PEPTIDE SYNTHESIS FROM AMINO ACIDS IN AQUEOUS SOLUTION

Novel Apparatuses for Incorporating Natural Selection Processes into Origins-of-Life Experiments to Produce Adaptively Evolving Chemical Ecosystems

Origins-of-life chemical experiments usually aim to produce specific chemical end-products such as amino acids, nucleic acids or sugars. The resulting chemical systems do not evolve or adapt because they lack natural selection processes. We have modified Miller origins-of-life apparatuses to incorporate several natural, prebiotic physicochemical selection factors that can be tested individually or in tandem: freezing-thawing cycles; drying-wetting cycles; ultraviolet light-dark cycles; and catalytic surfaces such as clays or minerals. Each process is already known to drive important origins-of-life chemical reactions such as the production of peptides and synthesis of nucleic acid bases and each can also destroy various reactants and products, resulting selection within the chemical system. No previous apparatus has permitted all of these selection processes to work together. Continuous synthesis and selection of products can be carried out over many months because the apparatuses can be re-gassed. Thus, long-term chemical evolution of chemical ecosystems under various combinations of natural selection may be explored for the first time. We argue that it is time to begin experimenting with the long-term effects of such prebiotic natural selection processes because they may have aided biotic life to emerge by taming the combinatorial chemical explosion that results from unbounded chemical syntheses.

The Role of Peptides in the Design of Electrochemical Biosensors for Clinical Diagnostics

Peptides represent a promising class of biorecognition elements that can be coupled to electrochemical transducers. The benefits lie mainly in their stability and selectivity toward a target analyte. Furthermore, they can be synthesized rather easily and modified with specific functional groups, thus making them suitable for the development of novel architectures for biosensing platforms, as well as alternative labelling tools. Peptides have also been proposed as antibiofouling agents. Indeed, biofouling caused by the accumulation of biomolecules on electrode surfaces is one of the major issues and challenges to be addressed in the practical application of electrochemical biosensors. In this review, we summarise trends from the last three years in the design and development of electrochemical biosensors using synthetic peptides. The different roles of peptides in the design of electrochemical biosensors are described. The main procedures of selection and synthesis are discussed. Selected applications in clinical diagnostics are also described.

Prebiotic Peptides: Molecular Hubs in the Origin of Life

The fundamental roles that peptides and proteins play in today's biology makes it almost indisputable that peptides were key players in the origin of life. Insofar as it is appropriate to extrapolate back from extant biology to the prebiotic world, one must acknowledge the critical importance that interconnected molecular networks, likely with peptides as key components, would have played in life's origin. In this review, we summarize chemical processes involving peptides that could have contributed to early chemical evolution, with an emphasis on molecular interactions between peptides and other classes of organic molecules. We first summarize mechanisms by which amino acids and similar building blocks could have been produced and elaborated into proto-peptides. Next, non-covalent interactions of peptides with other peptides as well as with nucleic acids, lipids, carbohydrates, metal ions, and aromatic molecules are discussed in relation to the possible roles of such interactions in chemical evolution of structure and function. Finally, we describe research involving structural alternatives to peptides and covalent adducts between amino acids/peptides and other classes of molecules. We propose that ample future breakthroughs in origin-of-life chemistry will stem from investigations of interconnected chemical systems in which synergistic interactions between different classes of molecules emerge.

Dry/Wet Cycling and the Thermodynamics and Kinetics of Prebiotic Polymer Synthesis

