Selective emergence and survival of early polypeptides in water

Oligopeptides essential to primitive cells could not be obtained just by raising the background noise of organic compounds produced by a prebiotic chemistry working at random. Selection pathways were required. Experimental evidence is given for selective condensation of amino acids in water as well as for selective resistance to degradation. It is shown that N-carboxyanhydrides are good candidates for chemical selection in water. They are formed when active esters of amino acids are left in the presence of bicarbonate ions or when N,N'-carbonyldiimidazole is used as condensing agent. Polymerization of a mixture of proteinaceous and non-proteinaceous amino acids leads to an enrichment in the proteinaceous ones plusα-aminobutyric acid. Selective resistance toward degradation ofβ-pleated sheet conformation is used to exemplify a possible accumulation of homochiral sequences made of hydrophilic and strong hydrophobic residues. Amino acids with branched aliphatic side-chains are selected but those having short linear aliphatic side-chains such asα-aminobutyric acid or norvaline are not.     

The atmosphere of the primitive Earth and the prebiotic synthesis of amino acids

The atmosphere of the Earth at the time of its formation is now generally believed to have been reducing, an idea proposed by Oparin and extensively discussed by Urey. This atmosphere would have contained CH₄, N₂ with traces of NH₃, water and hydrogen. Only traces of NH₃ would have been present because of its solubility in water. UV light and electric discharges were the major sources of energy for amino acid synthesis, with electric discharges being the most efficient, although most other sources of energy also give amino acids.The first prebiotic electric discharge synthesis of amino acids showed that surprisingly high yields of amino acids were synthesized. Eleven amino acids were identified, four of which occur in proteins. Hydroxy acids, simple aliphatic acids and urea were also identified. These experiments have been repeated recently, and 33 amino acids were identified, ten of which occur in proteins, including all of the hydrophobic amino acids.Methionine can be synthesized by electric discharges if H₂S or CH₃SH is added to the reduced gases. The prebiotic synthesis of phenylalanine, tyrosine and trytophan involves pyrolysis reactions combined with plausible solution reactions.Eighteen amino acids have been identified in the Murchison meteorite, a type II carbonaceous chondrite, of which six occur in proteins. All of the amino acids found in the Murchison meteorite have been found among the electric discharge products. Furthermore, the ratios of amino acids in the meteorite show a close correspondence to the ratios from the electric discharge synthesis, indicating that the amino acids on the parent body of the carbonaceous chondrites were synthesized by electric discharges or by an analogous process.     

Toward Homochiral Protocells in Noncatalytic Peptide Systems

The activation-polymerization-epimerization-depolymerization (APED) model of Plasson et al. has recently been proposed as a mechanism for the evolution of homochirality on prebiotic Earth. The dynamics of the APED model in two-dimensional spatially-extended systems is investigated for various realistic reaction parameters. It is found that the APED system allows for the formation of isolated homochiral proto-domains surrounded by a racemate. A diffusive slowdown of the APED network induced, for example, through tidal motion or evaporating pools and lagoons leads to the stabilization of homochiral bounded structures as expected in the first self-assembled protocells.     

Parity-Violating Energy Shifts of Murchison L-Amino Acids are Consistent with an Electroweak Origin of Meteorite L-Enantiomeric Excesses

In 1996, four α-methyl amino acids in the Murchison meteorite—L-isovaline, L-α-methylnorvaline, L-α-methyl-allo-isoleucine and L-α-methyl-isoleucine—were found to show significant enantiomeric excesses of the L form, ranging from 2% to 9%. Their deuterium to hydrogen isotope ratios suggest they formed in the pre-solar interstellar gas cloud rather than during a later aqueous processing phase on the asteroid parent body. In this paper we apply the techniques of the preceding two papers to compute the parity-violating energy shifts of these amino acids. We find that, in the gas phase, the PVESs of the neutral L forms of all four Murchison α-methyl amino acids are decisively negative, and there is even some correlation between the magnitudes of the L-excesses and the magnitudes of the PVESs—all of which is at least consistent with an electroweak origin of the Murchison enantiomeric excesses.     

