Peptides and the origin of life

Keynote Paper — AUTOPOIETIC GENE-ENZYME CYCLES AND THE EMERGENCE OF LIFE

Systems concepts are applied to solve the problem of how early life could have emerged from an initially abiotic organic environment. Proteinoid or lipid microspheres are proposed to have polymerized from a primordial organic soup and to contain various amino acids and several different nucleobases. A self-replicating "basic set" hypercycle consisting of 10 XNA gene strands and 10 enzymes is proposed that utilizes inorganic phosphates as an energy source. The genes would utilize triplet combinations of adenosine and uracil to code for a replicase enzyme, a polymerase enzyme and eight-code translator (synthetase) enzymes. It is shown that there is a high probability that the basic set genes would emerge. Fissioning of the basic set microspheres into a population of microspheres all containing the basic set, could eliminate the problem of a single gene monopolizing use of the replicator enzyme at the expense of the others and greatly enhance the survivability of the replicating population as a whole. A thermodynamic analysis of such a self-replicating system is also presented. It is shown that genetic mutations will, in the long run allow the basic set to evolve to increased diversity, higher rates of enzyme synthesis and greater rates of entropy production. Long-term evolution could have resulted in organisms similar to contemporary bacteria that utilize RNA genes with a four nucleobase codon system.

Peptide formation mechanism on montmorillonite under thermal conditions

The oligomerization of amino acids is an essential process in the chemical evolution of proteins, which are precursors to life on Earth. Although some researchers have observed peptide formation on clay mineral surfaces, the mechanism of peptide bond formation on the clay mineral surface has not been clarified. In this study, the thermal behavior of glycine (Gly) adsorbed on montmorillonite was observed during heating experiments conducted at 150 °C for 336 h under dry, wet, and dry-wet conditions to clarify the mechanism. Approximately 13.9 % of the Gly monomers became peptides on montmorillonite under dry conditions, with diketopiperazine (cyclic dimer) being the main product. On the other hand, peptides were not synthesized in the absence of montmorillonite. Results of IR analysis showed that the Gly monomer was mainly adsorbed via hydrogen bonding between the positively charged amino groups and negatively charged surface sites (i.e., Lewis base sites) on the montmorillonite surface, indicating that the Lewis base site acts as a catalyst for peptide formation. In contrast, peptides were not detected on montmorillonite heated under wet conditions, since excess water shifted the equilibrium towards hydrolysis of the peptides. The presence of water is likely to control thermodynamic peptide production, and clay minerals, especially those with electrophilic defect sites, seem to act as a kinetic catalyst for the peptide formation reaction.

Application of de novo sequencing tools to study abiogenic peptide formations by tandem mass spectrometry. The case of homo-peptides from glutamic acid complicated by substitutions of hydrogen by sodium or potassium atoms

RATIONALE

Peptides and proteins are among the most important components of living systems. Different attempts have been made to experimentally model the formation of peptides from amino acid monomers in investigation of the origin of life. Detailed characterization of peptides formed under various conditions in such reactions is very important for understanding processes of abiogenic peptide formation.

METHODS

We used liquid chromatography coupled with tandem mass spectrometry (MS/MS) for an accurate study of homo-peptides formed in a model reaction: glutamic acid oligomerization catalyzed by 1,1'-carbonyldiimidazole in aqueous solution with 1 M of sodium or potassium chloride and without any salts. We used de novo sequencing software for peptide identification. In addition we propose an approach that uses more spectral information for de novo sequencing then standard methods.

RESULTS

Peptides up to 9 amino acids long were found in the experiments with KCl, while in experiments with NaCl and without salts only peptides of up to 7 amino acids were detected. Due to high salt concentrations in samples a high number of singly charged peptide ions with up to 4 substitutions of hydrogen atoms by sodium or potassium atoms were observed. De novo sequencing software provided correct identifications even for peptide ions with substitutions.

CONCLUSIONS

Multiple substitutions of hydrogen by alkali metal atoms in peptide ions strongly change their fragmentation patterns. Proposed approach for de novo sequencing was found very effective, even for ions with substitutions. So, it may be useful in more complicated cases like sequencing abiogenic peptides consisting of different amino acids.

Physicochemical investigations of the metal complexes ofl-valine with doubly charged ions of nickel, copper and zinc: a combined experimental and computational approach

Molecular electrostatic potentials inl-Val and its metal complexes.