The endoergic nature of protein and nucleic acid assembly in aqueous media presents two questions that are fundamental to the understanding of life’s origins: (i) how did the polymers arise in an aqueous prebiotic world; and (ii) once formed in some manner, how were they sufficiently persistent to engage in further chemistry. We propose here a quantitative resolution of these issues that evolved from recent accounts in which RNA-like polymers were produced in evaporation/rehydration cycles. The equilibrium N_m + N_n ↔ N_m+n + H₂O is endoergic by about 3.3 kcal/mol for polynucleotide formation, and the system thus lies far to the left in the starting solutions. Kinetic simulations of the evaporation showed that simple Le Châtelier’s principle shifts were insufficient, but the introduction of oligomer-stabilizing factors of 5–10 kcal/mol both moved the process to the right and respectively boosted and retarded the elongation and hydrolysis rates. Molecular crowding and excluded volume effects in present-day cells yield stabilizing factors of that order, and we argue here that the crowded conditions in the evaporites generate similar effects. Oligomer formation is thus energetically preferred in those settings, but the process is thwarted in each evaporation step as diffusion becomes rate limiting. Rehydration dissipates disordered oligomer clusters in the evaporites, however, and subsequent dry/wet cycling accordingly “ratchets up” the system to an ultimate population of kinetically trappedthermodynamically preferred biopolymers.

Acylated cyanoimido-complexes trans-[Mo(NCN){NCNC(O)R}(dppe)(2)]Cl and their reactions with electrophiles: chemical, electrochemical and theoretical study

Treatment of a dichloromethane solution of trans-[Mo(NCN){NCNC(O)R}(dppe)(2)]Cl [R = Me (1a), Et (1b)] (dppe = Ph(2)PCH(2)CH(2)PPh(2)) with HBF(4), [Et(3)O][BF(4)] or EtC(O)Cl gives trans-[Mo(NCN)Cl(dppe)(2)]X [X = BF(4) (2a) or Cl (2b)] and the corresponding acylcyanamides NCN(R')C(O)Et (R' = H, Et or C(O)Et). X-ray diffraction analysis of 2a (X = BF(4)) reveals a multiple-bond coordination of the cyanoimide ligand. Compounds 1 convert to the bis(cyanoimide) trans-[Mo(NCN)(2)(dppe)(2)] complex upon reaction with an excess of NaOMe (with formation of the respective ester). In an aprotic medium and at a Pt electrode, compounds 1 (R = Me, Et or Ph) undergo a cathodically induced isomerization. Full quantitative kinetic analysis of the voltammetric behaviour is presented and allows the determination of the first-order rate constants and the equilibrium constant of the trans to cis isomerization reaction. The mechanisms of electrophilic addition (protonation) to complexes 1 and the precursor trans-[Mo(NCN)(2)(dppe)(2)], as well as the electronic structures, nature of the coordination bonds and electrochemical behaviour of these species are investigated in detail by theoretical methods which indicate that the most probable sites of the proton attack are the oxygen atom of the acyl group and the terminal nitrogen atom, respectively.

5(4H)-oxazolones as intermediates in the carbodiimide- and cyanamide-promoted peptide activations in aqueous solution

The early days: although considered a species to be avoided in peptide chemistry, the intermediacy of 5(4H)-oxazolones is demonstrated to be essential for the formation of peptides through cyanamide and carbodiimide activation in aqueous solution.

Catalytic effects of histidine enantiomers and glycine on the formation of dileucine and dimethionine in the salt-induced peptide formation reaction

The salt-induced peptide formation (SIPF) reaction takes place readily under mild reaction conditions and proceeds via a copper complex. Its ease of reaction and the universality for prebiotic scenarios add weights to the arguments in favour of the importance of peptide and proteins in the tug of war with the RNA world hypothesis. In addition, the SIPF reaction has a preference for L-form amino acids in dipeptide formation, casting light on the puzzle of biohomochirality, especially for the amino acids with aliphatic side chains. A detailed investigation on the behaviour of aliphatic leucine in the SIPF reaction is presented in this paper, including the catalytic effects of glycine, L- and D-histidine as well as the stereoselectivity under all the reaction conditions above. The results show a relatively low reactivity and stereoselectivity of leucine in the SIPF reaction, while both glycine and histidine enantiomers remarkably increase the yields of dileucine by factors up to 40. Moreover, a comparative study of the effectiveness of L- and D-histidine in catalysing the formation of dimethionine was also carried out and extends the scope of mutual catalysis by amino acid enantiomers in the SIPF reaction.