Enhanced Synthesis of Alkyl Amino Acids in Miller’s 1958 H<Subscript>2</Subscript>S Experiment

Stanley Miller’s 1958 H₂S-containing experiment, which included a simulated prebiotic atmosphere of methane (CH₄), ammonia (NH₃), carbon dioxide (CO₂), and hydrogen sulfide (H₂S) produced several alkyl amino acids, including the α-, β-, and γ-isomers of aminobutyric acid (ABA) in greater relative yields than had previously been reported from his spark discharge experiments. In the presence of H₂S, aspartic and glutamic acids could yield alkyl amino acids via the formation of thioimide intermediates. Radical chemistry initiated by passing H₂S through a spark discharge could have also enhanced alkyl amino acid synthesis by generating alkyl radicals that can help form the aldehyde and ketone precursors to these amino acids. We propose mechanisms that may have influenced the synthesis of certain amino acids in localized environments rich in H₂S and lightning discharges, similar to conditions near volcanic systems on the early Earth, thus contributing to the prebiotic chemical inventory of the primordial Earth.     

Chiral Amplification of Oligopeptides via Polymerization in Two-dimensional Crystallites on Water

A possible role that might have been played by ordered clusters at the air/water interface for the generation of homochiral oligopeptides under prebiotic conditions has been probed by a catalyzed polymerization of amphiphilic activated alpha-amino acids that assembled as two-dimensional (2-D) crystallites at this interface. Three type of processes are described: (i) polymerization of racemates of activated alpha-amino acids that undergo spontaneous resolution into enantiomorphous 2-D crystallites to yield racemic mixtures of oligopeptides enriched with the oligomers of homochiral sequence, (ii) enhanced formation of racemic mixtures of homochiral oligopeptides via lattice-controlled polymerization within 2-D racemic compounds and (iii) generation of homochiral oligopeptides of a single handedness from chiral non-racemic mixtures of monomers that self-assemble into two different phases, racemic crystallites composed from both enantiomers and enantiomorphous crystallites of the enantiomer in excess. The structures of the 2-D crystallites have been determined by grazing incidence X-ray diffraction and the diastereoisomeric composition of the oligopeptides by matrix-assisted laser-desorption time-of-flight mass spectrometry with enantio-labeling.     

Prebiotic Microreactors: A Synthesis of Purines and Dihydroxy Compounds in Aqueous Aerosol

We report the synthesis of purine bases and other heterocycles and the formation of amino acids, hydroxy acids and dihydroxy compounds by the spark activation of an atmosphere of methane, nitrogen and hydrogen, in the presence of an aqueous aerosol. With the aid of the interface air–water, the organic material obtained shows greater amounts and diversity of molecules with biological interest than the products obtained in the absence of an aerosol. Our results support the suggestion that aerosols may have played a significant role in the prebiotic origin of molecular diversity and evolution.     

Role of Ferrocyanides in the Prebiotic Synthesis of α-Amino Acids

We investigated the synthesis of α-amino acids under possible prebiotic terrestrial conditions in the presence of dissolved iron (II) in a simulated prebiotic ocean. An aerosol-liquid cycle with a prebiotic atmosphere is shown to produce amino acids via Strecker synthesis with relatively high yields. However, in the presence of iron, the HCN was captured in the form of a ferrocyanide, partially inhibiting the formation of amino acids. We showed how HCN captured as Prussian Blue (or another complex compound) may, in turn, have served as the HCN source when exposed to UV radiation, allowing for the sustained production of amino acids in conjunction with the production of oxyhydroxides that precipitate as by-products. We conclude that ferrocyanides and related compounds may have played a significant role as intermediate products in the prebiotic formation of amino acids and oxyhydroxides, such as those that are found in iron-containing soils and that the aerosol cycle of the primitive ocean may have enhanced the yield of the amino acid production.     

From earth's primitive atmosphere to chiral peptides--the origin of precursors for life

To re-enact the long way to the origin of life with today's chemical methods, many steps have to be investigated in the light of a primordial scenario deduced from geochemical research. After the formation of our planet and its atmosphere, prebiotic chemical evolution started its course with the formation of the first building blocks for the formation of biomolecules. In the case of proteins, those building blocks were amino acids that had to be formed in the primitive atmosphere, and then had to react to peptides and proteins as the main pillar of first life. In this paper, we describe the processes in the primordial atmosphere according to contemporary geochemical knowledge leading to the synthesis of amino acids until the formation of homochiral peptides, and, thus, show a plausible pathway towards the origin of life.     

Homochirality in Bio-Organic Systems and Glyceraldehyde in the Formose Reaction

The article explores the possibility that the ordering of bio-organic molecules into a homochiral assembly at the origin of life was performed not in aqueous solutions of amino acids or related materials but in racemic glyceraldehyde in the “formose” reaction at high concentration and temperature. Based on physical chemical evidence and computer simulations of condensed fluids, it is argued that the isomerization kinetics of glyceraldehyde is responszible of the symmetry break and the ordering of molecules into homochiral domains.     