Evolution and phylogeny of the corticotropin-releasing factor (CRF) family of peptides: expansion and specialization in the vertebrates

New sequence data on CRF family members from a number of genomes has led to the modification of our understanding of CRF evolution in the Metazoa. The corticotropin-releasing factor (CRF) family of peptides include four paralogous lineages in jawed vertebrates; CRF, urotensin-I/urocortin/sauvagine, urocortin 2 (Ucn2) and urocortin 3 (Ucn3). CRF and the urotensin-I/urocortin/sauvagine group represent a gene duplication from one lineage, whereas Ucns 2 and 3 are the result of a gene duplication in the other paralogous lineage. Both paralogous lineages are the result of a gene duplication from a single ancestral peptide that occurred after the divergence of the tunicates from the ancestor that led to the evolution of chordates and vertebrates. The presence of a single CRF-like peptide in tunicates and insects suggests that a single CRF-like ancestor was present before the separation of deuterostomes and protostomes. Currently there is no strong evidence that indicates that CRF-like peptides were present in metazoan taxa that evolved before this time although the structural similarity between some CRF peptides in insects, tunicates and vertebrates with the calcitonin family of peptides hints that prior to the formation of deuterostomes and protostomes the ancestral peptide possessed both CRF and calcitonin-like structural attributes. Here, we show evidences of conservation of CRF-like function dating back to early prokaryotes. This ancestral CRF-calcitonin-like peptide may have initially resulted from a horizontal gene transfer event from prokaryotes to a protistan species that later gave rise to the metazoans.

Origin of chordate peptides by horizontal protozoan gene transfer in early metazoans and protists: evolution of the teneurin C-terminal associated peptides (TCAP)

The teneurin C-terminal associated peptides (TCAP) are found at the extracellular face in C-terminal region of the teneurin transmembrane proteins. One of these peptides, TCAP-1 is independently transcribed as a smaller bioactive peptide that possesses a number of stress response-attenuating activities. The teneurin-TCAP system appears to be the result of a horizontal gene transfer from a prokaryotic proteinaceous polymorphic toxin to a choanoflagellate. In a basal metazoan, the TCAP region has been modified from a toxin to a soluble intercellular signaling system. New studies indicate that the teneurin-TCAP system form a complex signaling system associated with adhesion, cytoskeletal regulation and intracellular signaling. TCAP-1 is highly conserved in all vertebrates and in mammals, inhibits corticotropin-releasing factor (CRF)-associated stress. Using the TCAP-teneurin system as a model, it is likely that numerous peptide systems in the Chordata began as a result of horizontal gene transfer from prokaryotes early in metazoan ancestry.

Rate equation approach to understanding the ion-catalyzed formation of peptides

The salt-induced peptide formation is important for assessing and approaching schemes of molecular evolution. Here, we present experimental data and an exactly solvable kinetic model describing the linear polymerization of L-glutamic amino acid in water solutions with different concentrations of KCl and NaCl. The length distributions of peptides are well fitted by the model. Strikingly, we find that KCl considerably enhances the peptide yield, while NaCl does not show any catalytic effect in most cases under our experimental conditions. The greater catalytic effect of potassium ions is entirely interpreted by one and single parameter, the polymerization rate constant that depends on the concentration of a given salt in the reaction mixture. We deduce numeric estimates for the rate constant at different concentrations of the ions and show that it is always larger for KCl. This leads to an exponential increase of the potassium- to sodium-catalyzed peptide concentration ratio with length. Our results show that the ion-catalyzed peptides have a higher probability to emerge in excess potassium rather than in sodium-rich water solutions.

Survivability and abiotic reactions of selected amino acids in different hydrothermal system simulators

We tested the stability and reaction of several amino acids using hydrothermal system simulators: an autoclave and two kinds of flow reactors at 200-250 °C. This study generally showed that there is a variation in the individual amino acids survivability in the simulators. This is mainly attributed to the following factors; heat time, cold quenching exposure, metal ions and also silica. We observed that, in a rapid heating flow reactor, high aggregation and/or condensation of amino acids could occur even during a heat exposure of 2 min. We also monitored their stability in a reflow-type of simulator for 120 min at 20 min intervals. The non-hydrolyzed and hydrolyzed samples for this system showed a similar degradation only in the absence of metal ions.

Potassium ions are more effective than sodium ions in salt induced peptide formation

Prebiotic peptide formation under aqueous conditions in the presence of metal ions is one of the plausible triggers of the emergence of life. The salt-induced peptide formation reaction has been suggested as being prebiotically relevant and was examined for the formation of peptides in NaCl solutions. In previous work we have argued that the first protocell could have emerged in KCl solution. Using HPLC-MS/MS analysis, we found that K⁺ is more than an order of magnitude more effective in the L-glutamic acid oligomerization with 1,1'-carbonyldiimidazole in aqueous solutions than the same concentration of Na⁺, which is consistent with the diffusion theory calculations. We anticipate that prebiotic peptides could have formed with K⁺ as the driving force, not Na⁺, as commonly believed.

Formation of RNA phosphodiester bond by histidine-containing dipeptides

A new scenario for prebiotic formation of nucleic acid oligomers is presented. Peptide catalysis is applied to achieve condensation of activated RNA monomers into short RNA chains. As catalysts, L-dipeptides containing a histidine residue, primarily Ser-His, were used. Reactions were carried out in self-organised environment, a water-ice eutectic phase, with low concentrations of reactants. Incubation periods up to 30 days resulted in the formation of short oligomers of RNA. During the oligomerisation, an active intermediate (dipeptide-mononucleotide) is produced, which is the reactive species. Details of the mechanism and kinetics, which were elucidated with a set of control experiments, further establish that the imidazole side chain of a histidine at the carboxyl end of the dipeptide plays a crucial role in the catalysis. These results suggest that this oligomerisation catalysis occurs by a transamination mechanism. Because peptides are much more likely products of spontaneous condensation than nucleotide chains, their potential as catalysts for the formation of RNA is interesting from the origin-of-life perspective. Finally, the formation of the dipeptide-mononucleotide intermediate and its significance for catalysis might also be viewed as the tell-tale signs of a new example of organocatalysis.

