A Plausible Simultaneous Synthesis of Amino Acids and Simple Peptides on the Primordial Earth

Gamma-Ray-Induced Amino Acid Formation during Aqueous Alteration in Small Bodies: The Effects of Compositions of Starting Solutions

Organic compounds, such as amino acids, are essential for the origin of life, and they may have been delivered to the prebiotic Earth from extra-terrestrial sources, such as carbonaceous chondrites. In the parent bodies of carbonaceous chondrites, the radioactive decays of short-lived radionuclides, such as 26Al, cause the melting of ice, and aqueous alteration occurs in the early stages of solar system formation. Many experimental studies have shown that complex organic matter, including amino acids and high-molecular-weight organic compounds, is produced by such hydrothermal processes. On the other hand, radiation, particularly gamma rays from radionuclides, can contribute to the formation of amino acids from simple molecules such as formaldehyde and ammonia. In this study, we investigated the details of gamma-ray-induced amino acid formation, focusing on the effects of different starting materials on aqueous solutions of formaldehyde, ammonia, methanol, and glycolaldehyde with various compositions, as well as hexamethylenetetramine. Alanine and glycine were the most abundantly formed amino acids after acid hydrolysis of gamma-ray-irradiated products. Amino acid formation increased with increasing gamma-ray irradiation doses. Lower amounts of ammonia relative to formaldehyde produced more amino acids. Glycolaldehyde significantly increased amino acid yields. Our results indicated that glycolaldehyde formation from formaldehyde enhanced by gamma rays is key for the subsequent production of amino acids.

From the RNA-Peptide World: Prebiotic Reaction Conditions Compatible with Lipid Membranes for the Formation of Lipophilic Random Peptides in the Presence of Short Oligonucleotides, and More

Deciphering the origins of life on a molecular level includes unravelling the numerous interactions that could occur between the most important biomolecules being the lipids, peptides and nucleotides. They were likely all present on the early Earth and all necessary for the emergence of cellular life. In this study, we intended to explore conditions that were at the same time conducive to chemical reactions critical for the origins of life (peptide-oligonucleotide couplings and templated ligation of oligonucleotides) and compatible with the presence of prebiotic lipid vesicles. For that, random peptides were generated from activated amino acids and analysed using NMR and MS, whereas short oligonucleotides were produced through solid-support synthesis, manually deprotected and purified using HPLC. After chemical activation in prebiotic conditions, the resulting mixtures were analysed using LC-MS. Vesicles could be produced through gentle hydration in similar conditions and observed using epifluorescence microscopy. Despite the absence of coupling or ligation, our results help to pave the way for future investigations on the origins of life that may gather all three types of biomolecules rather than studying them separately, as it is still too often the case.

RNA folding studies inside peptide-rich droplets reveal roles of modified nucleosides at the origin of life

Compartmentalization of RNA in biopolymer-rich membraneless organelles is now understood to be pervasive and critical for the function of extant biology and has been proposed as a prebiotically plausible way to accumulate RNA. However, compartment-RNA interactions that drive encapsulation have the potential to influence RNA structure and function in compartment- and RNA sequence-dependent ways. Here, we detail next-generation sequencing (NGS) experiments performed in membraneless compartments called complex coacervates to characterize the fold of many different transfer RNAs (tRNAs) simultaneously under the potentially denaturing conditions of these compartments. Notably, we find that natural modifications favor the native fold of tRNAs in these compartments. This suggests that covalent RNA modifications could have played a critical role in metabolic processes at the origin of life.

Exploring the Lipid World Hypothesis: A Novel Scenario of Self-Sustained Darwinian Evolution of the Liposomes

According to the Lipid World hypothesis, life on Earth originated with the emergence of amphiphilic assemblies in the form of lipid micelles and vesicles (liposomes). However, the mechanism of appearance of the information molecules (ribozymes/RNA) accompanying that process, considered obligatory for Darwinian evolution, is unclear. We propose a novel scenario of self-sustained Darwinian evolution of the liposomes driven by ever-present natural phenomena: solar UV radiation, day/night cycle, gravity, and the formation of liposomes in an aqueous media. The central tenet of this scenario is the liposomes' encapsulation of the heavy solutes, followed by their gravitational submerging in the water. The submerged liposomes, being protected from the damaging UV radiation, acquire the longevity necessary for autocatalytic replication of amphiphiles, their mutation, and the selection of those amphiphilic assemblies that provide the greatest membrane stability. These two sets of adaptive compositional information (heavy content and amphiphilic assemblies design) generate a population of liposomes with self-replication/reproduction properties, which are amendable to mutation, inheritance, and selection, thereby establishing Darwinian progression. Temporary and spatial expansion of this liposomal population will provide the basis for the next evolutionary step-a transition of accidentally entrapped RNA precursor molecules into complex functional molecules, such as ribozymes/RNA.

RNA folding studies inside peptide-rich droplets reveal roles of modified nucleosides at the origin of life

Compartmentalization of RNA in biopolymer-rich membraneless organelles is now understood to be pervasive and critical for the function of extant biology and has been proposed as a prebiotically-plausible way to accumulate RNA. However, compartment-RNA interactions that drive encapsulation have the potential to influence RNA structure and function in compartment- and RNA sequence-dependent ways. Herein, we detail Next-Generation Sequencing (NGS) experiments performed for the first time in membraneless compartments called complex coacervates to characterize the fold of many different transfer RNAs (tRNAs) simultaneously under the potentially denaturing conditions of these compartments. Strikingly, we find that natural modifications favor the native fold of tRNAs in these compartments. This suggests that covalent RNA modifications could have played a critical role in metabolic processes at the origin of life.

One Sentence Summary

We demonstrate that RNA folds into native secondary and tertiary structures in protocell models and that this is favored by covalent modifications, which is critical for the origins of life.

