaline, galena, apatite, mica, sphalerite, quartz, chalcopyrite, and pyrite did not show enhancement activities. These facts suggest the importance of carbonate minerals for the accumulation of peptide in primitive Earth environments.

Effect of condensation agents and minerals for oligopeptide formation under mild and hydrothermal conditions in related to chemical evolution of proteins

The role of condensation agents and minerals for oligopeptide formation was inspected to see whether minerals possess catalytic activity under mild and hydrothermal conditions. Under mild conditions, oligopeptide formation from negatively charged amino acids (Asp and Glu) using different minerals and the elongation of alanine oligopeptides ((Ala) 2–(Ala) 5) were attempted using apatite minerals. Oligo(Asp) up to 10 amino acid units from Asp were observed in the presence of 1-ethyl-3-(3-dimethylaminopropyl carbodiimide (EDC). Notable influence of minerals was not detected for the oligo(Asp) formation. Oligo(Asp) was gradually degraded by the further incubation in the presence of EDC in both the absence and presence of minerals. The formation of oligo(Glu) was less efficient in the presence of carbonyldiimidazole. The elongation from (Ala) 3, (Ala) 4, and (Ala) 5 and the formation of diketopiperazine from (Ala) 2 proceeded immediately in the presence of EDC in the meantime of the sample preparations. In addition, it was unexpected that the disappearance of the products and the reformation of the reactants occurred by the further incubation for 24 h; for instance, (Ala) 5 decreased but (Ala) 4 increased with increasing the reaction time in the reaction of (Ala) 4 with EDC. These facts suggest that the activation of the reactant amino acids or peptides immediately occurs. Under the simulated hydrothermal conditions, EDC did not enhance the formation of oligopeptides from Asp, Glu or Ala nor the spontaneous formation of (Ala) 5 from (Ala) 4.

Oligopeptides and Copeptides of Homochiral Sequence, via β-Sheets, from Mixtures of Racemic α-Amino Acids, in a One-Pot Reaction in Water; Relevance to Biochirogenesis

As part of our studies on the biochirogenesis of peptides of homochiral sequence during early evolution, the formation of oligopeptides composed of 14-24 residues of the same handedness in the polymerization of dl-leucine (Leu), dl-phenylalanine (Phe), and dl-valine (Val) in aqueous solutions, by activation with N, N'-carbonyldiimidazole and then initiation with a primary amine, in a one-pot reaction, was demonstrated by MALDI-TOF MS using deuterium enantio-labeled alpha-amino acids. The formation of long isotactic peptides is rationalized by the following steps occurring in tandem: (i) creation of a library of short diasteroisomeric oligopeptides containing isotactic peptides in excess in comparison to a binomial kinetics, as a result of an asymmetric induction exerted by the N-terminal residue of a given handedness; (ii) precipitation of the less soluble racemic isotactic penta- and hexapeptides in the form of beta-sheets that are delineated by homochiral rims; (iii) regio-enantiospecific chain elongation occurring heterogeneously at the beta-sheets/solution interface. Polymerization of l-Leu with l-isoleucine (Ile) or l-Phe with l- (1) N-Me-histidine yielded mixtures of copeptides containing both residues. In contrast, in the polymerization of the corresponding mixtures of l- + d-alpha-amino acids, the long oligopeptides were composed mainly from oligo- l-Leu and oligo- d-Ile in the first system and oligo- d-Phe in the second. Furthermore, in the polymerization of mixtures of hydrophobic racemic alpha-amino acids dl-Leu, dl-Val, and dl-Phe and with added racemic dl-alanine and dl-tyrosine, copeptides of homochiral sequences are most dominantly represented. Possible routes for a spontaneous "mirror-symmetry breaking" process of the racemic mixtures of homochiral peptides are presented.

Conformational behavior of different possible ways of oligoglycine formation in a solvent-free environment

The possible ways for glycine oligopeptide formation in gas phase, both in the extended β-strand like conformation and folded 2 7-ribbon like conformations are analyzed using quantum chemical calculations. We focus on the sequential formation of peptide bond through upgradation of the immediate lower order molecule and observe the consequences in other related processes like oligoglycine formation through simultaneous peptide linkage of n glycine monomers and interchange of molecular conformation through peptide linkage. A comparison is made between the structures and binding energies obtained for both conformers. All binding energies are increased by the zero-point energy contribution. The role of electron correlation effects is briefly analyzed. The folded 2 7-ribbon-like conformations in vacuo are found to be more stable in comparison to the extended structure.