Methionine peptide formation under primordial earth conditions

According to recent research on the origin of life it seems more and more likely that amino acids and peptides were among the first biomolecules formed on earth and that a peptide/protein world was thus a key starting point in evolution towards life. Salt-induced Peptide Formation (SIPF) has repeatedly been shown to be the most universal and plausible peptide-forming reaction currently known under prebiotic conditions and forms peptides from amino acids with the help of copper ions and sodium chloride. In this paper we present experimental results for salt-induced peptide formation from methionine. This is the first time that a sulphur-containing amino acid was investigated in this reaction. The possible catalytic effects of glycine and L-histidine in this reaction were also investigated and a possible distinction between the L- and D-forms of methionine was studied as well.

Mixed dinitrogen-organocyanamide complexes of molybdenum(0) and their protic conversion into hydrazide and amidoazavinylidene derivatives

Organocyanamides, Ntbd1;CNR(2) (R = Me or Et), react with trans-[Mo(N(2))(2)(dppe)(2)] (1, dppe = Ph(2)PCH(2)CH(2)PPh(2)), in THF, to give the first mixed molybdenum dinitrogen-cyanamide complexes trans-[Mo(N(2))(NCNR(2))(dppe)(2)] (R = Me 2a or Et 2b) which are selectively protonated at N(2) by HBF(4) to yield the hydrazide(2-) complexes trans-[Mo(NNH(2))(NCNR(2))(dppe)(2)][BF(4)](2) (R = Me, 3a, or Et, 3b). On treatment with Ag[BF(4)], oxidation and metal fluorination occur, and the ligating cyanamide undergoes an unprecedented beta-protonation at the unsaturated C atom to form trans-[MoF(NCHNR(2))(dppe)(2)][BF(4)](2) (R = Me, 4a, or Et, 4b) compounds which present the novel amidoazavinylidene (or amidomethyleneamide) ligands. Complexes 4 are also formed from the corresponding compounds 3, with liberation of ammonia and hydrazine. The crystal structure of 2b was determined by single-crystal X-ray diffraction analysis which indicates that the N atom of the amide group has a trigonal planar geometry.

Azametallacycles from Ag(I)- or Cu(II)-promoted coupling reactions of dialkylcyanamides with oximes at Pt(II)

The dialkylcyanamide complexes cis-[PtCl(NCNR(2))(PPh(3))(2)][BF(4)] 1 and cis-[Pt(NCNR(2))(2)(PPh(3))(2)][BF(4)](2) 2 (R = Me or Et) have been prepared by treatment of a CH(2)Cl(2) solution of cis-[PtCl(2)(PPh(3))(2)] with the appropriate dialkylcyanamide and one or two equivalents of Ag[BF(4)], respectively. Compounds 2 can also be obtained from 1 by a similar procedure. Their reaction with oximes, HON=CR'R' ' (R'R' ' = Me(2) or C(4)H(8)), in CH(2)Cl(2) and in the presence of Ag[BF(4)] or Cu(CH(3)COO)(2), leads to the novel type of azametallacycles cis-[Pt(NH=C(ON=CR'R")-NR2)(PPh3)2][BF4]2 4 upon an unprecedented coupling of the organocyanamides with oximes, in a process that proceeds via the mixed oxime-organocyanamide species cis-[Pt(NCNR(2))(HON=CR'R' ')(PPh(3))(2)][BF(4)](2) 3, and is catalyzed by either Ag(+) or Cu(2+) which activate the ligating organocyanamide by Lewis acid addition to the amide group. In contrast, in the organonitrile complexes cis-[Pt(NCR)(2)(PPh(3))(2)][BF(4)](2) 5 (R = C(6)H(4)OMe-4 or Et), obtained in a similar way as 2 (but by using NCR instead of the cyanamide), the ligating NCR is not activated by the Lewis acid and does not couple with the oximes. The spectroscopic properties of those complexes are reported along with the molecular structures of 2b (R = Et), 4a1 (R = Me, R'R' ' = Me(2)), and 4b1 (R = Et, R'R' ' = Me(2)), as established by X-ray crystallography which indicates that in the former complex the amide-N-atoms are trigonal planar, whereas in the latter (4a1 and 4b1) the five-membered rings are planar with a localized N=C double bond (imine group derived from the cyanamide) and the exocyclic amide and alkylidene groups (in 4b1) are involved in two intramolecular H-bonds to the oxygen atom of the ring.