"Sea Water" Supplemented with Calcium Phosphate and Magnesium Sulfate in a Long-Term Miller-Type Experiment Yields Sugars, Nucleic Acids Bases, Nucleosides, Lipids, Amino Acids, and Oligopeptides

The standard approach to exploring prebiotic chemistry is to use a small number of highly purified reactants and to attempt to optimize the conditions required to produce a particular end product. However, purified reactants do not exist in nature. We have previously proposed that what drives prebiotic evolution are complex chemical ecologies. Therefore, we have begun to explore what happens if one substitutes "sea water", with its complex mix of minerals and salts, for distilled water in the classic Miller experiment. We have also adapted the apparatus to permit it to be regassed at regular intervals so as to maintain a relatively constant supply of methane, hydrogen, and ammonia. The "sea water" used in the experiments was created from Mediterranean Sea salt with the addition of calcium phosphate and magnesium sulfate. Tests included several types of mass spectrometry, an ATP-monitoring device capable of measuring femtomoles of ATP, and a high-sensitivity cAMP enzyme-linked immunoadsorption assay. As expected, amino acids appeared within a few days of the start of the experiment and accumulated thereafter. Sugars, including glucose and ribose, followed as did long-chain fatty acids (up to C₂₀). At three-to-five weeks after starting the experiment, ATP was repeatedly detected. Thus, we have shown that it is possible to produce a "one-pot synthesis" of most of the key chemical prerequisites for living systems within weeks by mimicking more closely the complexity of real-world chemical ecologies.

Setting the geological scene for the origin of life and continuing open questions about its emergence

The origin of life is one of the most fundamental questions of humanity. It has been and is still being addressed by a wide range of researchers from different fields, with different approaches and ideas as to how it came about. What is still incomplete is constrained information about the environment and the conditions reigning on the Hadean Earth, particularly on the inorganic ingredients available, and the stability and longevity of the various environments suggested as locations for the emergence of life, as well as on the kinetics and rates of the prebiotic steps leading to life. This contribution reviews our current understanding of the geological scene in which life originated on Earth, zooming in specifically on details regarding the environments and timescales available for prebiotic reactions, with the aim of providing experimenters with more specific constraints. Having set the scene, we evoke the still open questions about the origin of life: did life start organically or in mineralogical form? If organically, what was the origin of the organic constituents of life? What came first, metabolism or replication? What was the time-scale for the emergence of life? We conclude that the way forward for prebiotic chemistry is an approach merging geology and chemistry, i.e., far-from-equilibrium, wet-dry cycling (either subaerial exposure or dehydration through chelation to mineral surfaces) of organic reactions occurring repeatedly and iteratively at mineral surfaces under hydrothermal-like conditions.

A Computational Quantum-Based Perspective on the Molecular Origins of Life’s Building Blocks

The search for the chemical origins of life represents a long-standing and continuously debated enigma. Despite its exceptional complexity, in the last decades the field has experienced a revival, also owing to the exponential growth of the computing power allowing for efficiently simulating the behavior of matter—including its quantum nature—under disparate conditions found, e.g., on the primordial Earth and on Earth-like planetary systems (i.e., exoplanets). In this minireview, we focus on some advanced computational methods capable of efficiently solving the Schro¨dinger equation at different levels of approximation (i.e., density functional theory)—such as ab initio molecular dynamics—and which are capable to realistically simulate the behavior of matter under the action of energy sources available in prebiotic contexts. In addition, recently developed metadynamics methods coupled with first-principles simulations are here reviewed and exploited to answer to old enigmas and to propose novel scenarios in the exponentially growing research field embedding the study of the chemical origins of life.

Computational Analysis of a Prebiotic Amino Acid Synthesis with Reference to Extant Codon-Amino Acid Relationships

Novel density functional theory calculations are presented regarding a mechanism for prebiotic amino acid synthesis from alpha-keto acids that was suggested to happen via catalysis by dinucleotide species. Our results were analysed with comparison to the original hypothesis (Copley et al., PNAS, 2005, 102, 4442–4447). It was shown that the keto acid–dinucleotide hypothesis for possible prebiotic amino acid synthesis was plausible based on an initial computational analysis, and details of the structures for the intermediates and transition states showed that there was wide scope for interactions between the keto acid and dinucleotide moieties that could affect the free energy profiles and lead to the required proto-metabolic selectivity.

Electrochemically promoted oxidative α-cyanation of tertiary and secondary amines using cheap AIBN

The electrochemical α-cyanation of tertiary and secondary amines has been developed by using a cheap cyanide reagent, azobisisobutyronitrile (AIBN). The CN radical, generated through n-Bu₄NBr-meidated electrochemical oxidation, participates in a novel α-cyanation reaction under exogenous oxidant-free conditions.

Monomers of Glycine and Serine Have a Limited Ability to Hydrate in the Atmosphere

The role of atmospheric aerosols on climate change is one of the biggest uncertainties in most global climate models. Organic aerosols have been identified as potential cloud condensation nuclei (CCN), and amino acids are organic molecules that could serve as CCN. Amino acids make up a significant portion of the total organic material in the atmosphere, and herein we present a systematic study of hydration for two of the most common atmospheric amino acids, glycine and serine. We compute DLPNO/CCSD(T)//M08-HX/MG3S thermodynamic properties and atmospheric concentrations of Gly(H₂O)_n and Ser(H₂O)_n, where n = 1-5. We predict that serine-water clusters have higher concentrations at n = 1 and 5, while glycine-water clusters have higher concentrations at n = 2-4. However, both glycine and serine are inferred to exist primarily in their nonhydrated monomer forms in the absence of other species such as sulfuric acid.