Question 6: Coevolution Theory of the Genetic Code: A Proven Theory

The coevolution theory proposes that primordial proteins consisted only of those amino acids readily obtainable from the prebiotic environment, representing about half the twenty encoded amino acids of today, and the missing amino acids entered the system as the code expanded along with pathways of amino acid biosynthesis. The isolation of genetic code mutants, and the antiquity of pretran synthesis revealed by the comparative genomics of tRNAs and aminoacyl-tRNA synthetases, have combined to provide a rigorous proof of the four fundamental tenets of the theory, thus solving the riddle of the structure of the universal genetic code. Presented at: International School of Complexity – 4th Course: Basic Questions on the Origins of Life; “Ettore Majorana” Foundation and Centre for Scientific Culture, Erice, Italy, 1–6 October 2006.     

γ-Glutamyl compounds and their enzymatic production using bacterial γ-glutamyltranspeptidase

Summary. Some amino acids and peptides, which have low solubility in water, become much more soluble following γ-glutamylation. Compounds become more stable in the blood stream with γ-glutamylation. Several γ-glutamyl compounds are known to have favorable physiological effects on mammals. γ-Glutamylation can improve taste and can stabilize glutamine in aqueous solution. Because of such favorable features, γ-glutamyl compounds are very attractive. However, only a small number of γ-glutamyl amino acids have been studied although many other γ-glutamyl compounds may have characteristics that will benefit humans. This is mainly because γ-glutamyl compounds have not been readily available. An efficient and simple method of producing various γ-glutamyl compounds, especially γ-glutamyl amino acids, using bacterial γ-glutamyltranspeptidase has been developed. With this method, modifications of reactive groups of the substrate and energy source such as ATP are not required, and a wide-range of γ-glutamyl compounds can be synthesized. Moreover, bacterial γ-glutamyltranspeptidase, a catalyst for this method, is readily available from the strain over-producing this enzyme. The superiority of producing γ-glutamyl compounds with bacterial γ-glutamyltranspeptidase over other methods of production is discussed.     

A single aromatic core mutation converts a designed “primitive” protein from halophile to mesophile folding

The halophile environment has a number of compelling aspects with regard to the origin of structured polypeptides (i.e., proteogenesis) and, instead of a curious niche that living systems adapted into, the halophile environment is emerging as a candidate “cradle” for proteogenesis. In this viewpoint, a subsequent halophile‐to‐mesophile transition was a key step in early evolution. Several lines of evidence indicate that aromatic amino acids were a late addition to the codon table and not part of the original “prebiotic” set comprising the earliest polypeptides. We test the hypothesis that the availability of aromatic amino acids could facilitate a halophile‐to‐mesophile transition by hydrophobic core‐packing enhancement. The effects of aromatic amino acid substitutions were evaluated in the core of a “primitive” designed protein enriched for the 10 prebiotic amino acids (A,D,E,G,I,L,P,S,T,V)—having an exclusively prebiotic core and requiring halophilic conditions for folding. The results indicate that a single aromatic amino acid substitution is capable of eliminating the requirement of halophile conditions for folding of a “primitive” polypeptide. Thus, the availability of aromatic amino acids could have facilitated a critical halophile‐to‐mesophile protein folding adaptation—identifying a selective advantage for the incorporation of aromatic amino acids into the codon table.     

A Phase Solubility Study on the Chiral Discrimination of Ibuprofen by ??-Cyclodextrin Complexes

The effects of chiral discrimination in inclusion complexes formed by native β-cyclodextrin and its substituted form (namely methyl-β-cyclodextrin) with racemate or pure enantiomers of the non-steroidal anti-inflammatory drug ibuprofen have been investigated in water. Stability constants and complexation efficiency have been determined for these host–guest systems with a 1:1 molar ratio from phase solubility profiles, showing that in aqueous solution, methylated cyclodextrin is a better complex agent than native cyclodextrin, with more enhanced effects for the (R)-enantiomer. These results have been validated using NMR technique. In particular, ¹H NMR spectra in D₂O show a splitting of the signals for the methyl group and the aromatic protons close to the asymmetric centre of the racemate ibuprofen included in cyclodextrin cavity.     