Isoleucine as a possible bridge between exogenous delivery and terrestrial enhancement of homochirality

We report a highly enantioselective oligomerization of isoleucine stereomers in the salt-induced peptide formation reaction under plausibly prebiotic earth conditions. Up to 6.5-fold superiority in reactivity of L-isoleucine was observed, compared to its D-enantiomer, after 14 evaporation cycles in the presence of Cu(2+) and NaCl. Since isoleucine is among the proteinogenic amino acids that were found enantioenriched in meteorites, this present work may further correlate the extraterrestrial delivery and endogenous production of biological homochirality by virtue of a protein constituent rather than the rarely occurring α-methylated amino acids.

Chemical evolution from simple inorganic compounds to chiral peptides

Numerous experiments performed in the past 50 years have strongly changed ideas of how life could have emerged on the primitive Earth. This review deals with the synthesis of biomolecule precursors under the conditions prevailing on the primordial Earth, and describes possible scenarios for their combination and elongation to form peptides and proteins. Furthermore it proposes different answers to one of the big secrets of nature: why DNA-coded biohomochiral life emerged using amino acids in their l-form?

Pathways for the formation and evolution of peptides in prebiotic environments

α-Amino acids are easily accessible through abiotic processes and were likely present before the emergence of life. However, the role they could have played in the process remains uncertain. Chemical pathways that could have brought about features of self-organization in a peptide world are considered in this review and discussed in relation with their possible contribution to the origin of life. An overall scheme is proposed with an emphasis on possibilities that may have led to dynamically stable far from equilibrium states. This analysis defines new lines of investigation towards a better understanding of the contribution of the systems chemistry of amino acids and peptides to the emergence of life.

Theory, modelling and simulation in origins of life studies

Origins of life studies represent an exciting and highly multidisciplinary research field. In this review we focus on the contributions made by theory, modelling and simulation to addressing fundamental issues in the domain and the advances these approaches have helped to make in the field. Theoretical approaches will continue to make a major impact at the "systems chemistry" level based on the analysis of the remarkable properties of nonlinear catalytic chemical reaction networks, which arise due to the auto-catalytic and cross-catalytic nature of so many of the putative processes associated with self-replication and self-reproduction. In this way, we describe inter alia nonlinear kinetic models of RNA replication within a primordial Darwinian soup, the origins of homochirality and homochiral polymerization. We then discuss state-of-the-art computationally-based molecular modelling techniques that are currently being deployed to investigate various scenarios relevant to the origins of life.

Prebiotic chemistry in eutectic solutions at the water-ice matrix

A crystalline ice matrix at subzero temperatures can maintain a liquid phase where organic solutes and salts concentrate to form eutectic solutions. This concentration effect converts the confined reactant solutions in the ice matrix, sometimes making condensation and polymerisation reactions occur more favourably. These reactions occur at significantly high rates from a prebiotic chemistry standpoint, and the labile products can be protected from degradation. The experimental study of the synthesis of nitrogen heterocycles at the ice-water system showed the efficiency of this scenario and could explain the origin of nucleobases in the inner Solar System bodies, including meteorites and extra-terrestrial ices, and on the early Earth. The same conditions can also favour the condensation of monomers to form ribonucleic acid and peptides. Together with the synthesis of these monomers, the ice world (i.e., the chemical evolution in the range between the freezing point of water and the limit of stability of liquid brines, 273 to 210 K) is an under-explored experimental model in prebiotic chemistry.

Modulation of neuroplastic changes and corticotropin-releasing factor-associated behavior by a phylogenetically ancient and conserved peptide family

The co-evolution of peptides and early cells some 3.7 billion years ago provided bioactive peptides with a long history for the proliferation and refinement of peptide hormones. Central to the adaptation and evolution of cell types in metazoans is the development of peptide signaling systems that regulate stress mechanisms. The corticotropin-releasing factor (CRF) family of peptides represents the canonical family of peptides that are pivotal to the regulation of stress in vertebrates. However, these peptides appear to have evolved at least 2 billion years after the formation of the first postulated bioactive peptides, suggesting that before this, other peptide systems played a role in stress and energy metabolism. The teneurin C-terminal associated peptides (TCAPs) are a recently discovered family of highly conserved peptides that are processed from the teneurin transmembrane proteins. This peptide/protein system is ubiquitous in multicellular organisms and evolved before the CRF family. TCAP-1 is a potent regulator of CRF-associated physiology and behavior and may play a significant role in the regulation of cell-to-cell communication and neuroplasticity in neurons.