Binding of Dipeptides to Fatty Acid Membranes Explains Their Colocalization in Protocells but Does Not Select for Them Relative to Unjoined Amino Acids

Dipeptides, which consist of two amino acids joined by a peptide bond, have been shown to have catalytic functions. This observation leads to fundamental questions relevant to the origin of life. How could peptides have become colocalized with the first protocells? Which structural features would have determined the association of amino acids and peptides with membranes? Could the association of dipeptides with protocell membranes have driven molecular evolution, favoring dipeptides over individual amino acids? Using pulsed-field gradient nuclear magnetic resonance, we find that several prebiotic amino acids and dipeptides bind to prebiotic membranes. For amino acids, the side chains and carboxylate contribute to the interaction. For dipeptides, the extent of binding is generally less than that of the constituent amino acids, implying that other mechanisms would be necessary to drive molecular evolution. Nevertheless, our results are consistent with a scheme in which the building blocks of the biological polymers colocalized with protocells prior to the emergence of RNA and proteins.

Toward Molecular Cooperation by De Novo Peptides

Theoretical models of the chemical origins of life depend on self-replication or autocatalysis, processes that arise from molecular interactions, recruitment, and cooperation. Such models often lack details about the molecules and reactions involved, giving little guidance to those seeking to detect signs of interaction, recruitment, or cooperation in the laboratory. Here, we develop minimal mathematical models of reactions involving specific chemical entities: amino acids and their condensation reactions to form de novo peptides. Reactions between two amino acids form a dipeptide product, which enriches linearly in time; subsequent recruitment of such products to form longer peptides exhibit super-linear growth. Such recruitment can be reciprocated: a peptide contributes to and benefits from the formation of one or more other peptides; in this manner, peptides can cooperate and thereby exhibit autocatalytic or exponential growth. We have started to test these predictions by quantitative analysis of de novo peptide synthesis conducted by wet-dry cycling of a five-amino acid mixture over 21 days. Using high-performance liquid chromatography, we tracked abundance changes for >60 unique peptide species. Some species were highly transient, with the emergence of up to 17 new species and the extinction of nine species between samplings, while other species persisted across many cycles. Of the persisting species, most exhibited super-linear growth, a sign of recruitment anticipated by our models. This work shows how mathematical modeling and quantitative analysis of kinetic data can guide the search for prebiotic chemistries that have the potential to cooperate and replicate.

Halophilic to mesophilic adaptation of ubiquitin-like proteins

Elucidating how proteins adapt from halophilic to mesophilic environments will enable a better understanding of protein evolution and folding. In this study, by directed evolution and site-directed mutagenesis of the halophilic ubiquitin-like protein (ULP) Samp2, we find that substitution of the prebiotic amino acid Asp31 by Gly is uniquely effective in the mesophilic adaptation of ULP. Sequence analysis shows that substitution of Asp/Glu in halophilic ULPs by Gly in mesophilic ULPs has higher occurrence than other substitutions, supporting the unique role of the substitution in the mesophilic adaptation of ULP. Molecular dynamic simulations indicate that the mesophilic adaptation might result from the effect of the substitution on the conformational flexibility of ULP.

Ester-mediated peptide formation promoted by deep eutectic solvents: a facile pathway to proto-peptides

The ester-amide exchange reaction enables spontaneous formation of prebiotic proto-peptides under mild conditions. However, this reaction also leads to oligomers with a vast sequence diversity of ester and amide linkages. Here, we demonstrate using deep eutectic solvents as a universal strategy to regulate the reaction pathways and promote the formation of amino acid-enriched oligomers with peptide backbones.

Symmetry Breaking of Phospholipids

Either stereo reactants or stereo catalysis from achiral or chiral molecules are a prerequisite to obtain pure enantiomeric lipid derivatives. We reviewed a few plausibly organic syntheses of phospholipids under prebiotic conditions with special attention paid to the starting materials as pro-chiral dihydroxyacetone and dihydroxyacetone phosphate (DHAP), which are the key molecules to break symmetry in phospholipids. The advantages of homochiral membranes compared to those of heterochiral membranes were analysed in terms of specific recognition, optimal functions of enzymes, membrane fluidity and topological packing. All biological membranes contain enantiomerically pure lipids in modern bacteria, eukarya and archaea. The contemporary archaea, comprising of methanogens, halobacteria and thermoacidophiles, are living under extreme conditions reminiscent of primitive environment and may indicate the origin of one ancient evolution path of lipid biosynthesis. The analysis of the known lipid metabolism reveals that all modern cells including archaea synthetize enantiomerically pure lipid precursors from prochiral DHAP. Sn-glycerol-1-phosphate dehydrogenase (G1PDH), usually found in archaea, catalyses the formation of sn-glycerol-1-phosphate (G1P), while sn-glycerol-3-phosphate dehydrogenase (G3PDH) catalyses the formation of sn-glycerol-3-phosphate (G3P) in bacteria and eukarya. The selective enzymatic activity seems to be the main strategy that evolution retained to obtain enantiomerically pure lipids. The occurrence of two genes encoding for G1PDH and G3PDH served to build up an evolutionary tree being the basis of our hypothesis article focusing on the evolution of these two genes. Gene encoding for G3PDH in eukarya may originate from G3PDH gene found in rare archaea indicating that archaea appeared earlier in the evolutionary tree than eukarya. Archaea and bacteria evolved probably separately, due to their distinct respective genes coding for G1PDH and G3PDH. We propose that prochiral DHAP is an essential molecule since it provides a convergent link between G1DPH and G3PDH. The synthesis of enantiopure phospholipids from DHAP appeared probably firstly in the presence of chemical catalysts, before being catalysed by enzymes which were the products of later Darwinian selection. The enzymes were probably selected for their efficient catalytic activities during evolution from large libraries of vesicles containing amino acids, carbohydrates, nucleic acids, lipids, and meteorite components that induced symmetry imbalance.