Deracemization of Amino Acids by Partial Sublimation and via Homochiral Self-Organization

Deracemization of a 50/50 mixture of enantiomers of aliphatic amino acids (Ala, Leu, Pro, Val) can be achieved by a simple sublimation of a pre-solubilized solid mixture of the racemates with a huge amount of a less-volatile optically active amino acid (Asn, Asp, Glu, Ser, Thr). The choice of chirality correlates with the handedness of the enantiopure amino acids—Asn, Asp, Glu, Ser, and Thr. The deracemization, enantioenrichment and enantiodepletion observed in these experiments clearly demonstrate the preferential homochiral interactions and a tendency of natural amino acids to homochiral self-organization. These data may contribute toward an ultimate understanding of the pathways by which prebiological homochirality might have emerged.     

Amino Acid Homochirality may be Linked to the Origin of Phosphate-Based Life

Phosphorylation has to have been one of the key events in prebiotic evolution on earth. In this article, the emergence of phosphoryl amino acid 5′-nucleosides having a P–N bond is described as a model of the origin of amino acid homochirality and Genetic Code. It is proposed that the intramolecular interaction between the nucleotide base and the amino acid side-chain influences the stability of particular amino acid 5′-nucleotides, and the interaction also selects for the chirality of amino acids. The differences between l- and d-conformation energies (ΔE _conf) are evaluated by DFT methods at the B3LYP/6-31G(d) level. Although, as expected, these ΔE _conf values are not large, they do give differences in energy that can distinguish the chirality of amino acids. Based on our calculations, the chiral selection of the earliest amino acids for l-enantiomers seems to be determined by a clear stereochemical/physicochemical relationship. As later amino acids developed from the earliest amino acids, we deduce that the chirality of these late amino acids was inherited from that of the early amino acids. This idea reaches far back into evolution, and we hope that it will guide further experiments in this area.     

Evolutionary processes possibly limiting the kinds of amino acids in protein to twenty: a review.

Only 20 of more than 250 biosynthetic amino acids are common (coded) constituents of contemporary protein. In this paper, several stages of evolution, both prebiotic and biotic, are examined for means by which other (non-proteinous) amino acids may have been selected against. Simulated prebiotic experiments indicate that some non-proteinous amino acids were present prebiotically, that they could be incorporated during the formation of prebiotic protein, and that they would function in such protein. Biotic selection is thus indicated.Non-proteinous amino acids currently are available via biosynthetic pathways for potential incorporation into bioprotein. Codon-anticodon interaction, peptidyl transferases, and elongation and termination factors of protein synthesis do not show the specificity needed to preclude non-proteinous amino acids. Highly specific recognition among amino acids, tRNAs, and activating enzymes is concluded to be why the kinds of amino acids in contemporary protein are limited to twenty.Some of several theories concerning the origin, nature and evolution of the genetic code can readily accommodate non-proteinous amino acids. Some evidence suggests that such amino acids were eventually eliminated from protein because they were less suitable than related proteinous amino acids. However, deterministic or “direct interaction” theories currently lack sufficient experimental support to answer how non-proteinous amino acids were precluded; such theories, being testable, probably have the most potential for providing an answer.     

Assemblies of free amino acids as possible prebiotic catalysts

Our understanding of how life emerged on Earth has much to do with speculations about the ways in which prebiotic catalysts could have been formed. Since enzymes, the contemporary biological catalysts, are polymers of amino acids, we looked at the possible activity of free amino acids as catalysts. In this study it is shown experimentally that mixtures of free amino acids exert catalytic activities of -galactosidase, carbonic anhydrase, and catalase. We also observed different levels of catalytic activty of individual amino acids: some were more efficient than others. Apparently, assemblies of amino acids which were formed around substrate molecules through weak interactions, could, in principle, catalyze many prebiotic reactions. This might have been one step in the emergence of biological enzymes.     

The thermal polymerization of amino acids in the presence of sand.

Sand was tested as a model of a common "impurity" that could have influenced the formation of thermal prebiotic protein. Increasing proportions of sand (0-16 g) in admixture with one set of reactant amino acids (1g), when heated at 175 degrees C for 1.5 h, resulted in increasing yields of polyamino acids of increasing size and color intensity; amino acid composition was not greatly affected. Similar results were noted for three of five other sets of reactant amino acids (8 g sand per g amino acids). In no case did sand prevent the amino acids from polymerizing. The results are interpreted to indicate a broader range of conditions conducive to the formation of prebiotic protein and to further emphasize that environmental parameters should be considerided in the experimental modeling of prebiotic processes.