On the possible amyloid origin of protein folds

The diversity of protein folds is derived from the diversity of the underlying proteome. Such diversity must have originated from a so-called common ancestor: a hypothetical fold whose identity will, in all likelihood, never be known. Nonetheless, hypotheses exist to explain the evolution of protein folds. When formulating such hypotheses as done here, the entire repertoire of polypeptide structure, from well-defined tertiary structures and molten globule states to intrinsically disordered proteins and oligomeric aggregates, is worth considering. It is the aim of this short essay to discuss the hypothesis that one type of protein aggregate-the cross-β-sheet motif-was the first functional protein fold, that is, the common ancestor fold. Support for this hypothesis comes from the observations that (i) short peptides with simple amino acid sequences are able to form the cross-β-sheet structure, (ii) amyloids can be very stable under harsh conditions, (iii) amyloids can self-assemble in complex mixtures, (iv) amyloids have many potent activities that are attributable to the inherent repetitiveness of the structure, and (v) the proteomes of modern organisms appear to have evolved away from the more amyloidogenic sequences of older organisms, suggesting that amyloids were more ubiquitous earlier in the evolution of modern protein folds.

Amino acid fermentation at the origin of the genetic code

There is evidence that the genetic code was established prior to the existence of proteins, when metabolism was powered by ribozymes. Also, early proto-organisms had to rely on simple anaerobic bioenergetic processes. In this work I propose that amino acid fermentation powered metabolism in the RNA world, and that this was facilitated by proto-adapters, the precursors of the tRNAs. Amino acids were used as carbon sources rather than as catalytic or structural elements. In modern bacteria, amino acid fermentation is known as the Stickland reaction. This pathway involves two amino acids: the first undergoes oxidative deamination, and the second acts as an electron acceptor through reductive deamination. This redox reaction results in two keto acids that are employed to synthesise ATP via substrate-level phosphorylation. The Stickland reaction is the basic bioenergetic pathway of some bacteria of the genus Clostridium. Two other facts support Stickland fermentation in the RNA world. First, several Stickland amino acid pairs are synthesised in abiotic amino acid synthesis. This suggests that amino acids that could be used as an energy substrate were freely available. Second, anticodons that have complementary sequences often correspond to amino acids that form Stickland pairs. The main hypothesis of this paper is that pairs of complementary proto-adapters were assigned to Stickland amino acids pairs. There are signatures of this hypothesis in the genetic code. Furthermore, it is argued that the proto-adapters formed double strands that brought amino acid pairs into proximity to facilitate their mutual redox reaction, structurally constraining the anticodon pairs that are assigned to these amino acid pairs. Significance tests which randomise the code are performed to study the extent of the variability of the energetic (ATP) yield. Random assignments can lead to a substantial yield of ATP and maintain enough variability, thus selection can act and refine the assignments into a proto-code that optimises the energetic yield. Monte Carlo simulations are performed to evaluate the establishment of these simple proto-codes, based on amino acid substitutions and codon swapping. In all cases, donor amino acids are assigned to anticodons composed of U+G, and have low redundancy (1-2 codons), whereas acceptor amino acids are assigned to the the remaining codons. These bioenergetic and structural constraints allow for a metabolic role for amino acids before their co-option as catalyst cofactors. Reviewers: this article was reviewed by Prof. William Martin, Prof. Eörs Szathmáry (nominated by Dr. Gáspár Jékely) and Dr. Ádám Kun (nominated by Dr. Sandor Pongor)

Primal eukaryogenesis: on the communal nature of precellular States, ancestral to modern life

This problem-oriented, exploratory and hypothesis-driven discourse toward the unknown combines several basic tenets: (i) a photo-active metal sulfide scenario of primal biogenesis in the porespace of shallow sedimentary flats, in contrast to hot deep-sea hydrothermal vent conditions; (ii) an inherently complex communal system at the common root of present life forms; (iii) a high degree of internal compartmentalization at this communal root, progressively resembling coenocytic (syncytial) super-cells; (iv) a direct connection from such communal super-cells to proto-eukaryotic macro-cell organization; and (v) multiple rounds of micro-cellular escape with streamlined reductive evolution-leading to the major prokaryotic cell lines, as well as to megaviruses and other viral lineages. Hopefully, such nontraditional concepts and approaches will contribute to coherent and plausible views about the origins and early life on Earth. In particular, the coevolutionary emergence from a communal system at the common root can most naturally explain the vast discrepancy in subcellular organization between modern eukaryotes on the one hand and both archaea and bacteria on the other.