A sensitive quantitative analysis of abiotically synthesized short homopeptides using ultraperformance liquid chromatography and time-of-flight mass spectrometry

In the origins of life field understanding the abiotic polymerization of simple organic monomers (e.g., amino acids) into larger biomolecules (e.g., oligopeptides), remains a seminal challenge. Recently, preliminary observations showed a limited set of peptides formed in the presence of the plausible prebiotic phosphorylating agent, diamidophosphate (DAP), highlighting the need for an analytical tool to critically evaluate the ability of DAP to induce oligomerization of simple organics under aqueous conditions. However, performing accurate and precise, targeted analyses of short oligopeptides remains a distinct challenge in the analytical chemistry field. Here, we developed a new technique to detect and quantitate amino acids and their homopeptides in a single run using ultraperformance liquid chromatography-fluorescence detection/time of flight mass spectrometry. Over an 8-minute retention time window, 18 target analytes were identified and quantitated, 16 of which were chromatographically separated at, or near baseline resolution. Compound identity was confirmed by accurate mass analysis using a 10 ppm mass tolerance window. This method featured limits of detection < 5 nM (< 1 fmol on column) and limits of quantitation (LOQs) <15 nM (< 3 fmol on column). The LODs and LOQs were upwards of ∼28x and ∼788x lower, respectively, than previous methods for the same analytes, highlighting the quantifiable advantages of this new method. Both detectors provided good quantitative linearity (R2 > 0.985) for all analytes spanning concentration ranges ∼3 - 4 orders of magnitude. We performed a series of laboratory experiments to investigate DAP-mediated oligomerization of amino acids and peptides and analyzed experimental products with the new method. DAP readily polymerized amino acids and peptides under a range of simulated environmental conditions. This research underscores the potential of DAP to have generated oligopeptides on the primordial Earth, enhancing prebiotic chemical diversity and complexity at or near the origin of life.

pH-Dependent Adsorption of Peptides on Montmorillonite for Resisting UV Irradiation

Ultraviolet (UV) irradiation is considered an energy source for the prebiotic chemical synthesis of life's building blocks. However, it also results in photodegradation of biology-related organic compounds on early Earth. Thus, it is important to find a process to protect these compounds from decomposition by UV irradiation. Herein, pH effects on both the adsorption of peptides on montmorillonite (MMT) and the abilities of peptides to resist UV irradiation due to this adsorption were systematically studied. We found that montmorillonite (MMT) can adsorb peptides effectively under acidic conditions, while MMT-adsorbed peptides can be released under basic conditions. Peptide adsorption is positively correlated with the length of the peptide chains. MMT's adsorption of peptides and MMT-adsorbed peptide desorption are both rapid-equilibrium, and it takes less than 30 min to reach the equilibrium in both cases. Furthermore, compared to free peptides, MMT-adsorbed peptides under acidic conditions are well protected from UV degradation even after prolonged irradiation. These results indicate amino acid/peptides are able to concentrate from aqueous solution by MMT adsorption under low-pH conditions (concentration step). The MMT-adsorbed peptides survive under UV irradiation among other unprotected species (storage step). Then, the MMT-adsorbed peptides can be released to the aqueous solution if the environment becomes more basic (releasing step), and these free peptides are ready for polymerization to polypeptides. Hence, a plausible prebiotic concentration-storage-release cycle of amino acids/peptides for further polypeptide synthesis is established.

Thermodynamic and Evolutionary Coupling between the Native and Amyloid State of Globular Proteins

The amyloid-like aggregation propensity present in most globular proteins is generally considered to be a secondary side effect resulting from the requirements of protein stability. Here, we demonstrate, however, that mutations in the globular and amyloid state are thermodynamically correlated rather than simply associated. In addition, we show that the standard genetic code couples this structural correlation into a tight evolutionary relationship. We illustrate the extent of this evolutionary entanglement of amyloid propensity and globular protein stability. Suppressing a 600-Ma-conserved amyloidogenic segment in the p53 core domain fold is structurally feasible but requires 7-bp substitutions to concomitantly introduce two aggregation-suppressing and three stabilizing amino acid mutations. We speculate that, rather than being a corollary of protein evolution, it is equally plausible that positive selection for amyloid structure could have been a driver for the emergence of globular protein structure.

Templates direct the sequence-specific anchoring of the C-terminus of peptido RNAs

When amino acids and ribonucleotides react in aqueous condensation buffer, they form peptido RNA with a phosphoramidate bond between the N-terminus of the peptide and the 5'-terminal phosphate of a ribonucleotide. If peptido RNA was the product of spontaneous reactions of amino acids and nucleotides, there must have been a transition to peptidyl tRNAs, where the C-terminus of the peptide is ester-linked to the 2',3'-terminus of an oligonucleotide. Here we report how short peptido RNAs react with the 3'-terminus of oligodeoxynucleotides, templated by RNA strands. In our model system, the rate and yield of the anchoring of the C-terminus of the dipeptido dinucleotides to an amino group was found to depend on the sequence of the peptide, the 5'-terminal nucleotide of the dinucleotide and the RNA template. In all cases tested, highest yields were found for dinucleotides hybridizing next to the primer terminus. For the most reactive species, GlyPro-AA, anchoring yields ranged from 8-99%, depending on the template. When LeuLeu-AA, PhePhe-AA and GlyGly-AA were allowed to compete for anchoring on 3'-UUC-5' as templating sequence, they gave a product ratio of 1 : 2 : 6, and this selectivity was almost independent of the terminal base of the primer. Our results show the control that a simple duplex context has over the covalent anchoring of peptido RNAs at a position known from peptidyl tRNAs. Processes of this type may have bridged the gap between untemplated condensation reactions and the highly specific processes of ribosomal protein synthesis.

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.