Hydrothermal biochemistry: from formaldehyde to oligopeptides

Hydrothermal reactions of formaldehyde (CH2O), which is mainly formed by CO2, are considered to be of most importance in the abiotic synthesis of complex organic molecules in chemical evolution on the primitive Earth. We show the hydrothermal formation of amino acids and oligopeptides in neutral or weak acidic solutions from CH2O in the presence of metals and metal oxides. In these hydrothermal processes, metal or metal oxides selectively catalyzed a series of hydrothermal reactions from CH2O to amino acids, whereas the further reactions for the formation of oligopeptides proceeded without any catalyst. Our experimental observation may provide a possible clue to understanding the initial chemical evolution in Earth’s primitive atmosphere of the origin of life.

Homochiral oligopeptides via surface recognition and enantiomeric cross impediment in the polymerization of racemic phenylalanine N‐carboxyanhydride crystals suspended in water

As part of our program on the search of possible prebiotic routes for the formation of oligopeptides of homochiral sequence (isotactic) from racemic precursors in aqueous environment, we report the polymerization of racemic crystals of phenylalanine N-carboxyanhydrides, enantioselectively tagged with five deuterium atoms, suspended in water containing various amine initiators. Racemic mixtures of isotactic oligopeptides, comprising up to 25 repeat units of the same handedness, as the dominant component for each length, were observed in a MALDI-TOF mass spectrometry analysis. The racemic mixtures of the peptides could be desymmetrized by initiating the polymerization reaction with water-soluble methyl esters of either enantiopure alpha-amino acids or dipeptides. A three-step mechanism is proposed to account for these results: (i) Surface recognition of the chiral initiator by the chiral sites present at specific faces of the crystal; (ii) Oligopeptide elongation at the polymer/crystal interface; and (iii) Self-assembly of the short isotactic peptides into racemic antiparallel beta-sheets as templates followed by cross-enantiomeric impediment in the growth of enantiomeric chains at the peptide beta-sheet/crystal interface.

Comparative behaviour of proteinases from the latex of Carica papaya and Funastrum clausum as catalysts for the synthesis of Z-Ala-Phe-OMe

The proteolytic extract obtained from the latex of Funastrum clausum (Jacq.) Schlechter ( Asclepiadaceae), a South American climbing plant, was assayed as a novel catalyst for peptide synthesis and compared with commercial papain under the same conditions. After immobilization on polyamide, the synthesis of the bitter peptide precursor Z-Ala-Phe-OMe was performed and different conditions were tried. Acetonitrile and ethyl acetate with low water content were tested as organic solvents. Equilibrium- and kinetically-controlled synthesis were tried by using either Z-Ala-OH or Z-Ala-OMe as acyl donors, respectively. The best conditions for the synthesis of the desired product varied according to the catalyst used. For papain, thermodynamic control in acetonitrile ( a w ≅ 0.12) in the presence of triethylamine (TEA) or boric acid–borate buffer (40 mM), and equilibrium- and kinetic-controlled synthesis in ethyl acetate ( a w ≅ 0.75) proved to be the best conditions. The thermodynamic control in either acetonitrile with a w ≅ 0.12 (40 mM TEA or Na 2CO 3) or ethyl acetate ( a w ≅ 0.75) were the best conditions found for funastrain. In all cases, the formation of oligopeptides up to three Phe was observed. The proteolytic extract of F. clausum latex showed more selectivity than papain towards the conversion to Z-Ala-Phe-OMe leading to less proportion of oligopeptides.

Analysis of peptides synthesized in the presence of SAz-1 montmorillonite and Cu 2+ exchanged hectorite

We have investigated the synthesis of oligopeptides containing glycine and tyrosine in the presence of the clay minerals montmorillonite (non-exchanged, SAz-1) and Cu 2+ exchanged hectorite. In both cases, homopolymers of the two amino acids are formed, as are mixed peptides. In the case of Cu 2+ hectorite, mixed oligopeptides up to trimers are detected in small amounts. For montmorillonite, heterogeneous oligopeptides up to hexamers are detected. Our experiments indicate montmorillonite is more effective in promoting oligopeptide formation than Cu 2+ hectorite. Analysis of the oligopeptide sequences formed on the montmorillonite surfaces indicates preferential synthesis of certain Gly-Tyr sequences over others.

Research on the Origin of Life: Membrane-Assisted Polycondensations of Amino Acids and Peptides

The question as to whether and to what extent the phospholipid membrane of liposomes can assist in the polymerization of amino acids and peptides has been investigated. It has been found that the membrane can select hydrophobic amino acids and peptides, thus operating as a selection tool in the polymerization reaction and thus permitting the formation of oligopeptides not possible in water – in the absence of liposomes – as a result of the too low solubility.

ChemInform Abstract: Metal Complexes of Biologically Important Ligands. Part 105. Catalytic Formation of Oligopeptides from α‐Amino Acid Esters with (p‐Cymene)ruthenium(II) Complexes.

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