The origin of large molecules in primordial autocatalytic reaction networks

Large molecules such as proteins and nucleic acids are crucial for life, yet their primordial origin remains a major puzzle. The production of large molecules, as we know it today, requires good catalysts, and the only good catalysts we know that can accomplish this task consist of large molecules. Thus the origin of large molecules is a chicken and egg problem in chemistry. Here we present a mechanism, based on autocatalytic sets (ACSs), that is a possible solution to this problem. We discuss a mathematical model describing the population dynamics of molecules in a stylized but prebiotically plausible chemistry. Large molecules can be produced in this chemistry by the coalescing of smaller ones, with the smallest molecules, the ‘food set’, being buffered. Some of the reactions can be catalyzed by molecules within the chemistry with varying catalytic strengths. Normally the concentrations of large molecules in such a scenario are very small, diminishing exponentially with their size. ACSs, if present in the catalytic network, can focus the resources of the system into a sparse set of molecules. ACSs can produce a bistability in the population dynamics and, in particular, steady states wherein the ACS molecules dominate the population. However to reach these steady states from initial conditions that contain only the food set typically requires very large catalytic strengths, growing exponentially with the size of the catalyst molecule. We present a solution to this problem by studying ‘nested ACSs’, a structure in which a small ACS is connected to a larger one and reinforces it. We show that when the network contains a cascade of nested ACSs with the catalytic strengths of molecules increasing gradually with their size (e.g., as a power law), a sparse subset of molecules including some very large molecules can come to dominate the system.

The phylogenomic roots of modern biochemistry: origins of proteins, cofactors and protein biosynthesis

The complexity of modern biochemistry developed gradually on early Earth as new molecules and structures populated the emerging cellular systems. Here, we generate a historical account of the gradual discovery of primordial proteins, cofactors, and molecular functions using phylogenomic information in the sequence of 420 genomes. We focus on structural and functional annotations of the 54 most ancient protein domains. We show how primordial functions are linked to folded structures and how their interaction with cofactors expanded the functional repertoire. We also reveal protocell membranes played a crucial role in early protein evolution and show translation started with RNA and thioester cofactor-mediated aminoacylation. Our findings allow elaboration of an evolutionary model of early biochemistry that is firmly grounded in phylogenomic information and biochemical, biophysical, and structural knowledge. The model describes how primordial α-helical bundles stabilized membranes, how these were decorated by layered arrangements of β-sheets and α-helices, and how these arrangements became globular. Ancient forms of aminoacyl-tRNA synthetase (aaRS) catalytic domains and ancient non-ribosomal protein synthetase (NRPS) modules gave rise to primordial protein synthesis and the ability to generate a code for specificity in their active sites. These structures diversified producing cofactor-binding molecular switches and barrel structures. Accretion of domains and molecules gave rise to modern aaRSs, NRPS, and ribosomal ensembles, first organized around novel emerging cofactors (tRNA and carrier proteins) and then more complex cofactor structures (rRNA). The model explains how the generation of protein structures acted as scaffold for nucleic acids and resulted in crystallization of modern translation.

Structures and physical properties of gaseous metal cationized biological ions

Metal chelation can alter the activity of free biomolecules by modifying their structures or stabilizing higher energy tautomers. In recent years, mass spectrometric techniques have been used to investigate the effects of metal complexation with proteins, nucleobases and nucleotides, where small conformational changes can have significant physiological consequences. In particular, infrared multiple photon dissociation spectroscopy has emerged as an important tool for determining the structure and reactivity of gas-phase ions. Unlike other mass spectrometric approaches, this method is able to directly resolve structural isomers using characteristic vibrational signatures. Other activation and dissociation methods, such as blackbody infrared radiative dissociation or collision-induced dissociation can also reveal information about the thermochemistry and dissociative pathways of these biological ions. This information can then be used to provide information about the structures of the ionic complexes under study. In this article, we review the use of gas-phase techniques in characterizing metal-bound biomolecules. Particular attention will be given to our own contributions, which detail the ability of metal cations to disrupt nucleobase pairs, direct the self-assembly of nucleobase clusters and stabilize non-canonical isomers of amino acids.

An exit cavity was crucial to the polymerase activity of the early ribosome

The emergence of an RNA entity capable of synthesizing peptides was a key prebiotic development. It is hypothesized that a precursor of the modern ribosomal exit tunnel was associated with this RNA entity (e.g., "protoribosome" or "bonding entity") from the earliest time and played an essential role. Various compounds that can bind and activate amino acids, including extremely short RNA chains carrying amino acids, and possibly di- or tripeptides, would have associated with the internal cavity of the protoribosome. This cavity hosts the site for peptide bond formation and adjacent to it a relatively elongated feature that could have evolved to the modern ribosomal exit tunnel, as it is wide enough to allow passage of an oligopeptide. When two of the compounds carrying amino acids or di- or tripeptides (to which we refer, for simplicity, as small aminoacylated RNAs) were in proximity within the heart of the protoribosome, a peptide bond could form spontaneously. The growing peptide would enter the nearby cavity and would not disrupt the attachment of the substrates to the protoribosome or interfere with the subsequent attachment of additional small aminoacylated RNAs. Additionally, the presence of the peptide in the cavity would increase the lifetime of the oligopeptide in the protoribosome. Thus, subsequent addition of another amino acid would be more likely than detachment from the protoribosome, and synthesis could continue. The early ability to synthesize peptides may have resulted in an abbreviated RNA World.