How Small Heterocycles Make a Reaction Network of Amino Acids and Nucleotides Efficient in Water

Organisms use enzymes to ensure a flow of substrates through biosynthetic pathways. How the earliest form of life established biosynthetic networks and prevented hydrolysis of intermediates without enzymes is unclear. Organocatalysts may have played the role of enzymes. Quantitative analysis of reactions of adenosine 5'-monophosphate and glycine that produce peptides, pyrophosphates, and RNA chains reveals that organocapture by heterocycles gives hydrolytically stabilized intermediates with balanced reactivity. We determined rate constants for 20 reactions in aqueous solutions containing a carbodiimide and measured product formation with cyanamide as a condensing agent. Organocapture favors reactions that are kinetically slow but productive, and networks, over single transformations. Heterocycles can increase the metabolic efficiency more than two-fold, with up to 0.6 useful bonds per fuel molecule spent, boosting the efficiency of life-like reaction systems in the absence of enzymes.

Interactions of Amino Acids and Aminoxazole Derivatives: Cocrystal Formation and Prebiotic Implications Enabled by Computational Analysis

In line with the postulated intermediacy of aminoxazoles derived from small sugars toward the direct assembly of nucleoside precursors, we show here a potential prebiotic scenario where aminoxazolines might have also played further roles as complexing and/or sequestering agents of other primeval blocks, namely amino acids. To this end, a bis-aminoxazoline derivative, generated from dihydroxyacetone and cyanamide, gives rise to stable co-crystal forms with dicarboxylic amino acids (Asp and Glu), while ionic interactions owing to proton transfer are inferred from spectroscopic data in aqueous solution. The structure of a 1:2 aminoxazoline: aspartic acid complex, discussed in detail, was elucidated by X-ray diffractometry. Optimized geometries of such ionic structures with bulk aqueous solvation were assessed by DFT calculations, which disclose preferential arrangements that validate the experimental data. Peripherally, we were able to detect in a few cases amino acid dimerization (i.e. dipeptide formation) after prolonged incubation with the bis-aminoxazole derivative. A mechanistic simulation aided by computation provides some predictive conclusions for future explorations and catalytic design.

Compositional characterization of complex protopeptide libraries via triboelectric nanogenerator Orbitrap mass spectrometry

RATIONALE

Understanding of the molecular processes that led to the first biomolecules on Earth is one of the key aspects of origins-of-life research. Depsipeptides, or polymers with mixed amide and ester backbones, have been proposed as plausible prebiotic precursors for peptide formation. Chemical characterization of depsipeptides in complex prebiotic-like mixtures should benefit from more efficient ion sources and ultrahigh-resolution mass spectrometry (UHR-MS) for elemental composition elucidation.

METHODS

A sliding freestanding (SF) Triboelectric Nanogenerator (TENG) was coupled to glass nanoelectrospray emitters for the analysis of a depsipeptide library created using 11 amino acids and 3 alpha-hydroxy acids subjected to environmentally driven polymerization. The TENG nanoelectrospray ionization (nanoESI) source was coupled to an UHR Orbitrap mass spectrometer operated at 1,000,000 resolution for detecting depsipeptides and oligoesters in such libraries. Tandem mass spectrometry (MS/MS) experiments were performed on an Orbitrap Q-Exactive mass spectrometer.

RESULTS

Our previous proteomics-like approach to depsipeptide library characterization showed the enormous complexity of these dynamic combinatorial systems. Here, direct infusion UHR-MS along with de novo sequencing enabled the identification of 524 sequences corresponding to 320 different depsipeptide compositions. Van Krevelen and mass defect diagrams enabled better visualization of the chemical diversity in these synthetic libraries.

CONCLUSIONS

TENG nanoESI coupled to UHR-MS is a powerful method for depsipeptide library characterization in an origins-of-life context.

Quantitative Analysis of Glycine Oligomerization by Ion-Pair Chromatography

This paper describes a method for the quantitative analysis of mixtures of glycine and its oligomers by ion-pair high-performance liquid chromatography (IP-HPLC), with a particular focus on applications in origins-of-life research. We demonstrate the identification of glycine oligomers (Gly _n ) up to 14 residues long-the approximate detectable limit of their solubility in water-and measurement of the concentration of these species in the product mixture of an oligomerization reaction. The molar response factors for higher oligomers of glycine-which are impractical to obtain as pure samples-are extrapolated from direct analysis of pure standards of n = 3-6, which established a clear linear trend. We compare and contrast our method to those in previous reports with respect to accuracy and practicality. While the data reported here are specific to the analysis of oligomers of glycine, the approach should be applicable to the design of methods for the analysis of oligomerization of other amino acids.

Reduced alphabet of prebiotic amino acids optimally encodes the conformational space of diverse extant protein folds

Background

There is wide agreement that only a subset of the twenty standard amino acids existed prebiotically in sufficient concentrations to form functional polypeptides. We ask how this subset, postulated as {A,D,E,G,I,L,P,S,T,V}, could have formed structures stable enough to found metabolic pathways. Inspired by alphabet reduction experiments, we undertook a computational analysis to measure the structural coding behavior of sequences simplified by reduced alphabets. We sought to discern characteristics of the prebiotic set that would endow it with unique properties relevant to structure, stability, and folding.

Results

Drawing on a large dataset of single-domain proteins, we employed an information-theoretic measure to assess how well the prebiotic amino acid set preserves fold information against all other possible ten-amino acid sets. An extensive virtual mutagenesis procedure revealed that the prebiotic set excellently preserves sequence-dependent information regarding both backbone conformation and tertiary contact matrix of proteins. We observed that information retention is fold-class dependent: the prebiotic set sufficiently encodes the structure space of α/β and α + β folds, and to a lesser extent, of all-α and all-β folds. The prebiotic set appeared insufficient to encode the small proteins. Assessing how well the prebiotic set discriminates native vs. incorrect sequence-structure matches, we found that α/β and α + β folds exhibit more pronounced energy gaps with the prebiotic set than with nearly all alternatives.