Mutual amino acid catalysis in salt-induced peptide formation supports this mechanism's role in prebiotic peptide evolution

The presence of some amino acids and dipeptides under the conditions of the salt-induced peptide formation reaction (aqueous solution at 85 degrees C, Cu(II) and NaCl) has been found to catalyze the formation of homopeptides of other amino acids, which are otherwise produced only in traces or not at all by this reaction. The condensation of Val, Leu and Lys to form their homodipeptides can occur to a considerable extent due to catalytic effects of other amino acids and related compounds, among which glycine, histidine, diglycine and diketopiperazine exhibit the most remarkable activity. These findings also lead to a modification of the table of amino acid sequences preferentially formed by the salt-induced peptide formation (SIPF) reaction, previously used for a comparison with the sequence preferences in membrane proteins of primitive organisms.

Polymerization of beta-amino acids in aqueous solution

We have compared carbonyl diimidazole (CDI) and 1-ethyl-3-(3-dimethylaminopropyl) carbodiimide (EDAC) as activating agents for the oligomerization of negatively-charged alpha- and beta-amino acids in homogeneous aqueous solution. alpha-Amino acids can be oligomerized efficiently using CDI, but not by EDAC. beta-Amino acids can be oligomerized efficiently using EDAC, but not by CDI. Aspartic acid, an alpha- and beta-dicarboxylic acid is oligomerized efficiently by both reagents. These results are explained in terms of the mechanisms of the reactions, and their relevance to prebiotic chemistry is discussed.

The Bakerian Lecture, 1965 - Chemical evolution

How did life come to be on the surface of the Earth? Darwin himself recognized that his basic idea of evolution by variation and natural selection must be a continuous process extending backward in time through that period in which the first living things arose and into the period of ‘chemical evolution´ which preceded it. We are approaching the examination of these events by two routes. One is to seek for evidence in the ancient rocks of the Earth which were laid down before the time in which organisms capable of leaving their skeletons in the rocks to be fossilized were in existence. This period is somewhat more than ca. 600 My ago. The Earth is believed to have taken its present form approximately 4700 My ago. We have found in rocks whose age is about 1000 My certain organic molecules which are closely related to the green pigments of plants, chlorophyll. This seems to establish that green plants were already flourishing before that time. We have now found in rocks of still greater age, namely, 2500 My, the same kinds of molecules mentioned above which can be attributed to the presence of living organisms. If these molecules are as old as the rocks, we have thus shortened the time available for the generation of the complex biosynthetic sequences which give rise to these specific hydro- ­ carbons (polyisoprenoids) to less than 2000 My. The second approach is to attempt to reproduce in the laboratory those chemical processes induced by energy of various kinds— radiation from the sun, from radioactivity, from electrical storm, etc.— which could give rise to simple organic molecules and polymeric combinations of them, ultimately leading to systems which could be called alive. This attempt has also succeeded along a variety of lines, and many of the present-day biologically important molecules have been constructed abiogenically from the primeval atmosphere, thus providing laboratory evidence for the hypothetical processes. The latest step in this approach has been to demonstrate the formation of polypeptides in dilute aqueous solutions through the agency of molecules formed in the primitive atmosphere of the Earth. Finally we must seek evidence for the same processes in material found elsewhere than on the Earth, such as other parts of our solar system , e.g. the Moon and Mars. We can expect to know whether such materials exist at all in the rocks of the Moon within this decade. We may even know something more definite about the botany of Mars during this same period.

Chemical studies on the possible existence of life on Mars

Although there is no direct evidence yet for the existence of life on Mars, it is reasonable to conclude that the emergence of life on Earth, which appears to have been controlled by universal laws of physics and chemistry, may have been repeated elsewhere in the universe. The dual approach of synthesis and analysis in our experimental studies has provided ample evidence in support of this hypothesis.