Metabolism and motility in prebiotic structures

Easily accessible, primitive chemical structures produced by self-assembly of hydrophobic substances into oil droplets may result in self-moving agents able to sense their environment and move to avoid equilibrium. These structures would constitute very primitive examples of life on the Earth, even more primitive than simple bilayer vesicle structures. A few examples of simple chemical systems are presented that self-organize to produce oil droplets capable of movement, environment remodelling and primitive chemotaxis. These chemical agents are powered by an internal chemical reaction based on the hydrolysis of an oleic anhydride precursor or on the hydrolysis of hydrogen cyanide (HCN) polymer, a plausible prebiotic chemistry. Results are presented on both the behaviour of such droplets and the surface-active properties of HCN polymer products. Such motile agents would be capable of finding resources while escaping equilibrium and sustaining themselves through an internal metabolism, thus providing a working chemical model for a possible origin of life.

Reactivity of alanylalanine diastereoisomers in neutral and acid aqueous solutions: a versatile stereoselectivity

A good comprehension of the reactivity of peptides in aqueous solution is fundamental in prebiotic chemistry, namely for understanding their stability and behavior in primitive oceans. Relying on the stereoselectivity of the involved reactions, there is a huge interest in amino acid derivatives for explaining the spontaneous emergence of homochirality on primitive Earth. The corresponding kinetic and thermodynamic parameters are however still poorly known in the literature. We studied the reactivity of alanylalanine in acidic to neutral conditions as a model system. The hydrolysis into amino acids, the epimerization of the N-terminal residue, and the cyclization into diketopiperazine could be successfully identified and studied. This kinetic investigation highlighted interesting behaviors. Complex mechanisms were observed in very acidic conditions. The relative kinetic stability of the diastereoisomers of the dipeptide is highly dependent of the pH, with the possibility to dynamically destabilize the thermodynamically more stable diastereoisomers. The existence of the cyclization of dipeptides adds complexity to the system. On one hand it brings additional stereoselectivities; on the other hand fast racemization of heterochiral dipeptides is obtained.

Stability of amino acids and their oligomerization under high-pressure conditions: implications for prebiotic chemistry

The polymerization of amino acids leading to the formation of peptides and proteins is a significant problem for the origin of life. This problem stems from the instability of amino acids and the difficulty of their oligomerization in aqueous environments, such as seafloor hydrothermal systems. We investigated the stability of amino acids and their oligomerization reactions under high-temperature (180-400°C) and high-pressure (1.0-5.5 GPa) conditions, based on the hypothesis that the polymerization of amino acids occurred in marine sediments during diagenesis and metamorphism, at convergent margins on early Earth. Our results show that the amino acids glycine and alanine are stabilized by high pressure. Oligomers up to pentamers were formed, which has never been reported for alanine in the absence of a catalyst. The yields of peptides at a given temperature and reaction time were higher under higher-pressure conditions. Elemental, infrared, and isotopic analyses of the reaction products indicated that deamination is a key degradation process for amino acids and peptides under high-pressure conditions. A possible NH(3)-rich environment in marine sediments on early Earth may have further stabilized amino acids and peptides by inhibiting their deamination.

Ultrasmall peptides self-assemble into diverse nanostructures: morphological evaluation and potential implications

In this study, we perform a morphological evaluation of the diverse nanostructures formed by varying concentration and amino acid sequence of a unique class of ultrasmall self-assembling peptides. We modified these peptides by replacing the aliphatic amino acid at the C-aliphatic terminus with different aromatic amino acids. We tracked the effect of introducing aromatic residues on self-assembly and morphology of resulting nanostructures. Whereas aliphatic peptides formed long, helical fibers that entangle into meshes and entrap >99.9% water, the modified peptides contrastingly formed short, straight fibers with a flat morphology. No helical fibers were observed for the modified peptides. For the aliphatic peptides at low concentrations, different supramolecular assemblies such as hollow nanospheres and membrane blebs were found. Since the ultrasmall peptides are made of simple, aliphatic amino acids, considered to have existed in the primordial soup, study of these supramolecular assemblies could be relevant to understanding chemical evolution leading to the origin of life on Earth. In particular, we propose a variety of potential applications in bioengineering and nanotechnology for the diverse self-assembled nanostructures.

Pumice as a remarkable substrate for the origin of life

The context for the emergence of life on Earth sometime prior to 3.5 billion years ago is almost as big a puzzle as the definition of life itself. Hitherto, the problem has largely been addressed in terms of theoretical and experimental chemistry plus evidence from extremophile habitats like modern hydrothermal vents and meteorite impact structures. Here, we argue that extensive rafts of glassy, porous, and gas-rich pumice could have had a significant role in the origin of life and provided an important habitat for the earliest communities of microorganisms. This is because pumice has four remarkable properties. First, during eruption it develops the highest surface-area-to-volume ratio known for any rock type. Second, it is the only known rock type that floats as rafts at the air-water interface and then becomes beached in the tidal zone for long periods of time. Third, it is exposed to an unusually wide variety of conditions, including dehydration. Finally, from rafting to burial, it has a remarkable ability to adsorb metals, organics, and phosphates as well as to host organic catalysts such as zeolites and titanium oxides. These remarkable properties now deserve to be rigorously explored in the laboratory and the early rock record.