Conclusions

The prebiotic set optimally encodes local backbone structures that appear in the folded environment and near-optimally encodes the tertiary contact matrix of extant proteins. The fold-class-specific patterns observed from our structural analysis confirm the postulated timeline of fold appearance in proteogenesis derived from proteomic sequence analyses. Polypeptides arising in a prebiotic environment will likely form α/β and α + β-like folds if any at all. We infer that the progressive expansion of the alphabet allowed the increased conformational stability and functional specificity of later folds, including all-α, all-β, and small proteins. Our results suggest that prebiotic sequences are amenable to mutations that significantly lower native conformational energies and increase discrimination amidst incorrect folds. This property may have assisted the genesis of functional proto-enzymes prior to the expansion of the full amino acid alphabet.

Selective incorporation of proteinaceous over nonproteinaceous cationic amino acids in model prebiotic oligomerization reactions

One of the long-standing questions in origins-of-life research centers on how the proteinaceous side chains and the protein backbone were selected during the earliest phases of evolution. Here we have studied oligomerization reactions of a group of positively charged amino acids, both proteinaceous and nonproteinaceous. Amino acids spontaneously oligomerized without the use of enzymes or activating agents, under mild, hydroxy acid-catalyzed, dry-down conditions. We observed that the proteinaceous amino acids oligomerized more extensively and with greater preference for reactivity through their α-amine compared with nonproteinaceous amino acids, forming predominantly linear, protein-like backbone topologies. These findings provide a purely chemical basis for selection of the positively charged amino acids found in today’s proteins.

Numerous long-standing questions in origins-of-life research center on the history of biopolymers. For example, how and why did nature select the polypeptide backbone and proteinaceous side chains? Depsipeptides, containing both ester and amide linkages, have been proposed as ancestors of polypeptides. In this paper, we investigate cationic depsipeptides that form under mild dry-down reactions. We compare the oligomerization of various cationic amino acids, including the cationic proteinaceous amino acids (lysine, Lys; arginine, Arg; and histidine, His), along with nonproteinaceous analogs of Lys harboring fewer methylene groups in their side chains. These analogs, which have been discussed as potential prebiotic alternatives to Lys, are ornithine, 2,4-diaminobutyric acid, and 2,3-diaminopropionic acid (Orn, Dab, and Dpr). We observe that the proteinaceous amino acids condense more extensively than these nonproteinaceous amino acids. Orn and Dab readily cyclize into lactams, while Dab and Dpr condense less efficiently. Furthermore, the proteinaceous amino acids exhibit more selective oligomerization through their α-amines relative to their side-chain groups. This selectivity results in predominantly linear depsipeptides in which the amino acids are α-amine−linked, analogous to today’s proteins. These results suggest a chemical basis for the selection of Lys, Arg, and His over other cationic amino acids for incorporation into proto-proteins on the early Earth. Given that electrostatics are key elements of protein−RNA and protein−DNA interactions in extant life, we hypothesize that cationic side chains incorporated into proto-peptides, as reported in this study, served in a variety of functions with ancestral nucleic acid polymers in the early stages of life.

Investigating Prebiotic Protocells for A Comprehensive Understanding of the Origins of Life: A Prebiotic Systems Chemistry Perspective

Protocells are supramolecular systems commonly used for numerous applications, such as the formation of self-evolvable systems, in systems chemistry and synthetic biology. Certain types of protocells imitate plausible prebiotic compartments, such as giant vesicles, that are formed with the hydration of thin films of amphiphiles. These constructs can be studied to address the emergence of life from a non-living chemical network. They are useful tools since they offer the possibility to understand the mechanisms underlying any living cellular system: Its formation, its metabolism, its replication and its evolution. Protocells allow the investigation of the synergies occurring in a web of chemical compounds. This cooperation can explain the transition between chemical (inanimate) and biological systems (living) due to the discoveries of emerging properties. The aim of this review is to provide an overview of relevant concept in prebiotic protocell research.

Absolute asymmetric Strecker synthesis in a mixed aqueous medium: reliable access to enantioenriched α-aminonitrile

Without using chiral sources, the Strecker reaction of achiral hydrogen cyanide, p-tolualdehyde and benzhydrylamine gave enantioenriched l- or d-N-benzhydryl-α-(p-tolyl)glycine nitriles with up to >99% ee in a mixed solvent of water and methanol. Therefore, total spontaneous resolution of α-aminonitriles could occur through a prebiotic mechanism of α-amino acid synthesis. Moreover, it was demonstrated that the repetition of partial dissolution and crystallization of a suspended conglomerate of aminonitrile under solution-phase racemization could generate the enantiomeric imbalance to afford, in combination with the amplification of chirality, an enantioenriched product in every case. Among the 73 experiments that were carried out, d- and l-enriched isomers occurred 36 and 37 times, respectively. This stochastic behavior, under achiral or racemic starting conditions, meets the requirements of the spontaneous absolute asymmetric Strecker synthesis. The implications of the present results for the origin of chirality of α-amino acids are discussed.

Matrix-assisted laser desorption/ionization time-of-flight mass spectrometry of model prebiotic peptides: Optimization of sample preparation

RATIONALE

Depsipeptides, or peptides with a mixture of amide and ester linkages, may have evolved into peptides on primordial Earth. Previous studies on depsipeptides utilized electrospray ionization ion mobility quadrupole time-of-flight (ESI-IM-QTOF) tandem mass spectrometry; such analysis was thorough yet time-consuming. Here, a complementary matrix-assisted laser desorption/ionization time-of-flight (MALDI-TOF) approach was optimized for rapid characterization of depsipeptide length and monomer composition.

METHODS

Depsipeptide mixtures of varying hydrophobicity were formed by subjecting aqueous mixtures of α-hydroxy acids and α-amino acids to evaporative cycles. Ester and amide content of depsipeptides was orthogonally confirmed using infrared spectroscopy. MALDI-TOF MS analysis was performed on a Voyager DE-STR in reflection geometry and positive ion mode. Optimization parameters included choice of matrix, sample solvent, matrix-to-analyte ratio, and ionization additives.