Cyanamide mediated syntheses of peptides containing histidine and hydrophobic amino acids

Using the model of a primitive earth evaporation pond, the synthesis of three histidyl peptides in yields up to 11% was demonstrated when aqueous solutions of histidine, leucine, ATP, cyanamide, and MgCl2 were evaporated and heated for 24 h at 80 degrees C. In addition, peptides were formed in yields of up to 56%, 35%, and 21%, respectively for phenylalanine, leucine, and alanine when aqueous solutions of the appropriate amino acid were evaporated and heated with cyanamide and one or more of the following components: ATP, AMP, 4-amino-5-imidazole carboxamide, or MgCl2. The greatest peptide yield occurred at pH 3. But peptide formation was demonstrated for a system of Leu, cyanamide, and MgCl2 adjusted to pH 7 with NH4OH. Peptide synthesis was also studied in the presence of CaCl2, ZnCl2, different adenosine nucleotides, and UTP to compare their effects on peptide synthesis. The optimum conditions for cyanamide mediated peptide synthesis were also studied in terms of pH, reaction time, reaction temperature, and cyanamide concentration. The major side product in nearly all reactions studied appears to be an amino acid-cyanamide adduct. Peptides were analyzed and identified by thin layer chromatography, acid hydrolysis, and enzymatic degradation.

The role of metal ions in chemical evolution: polymerization of alanine and glycine in a cation-exchanged clay environment

The effect of the exchangeable cation on the condensation of glycine and alanine was investigated using a series of homoinic bentonites. A cycling procedure of drying, warming and wetting was employed. Peptide bond formation was observed, and the effectiveness of metal ions to catalyze the condensation was Cu2+ greater than Ni2+ approximately Zn2+ greater than Na+. Glycine showed 6% of the monomer incorporated into oligomers with the largest detected being the pentamer. Alanine showed less peptide bond formation (a maximum of 2%) and only the dimer was observed.

Synthesis of protein, nucleosides and other organic compounds from cyanamide and potassium nitrite under possible primitive earth conditions

The mixing of cyanamide and KNO2 produced changes from white solids to yellow liquid and then to orange solid. The gases cyanogen and ammonia were formed. No external energy was used. The reactions were carried out with a small amount of O2. The presence of proteins in the reaction product formed 13 months after the mixing was indicated by the positive reactions of the cyanamide-KNO2 reaction product with ninhydrin, microbiuret, and Folin reagent; the ultraviolet absorption at about 280 nm; the yield of 24% of 15 amino acids; and molecular weight measurements of more than 160,000. The presence of nucleosides, nucleic acid bases, hydrocarbons, and organic esters in the reaction product formed 2 months after the mixing was indicated by ultraviolet absorption at about 260 nm, and the results of ligand-exchange chromatography, paper chromatography, infrared analysis, mass spectral analysis, and NMR spectroscopy. Possible cyanamide-mediated dehydration reactions and mechanisms are discussed.

Cyanamide mediated syntheses under plausible primitive earth conditions. II. The polymerization of deoxythymidine 5'-triphosphate

When an aqueous solution (pH 7.0) of 3H deoxythymidine 5'-triphosphate, deoxythymidine 5'-phosphate, 4-amino-5-imidazolecarboxamide, cyanamide and ammonium chloride was dried and heated at 60 degrees C for 18 h, oligomers were obtained in a yield of approximately 80%. After the chemical degradation of any pyrophosphate bonds present in these oligomers, linear polynucleotides of up to 7-8 units in length were isolated by DEAE cellulose column chromatography and identified by enzymatic digestion procedures. The di- and trinucleotide fractions were degraded 87% and 100% by snake venom phosphodiesterase and 39% and 9% by spleen phosphodiesterase. This synthesis of deoxythymidine oligonucleotides was conducted under potentially prebiotic conditions and may offer a possible method for the synthesis of deoxyoligonucleotides on the primitive Earth.