Activation of carboxyl group with cyanate: peptide bond formation from dicarboxylic acids

The reaction of cyanate with C-terminal carboxyl groups of peptides in aqueous solution was considered as a potential pathway for the abiotic formation of peptide bonds under the condition of the primitive Earth. The catalytic effect of dicarboxylic acids on cyanate hydrolysis was definitely attributed to intramolecular nucleophilic catalysis by the observation of the 1H-NMR signal of succinic anhydride when reacting succinic acid with KOCN in aqueous solution (pH 2.2-5.5). The formation of amide bonds was noticed when adding amino acids or amino acid derivatives into the solution. The reaction of N-acyl aspartic acid derivatives was observed to proceed similarly and the scope of the cyanate-promoted reaction was analyzed from the standpoint of prebiotic peptide formation. The role of cyanate in activating peptide C-terminus constitutes a proof of principle that intramolecular reactions of adducts of peptides C-terminal carboxyl groups with activating agents represent a pathway for peptide activation in aqueous solution, the relevance of which is discussed in connexion with the issue of the emergence of homochirality.

Emergence of self-reproduction in cooperative chemical evolution of prebiological molecules

The paper presents a model of coevolution of short peptides (P) and short oligonucleotides (N) at an early stage of chemical evolution leading to the origin of life. The model describes polymerization of both P and N types of molecules on mineral surfaces in aqueous solution at moderate temperatures. It is assumed that amino acid and nucleotide monomers were available in a prebiotic milieu, that periodic variation in environmental conditions between dry/warm and wet/cool took place and that energy sources were available for the polymerization. An artificial chemistry approach in combination with agent-based modeling was used to explore chemical evolution from an initially random mixture of monomers. It was assumed that the oligonucleotides could serve as templates for self-replication and for translation of peptide compositional sequences, and that certain peptides could serve as weak catalysts. Important features of the model are the short lengths of the peptide and oligonucleotide molecules that prevent an error catastrophe caused by copying errors and a finite diffusion rate of the molecules on a mineral surface that prevents excessive development of parasitism. The result of the simulation was the emergence of self-replicating molecular systems consisting of peptide catalysts and oligonucleotide templates. In addition, a smaller but significant number of molecules with alternative compositions also survived due to imprecise reproduction and translation of templates providing variability for further evolution. In a more general context, the model describes not only peptide-oligonucleotide molecular systems, but any molecular system containing two types of polymer molecules: one of which serves as templates and the other as catalysts.The presented coevolutionary system suggests a possible direction towards finding the origin of molecular functionality in a prebiotic environment.

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.

Creating prebiotic sanctuary: self-assembling supramolecular Peptide structures bind and stabilize RNA

Any attempt to uncover the origins of life must tackle the known 'blind watchmaker problem'. That is to demonstrate the likelihood of the emergence of a prebiotic system simple enough to be formed spontaneously and yet complex enough to allow natural selection that will lead to Darwinistic evolution. Studies of short aromatic peptides revealed their ability to self-assemble into ordered and stable structures. The unique physical and chemical characteristics of these peptide assemblies point out to their possible role in the origins of life. We have explored mechanisms by which self-assembling short peptides and RNA fragments could interact together and go through a molecular co-evolution, using diphenylalanine supramolecular assemblies as a model system. The spontaneous formation of these self-assembling peptides under prebiotic conditions, through the salt-induced peptide formation (SIPF) pathway was demonstrated. These peptide assemblies possess the ability to bind and stabilize ribonucleotides in a sequence-depended manner, thus increase their relative fitness. The formation of these peptide assemblies is dependent on the homochirality of the peptide monomers: while homochiral peptides (L-Phe-L-Phe and D-Phe-D-Phe) self-assemble rapidly in aqueous environment, heterochiral diastereoisomers (L-Phe-D-Phe and D-Phe-L-Phe) do not tend to self-assemble. This characteristic consists with the homochirality of all living matter. Finally, based on these findings, we propose a model for the role of short self-assembling peptides in the prebiotic molecular evolution and the origin of life.

Effect of metal Ions (Ni²⁺, Cu²⁺ and Zn²⁺) and water coordination on the structure of L-phenylalanine, L-tyrosine, L-tryptophan and their zwitterionic forms

Methods of quantum chemistry have been applied to double-charged complexes involving the transition metals Ni²⁺, Cu²⁺ and Zn²⁺ with the aromatic amino acids (AAA) phenylalanine, tyrosine and tryptophan. The effect of hydration on the relative stability and geometry of the individual species studied has been evaluated within the supermolecule approach. The interaction enthalpies, entropies and Gibbs energies of nine complexes Phe•M, Tyr•M, Trp•M, (M = Ni²⁺, Cu²⁺ and Zn²⁺) were determined at the Becke3LYP density functional level of theory. Of the transition metals studied the bivalent copper cation forms the strongest complexes with AAAs. For Ni²⁺and Cu²⁺ the most stable species are the NO coordinated cations in the AAA metal complexes, Zn²⁺cation prefers a binding to the aromatic part of the AAA (complex II). Some complexes energetically unfavored in the gas-phase are stabilized upon microsolvation.