RESULTS

It was determined that evaporated depsipeptide samples should be mixed with 2,5-dihydroxybenzoic acid (DHB) matrix in order to detect the highest number of unique signals. Low matrix-to-analyte ratios were found to generate higher quality spectra, likely due to a combination of matrix suppression and improved co-crystallization. Using this optimized protocol, a new depsipeptide mixture was characterized.

CONCLUSIONS

Understanding the diversity and chemical evolution of proto-peptides is of interest to origins-of-life research. Here, we have demonstrated MALDI-TOF MS can be used to rapidly screen the length and monomer composition of model prebiotic peptides containing a mixture of ester and amide backbone linkages.

Amyloid and the origin of life: self-replicating catalytic amyloids as prebiotic informational and protometabolic entities

A crucial stage in the origin of life was the emergence of the first molecular entity that was able to replicate, transmit information, and evolve on the early Earth. The amyloid world hypothesis posits that in the pre-RNA era, information processing was based on catalytic amyloids. The self-assembly of short peptides into β-sheet amyloid conformers leads to extraordinary structural stability and novel multifunctionality that cannot be achieved by the corresponding nonaggregated peptides. The new functions include self-replication, catalytic activities, and information transfer. The environmentally sensitive template-assisted replication cycles generate a variety of amyloid polymorphs on which evolutive forces can act, and the fibrillar assemblies can serve as scaffolds for the amyloids themselves and for ribonucleotides proteins and lipids. The role of amyloid in the putative transition process from an amyloid world to an amyloid-RNA-protein world is not limited to scaffolding and protection: the interactions between amyloid, RNA, and protein are both complex and cooperative, and the amyloid assemblages can function as protometabolic entities catalyzing the formation of simple metabolite precursors. The emergence of a pristine amyloid-based in-put sensitive, chiroselective, and error correcting information-processing system, and the evolvement of mutualistic networks were, arguably, of essential importance in the dynamic processes that led to increased complexity, organization, compartmentalization, and, eventually, the origin of life.

Giant vesicles from rehydrated crude mixtures containing unexpected mixtures of amphiphiles formed under plausibly prebiotic conditions

Giant lipid vesicles resemble compartments of biological cells, mimicking them in their dimension, membrane structure and partly in their membrane composition. The spontanenous appearance of closed membranes composed of bilayers of self-assembling amphiphiles was likely a prerequisite for Darwinian competitive behavior to set in at the molecular level. Such compartments should be dynamic in their membrane composition (evolvable), and sufficiently stable to harbor macromolecules (leak-free), yet semi-permeable for reactive small molecules to get across the membrane (stay away from chemical equilibrium). Here we describe bottom-up experiments simulating prebiotic environments that support the formation of simple amphiphilic molecules capable of self-assembling into vesicular objects on the micrometer scale. Long-chain alkyl phosphates, together with related amphiphilic compounds, were formed under simulated prebiotic phosphorylation conditions by using cyanamide, a recognized prebiotic chemical activator and a precursor for several compound classes. Crude dry material of the thus obtained prebiotic mixtures formed multilamellar giant vesicles once rehydrated at the appropriate pH and in the presence of plausibly prebiotic co-surfactants, as observed by optical microscopy. The size and the shape of lipid aggregates tentatively suggest that prebiotic lipid assemblies could encapsulate peptides or nucleic acids that could be formed under similar chemical prebiotic conditions. The formation of prebiotic amphiphiles was monitored by using TLC, IR, NMR and ESI-MS and UPLC-HRMS. In addition we provide a spectroscopic analysis of cyanamide under simulated prebiotic conditions in the presence of phosphate sources and spectroscopic analysis of O-phosphorylethanolamine as a plausible precursor for phosphoethanolamine lipids.

On the lack of evolutionary continuity between prebiotic peptides and extant enzymes

The significance of experiments that claim to simulate the properties of prebiotic small peptides and polypeptides as models of the polymers that may have preceded proteins is critically addressed. As discussed here, most of these experiments are based only on a small number of a larger set of amino acids that may have been present in the prebiotic environment, supported by both experimental simulations and the repertoire of organic compounds reported in carbonaceous chondrites. Model experiments with small peptides may offer some insights into the processes that contributed to generate the chemical environment leading to the emergence of informational oligomers, but not to the origin of proteins. The large body of circumstantial evidence indicating that catalytic RNA played a key role in the origin of protein synthesis during the early stages of cellular evolution implies that the emergence of the genetic code and of protein biosynthesis are no longer synonymous with the origin of life. Hence, reports on the abiotic synthesis of small catalytic peptides under potential prebiotic conditions do not provide information on the origin of triplet encoded protein biosynthesis, but in some cases may serve as models to understand the properties of the earliest proteins.

Mechanochemical Activation of Iron Cyano Complexes: A Prebiotic Impact Scenario for the Synthesis of α-Amino Acid Derivatives

Mechanochemical activation of iron cyano complexes by ball milling results in the formation of HCN, which can be trapped and incorporated into α-aminonitriles. This prebiotic impact scenario can be extended by mechanochemically transforming the resulting α-aminonitriles into α-amino amides using a chemical route related to early Earth conditions.