Cyanamide mediated syntheses under plausible primitive earth conditions. IV. The synthesis of acylglycerols

The synthesis of palmitoylglycerols in good yields occurs when a solution of glycerol, ammonium palmitate, cyanamide and imidazole is dried and heated at ambient humidity at temperatures ranging from 60 degrees--100 degrees C for 16 h. Much less product is formed in the absence of either or both cyanamide or imidazole. This work suggests that acylglycerols could have been synthesized on the primitive Earth under plausible prebiotic conditions which were similar but not identical to those which have been shown to condense deoxynucleotides into oligodeoxynucleotides and amino acids into peptides.

Cyanamide mediated syntheses under plausible primitive earth conditions. III. Synthesis of peptides

Peptides were formed in yields of 5%, 17% and 66%, respectively, when aqueous solutions of glycine, isoleucine or phenylalanine were dried and heated for 24 h at 90 degrees C with adenosine 5'-triphosphate, 4-amino-5-imidazolecarboxamide and cyanamide. Glycine and L-phenylalanine produced mixtures of di-, tri- and tetrapeptides, while L-isoleucine gave only the dipeptide in detectable quantities. The dipeptides of L-isoleucine and L-phenylalanine were identified by mass spectrometry and enzymatic and enzymatic degradation.

Novel prebiotic systems: nucleotide oligomerization in surfactant entrapped water pools

Oligomerization of 5' -TMP in water pools entrapped by dodecyl-ammonium chloride surfactant aggregates in benzene: hexane in the presence of dicyanodiimide at temperatures ranging from 21 degree -72 degree resulted in the formation of linear and cyclic oligonucleotides containing up to pentamers. Effects of temperature, time and surfactants have been examined. Rate constants for the formation of oligomers have been determined at five different temperatures. These data afforded values of (formula: see text). Prebiotic significance of these results are discussed.

Prebiotic condensation reactions in an aqueous medium: a review of condensing agents

Biopolymers are formed by dehydration-type condensation reactions. In aqueous solutions dehydration reactions are very unlikely to happen spontaneously. However, coupling of dehydration-condensation to the hydrolysis of condensing agents could facilitate the synthesis of biopolymers in an aqueous solution. The literature shows that the peptides, nucleosides, nucleotides and oligonucleotides can be formed in this way. A careful study of the literature pertaining to prebiotic condensing agents was conducted in order to determine the most plausible prebiotic synthesis of biopolymers. The condensing agents taken into consideration are cyanamide, carbodimide, dicyanamide, dicyandiamide, hydrogen-cyanide-tetramer, cyanogen and the linear- and cyclic polyphosphates. From both a chemical as well as biological point of view the polyphosphates appear to be the most plausible general prebiotic condensing agent.

Polycondensation of alpha-amino acids by pyrosulfuric acid

The thermal polycondensation of amino acids common to protein is promoted at 80 degrees C by pyrosulfuric acid. This is in contrast to the noncondensation at 100 degrees C in the presence of concentrated sulfuric acid. These results are in accord with an anhydride mechanism, as proposed earlier for copolycondensation promoted by polyphosphoric acid. The amino acid composition, molecular weight, near-homogeneity, are infrared absorption of the polymer formed are described. The potential significance of planetary pyrosulfuric acid is discussed.

Abiotic origin of biopolymers

A variety of methods have been investigated in different laboratories for the polymerization of amino acids and nucleotides under abiotic conditions. They include (1) thermal polymerization, (2) direct polymerization of certain amino acid nitriles, amides or esters, (3) pi, Tokyo 194, Japan.

Methyleneaminoacetonitrile: possible role in chemical evolution-II

Methyleneaminoacetonitrile (MAAN) when reacted with other amino acids, gives rise to the formation of peptides in addition to the usual hydrolytic products. It acts as a precursor of glycine and also as a dehydration condensing agent. It has been shown that MAAN is easily formed by the reaction of hydrogen cyanide, ammonia and formaldehyde as well as by the reaction of formaldehyde with aminoacetonitrile, in dilute ammoniacal solution.