Concentration of specific amino acids at the catalytic/active centers of highly-conserved "housekeeping" enzymes of central metabolism in archaea, bacteria and Eukaryota: is there a widely conserved chemical signal of prebiotic assembly?

In alignments of 1969 protein sequences the amino acid glycine and others were found concentrated at most-conserved sites within approximately 15 A of catalytic/active centers (C/AC) of highly conserved kinases, dehydrogenases or lyases of Archaea, Bacteria and Eukaryota. Lysine and glutamic acid were concentrated at least-conserved sites furthest from their C/ACs. Logistic-regression analyses corroborated the "movement" of glycine towards and lysine away from their C/ACs: the odds of a glycine occupying a site were decreased by 19%, while the odds for a lysine were increased by 53%, for every 10 A moving away from the C/AC. Average conservation of MSA consensus sites was highest surrounding the C/AC and directly decreased in transition toward model's peripheries. Findings held with statistical confidence using sequences restricted to individual Domains or enzyme classes or to both. Our data describe variability in the rate of mutation and likelihoods for phylogenetic trees based on protein sequence data and endorse the extension of substitution models by incorporating data on conservation and distance to C/ACs rather than only using cumulative levels. The data support the view that in the most-conserved environment immediately surrounding the C/AC of taxonomically distant and highly conserved essential enzymes of central metabolism there are amino acids whose identity and degree of occupancy is similar to a proposed amino acid set and frequency associated with prebiotic evolution.

Effect of metal ions (Li+, Na+, K+, Mg2+, Ca2+, Ni2+, Cu2+ and Zn2+) and water coordination on the structure and properties of L-histidine and zwitterionic L-histidine

Interactions between metal ions and amino acids are common both in solution and in the gas phase. The effect of metal ions and water on the structure of L-histidine is examined. The effect of metal ions (Li+, Na+, K+, Mg2+, Ca2+, Ni2+, Cu2+ and Zn2+) and water on structures of His·M(H2O)m, m=0.1 complexes have been determined theoretically employing density functional theories using extended basis sets. Of the five stable complexes investigated the relative stability of the gas-phase complexes computed with DFT methods (with one exception of K+ systems) suggest metallic complexes of the neutral L-histidine to be the most stable species. The calculations of monohydrated systems show that even one water molecule has a profound effect on the relative stability of individual complexes. Proton dissociation enthalpies and Gibbs energies of L-histidine in the presence of the metal cations Li+, Na+, K+, Mg2+, Ca2+, Ni2+, Cu2+ and Zn2+ were also computed. Its gas-phase acidity considerably increases upon chelation. Of the Lewis acids investigated, the strongest affinity to L-histidine is exhibited by the Cu2+ cation. The computed Gibbs energies ΔG are negative, span a rather broad energy interval (from -130 to -1,300 kJ/mol), and upon hydration are appreciably lowered.

Peptide-dominated membranes preceding the genetic takeover by RNA: latest thinking on a classic controversy

It is commonly presumed that abiotic membranes were colonized by proteins later on. Yet, hydrophobic peptides could have formed primordial protein-dominated membranes on their own. In a metabolism-first context, "autocatalytically closed" sets of statistical peptides could organize a self-maintaining protometabolism, assisted by an unfolding set of ribotide-related cofactors. Pairwise complementary ribotide cofactors may have formed docking guides for stochastic peptide formation, before replicating RNA emerged from this subset. Tidally recurring wet-drying cycles and an early onset of photosynthetic activities are considered most likely to meet the thermodynamic requirements. Conceivably, the earliest peptide-dominated vesicles were engaged in light harvesting, together with isoprenoid-tethered pigments, rather than providing an external boundary. Early on, the bulk of prebiotic organic matter can have formed a contiguous layer covering the mineral sediment, held in place by colloidal coherence of a hydrogel matrix. This unconventional scenario assumes a late onset of cellular individualization - perhaps from within, resembling endosporogenesis.

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.

Structural evolution of urotensin-I: reflections of life before corticotropin releasing factor

Peptides have a long evolutionary history that predates the appearance of metazoans. The corticotropin releasing factor (CRF) family of peptides is among the most ancient peptide lineages. The identification and characterization of urotensin-I and related orthologues led the way for the elucidation of the entire CRF peptide family. A comparative analysis of the CRF paralogue sequences suggest that CRF is the most derived of these peptides and has lost many of its ancestral characteristics after it became associated with the hypothalamic-pituitary-adrenal/interrenal (HPA/I axis). In vertebrates, the urotensin-I group of orthologues, which includes sauvagine and urocortin, possess a number of shared characteristics that may be indicative of the ancestral peptide. Given the early origin of the CRF family peptides, it is likely that other peptide lineages are distantly related to the CRF family. In silico or cDNA library screening using probes based on urotensin-I/urocortin characteristics have been used to identify novel CRF family and related sequences that provide clues the evolutionary origin of the CRF family.