Cavitation-Induced Synthesis of Biogenic Molecules on Primordial Earth

Despite decades of research, how life began on Earth remains one of the most challenging scientific conundrums facing modern science. It is agreed that the first step was synthesis of organic compounds essential to obtain amino acids and their polymers. Several possible scenarios that could accomplish this step, using simple inorganic molecules, have been suggested and studied over the years. The present study examines, using atomistic reactive molecular dynamics simulations, the long-standing suggestion that natural cavitation in primordial oceans was a dominant mechanism of organic molecule synthesis. The simulations allow, for the first time, direct observation of the rich and complex sonochemistry occurring inside a collapsing bubble filled with water and dissolved gases of the early atmosphere. The simulation results suggest that dissolved CH₄ is the most efficient carbon source to produce amino acids, while CO and CO₂ lead to amino acid synthesis with lower yields. The efficiency of amino acid synthesis also depends on the nitrogen source used (i.e., N₂, NH₃) and on the presence of HCN. Moreover, cavitation may have contributed to the increase in concentration of NH₃ in primordial oceans and to the production and liberation of molecular O₂ into the early atmosphere. Overall, the picture that emerges from the simulations indicates that collapsing bubbles may have served as natural bioreactors in primordial oceans, producing the basic chemical ingredients required for the beginning of life.

Small and Random Peptides: An Unexplored Reservoir of Potentially Functional Primitive Organocatalysts. The Case of Seryl-Histidine

Catalysis is an essential feature of living systems biochemistry, and probably, it played a key role in primordial times, helping to produce more complex molecules from simple ones. However, enzymes, the biocatalysts par excellence, were not available in such an ancient context, and so, instead, small molecule catalysis (organocatalysis) may have occurred. The best candidates for the role of primitive organocatalysts are amino acids and short random peptides, which are believed to have been available in an early period on Earth. In this review, we discuss the occurrence of primordial organocatalysts in the form of peptides, in particular commenting on reports about seryl-histidine dipeptide, which have recently been investigated. Starting from this specific case, we also mention a peptide fragment condensation scenario, as well as other potential roles of peptides in primordial times. The review actually aims to stimulate further investigation on an unexplored field of research, namely one that specifically looks at the catalytic activity of small random peptides with respect to reactions relevant to prebiotic chemistry and early chemical evolution.

On the Uniqueness of the Standard Genetic Code

In this work, we determine the biological and mathematical properties that are sufficient and necessary to uniquely determine both the primeval RNY (purine-any base-pyrimidine) code and the standard genetic code (SGC). These properties are: the evolution of the SGC from the RNY code; the degeneracy of both codes, and the non-degeneracy of the assignments of aminoacyl-tRNA synthetases (aaRSs) to amino acids; the wobbling property; the consideration that glycine was the first amino acid; the topological and symmetrical properties of both codes.

Homocysteine Editing, Thioester Chemistry, Coenzyme A, and the Origin of Coded Peptide Synthesis †

Aminoacyl-tRNA synthetases (AARSs) have evolved “quality control” mechanisms which prevent tRNA aminoacylation with non-protein amino acids, such as homocysteine, homoserine, and ornithine, and thus their access to the Genetic Code. Of the ten AARSs that possess editing function, five edit homocysteine: Class I MetRS, ValRS, IleRS, LeuRS, and Class II LysRS. Studies of their editing function reveal that catalytic modules of these AARSs have a thiol-binding site that confers the ability to catalyze the aminoacylation of coenzyme A, pantetheine, and other thiols. Other AARSs also catalyze aminoacyl-thioester synthesis. Amino acid selectivity of AARSs in the aminoacyl thioesters formation reaction is relaxed, characteristic of primitive amino acid activation systems that may have originated in the Thioester World. With homocysteine and cysteine as thiol substrates, AARSs support peptide bond synthesis. Evolutionary origin of these activities is revealed by genomic comparisons, which show that AARSs are structurally related to proteins involved in coenzyme A/sulfur metabolism and non-coded peptide bond synthesis. These findings suggest that the extant AARSs descended from ancestral forms that were involved in non-coded Thioester-dependent peptide synthesis, functionally similar to the present-day non-ribosomal peptide synthetases.

Quantitation of α-hydroxy acids in complex prebiotic mixtures via liquid chromatography/tandem mass spectrometry

RATIONALE

Spark discharge experiments, like those performed by Stanley Miller in the 1950s, generate complex, analytically challenging mixtures that contain biopolymer building blocks. Recently, α-amino acids and α-hydroxy acids (AHAs) were subjected to environmental cycling to form simple depsipeptides (peptides with both amide and ester linkages). The synthesis of AHAs under possible primordial environments must be examined to better understand this chemistry.

METHODS

We report a direct, quantitative method for AHAs using ultrahigh-performance liquid chromatography and triple quadrupole mass spectrometry. Hexylamine ion-pairing chromatography and selected reaction monitoring detection were combined for the rapid analysis of ten AHAs in a single run. Additionally, prebiotic simulation experiments, including the first-ever reproduction of Miller's 1958 cyanamide spark discharge experiment, were performed to evaluate AHA synthesis over a wide range of possible primitive terrestrial environments.

RESULTS

The quantitating transition for each of the AHAs targeted in this study produced a limit of detection in the nanomolar concentration range. For most species, a linear response over a range spanning two orders of magnitude was found. The AHAs glycolic acid, lactic acid, malic acid, and α-hydroxyglutaric acid were detected in electric discharge experiments in the low micromolar concentration range.

CONCLUSIONS

The results of this work suggest that the most abundant building blocks available for prebiotic depsipeptide synthesis would have been glycolic, lactic, malic, and α-hydroxyglutaric acids, and their corresponding amino acids, glycine, alanine, and aspartic and glutamic acids. Copyright © 2016 John Wiley & Sons, Ltd.

Bringing Prebiotic Nucleosides and Nucleotides Down to Earth

There may be more than one way leading to RNA: Recent discoveries in the synthesis of nucleoside and nucleotide precursors are described and put into the wider context of prebiotic systems chemistry. Mixing Butlerow's carbohydrate precursors with Traube's 5-formylaminopyrimidines has led to the formation of prebiotic purine nucleosides whereas the mixing of 5-phosphoribose with barbituric acid and melamine gave supramolecular fibers from stacks of Whitesides' rosettas.