Indications towards a stereoselectivity of the salt-induced peptide formation reaction

Bivalent Surface Attachment via Cysteine Thiol Results in Efficient and Stereoselective Abiotic Peptide Synthesis

Surface-catalyzed peptide bond formation may have been an important source of peptides for abiogenesis, but model peptide synthesis reactions using the consensus set of 10 abiotic amino acids give only modest rates of peptide bond formation. Additionally, the peptides are typically limited in length to a small number of amino acids and stereoselective amino acid incorporation is weak or absent. An abiotic route for the high-yield synthesis of cysteine from serine was recently reported by Foden et al. (Science 2020, 370, 865-869), indicating that, in some environments, prebiotic cysteine may also have been available. Here, we show that the presence of cysteine dramatically increases the yields of surface-catalyzed peptide synthesis reactions in a hydrothermal vent solvent model containing achiral silicate minerals and that the reaction exhibits a strong stereoselective bias toward l-cysteine. Solid state NMR confirmed that cysteine associates bivalently with silicates at alkaline pH via both the carboxylate and the sulfur groups. Polarization-resolved IRRAS indicates that the bivalent adsorption stereospecifically orients the reactive amino group, providing a mechanism for stereoselective incorporation of l-cysteine. Stereoselective rates of peptide bond formation in surface-catalyzed peptide bond formation are expected to occur for any amino acid able to form sufficiently strong side chain-silicate interactions at alkaline pH. The high nucleophilicity of the thiol group produces unusually high reaction rates and stereoselectivity in such reactions, in addition to conferring transition metal ion binding to the peptide products. The potential benefits of reactive sulfur species for abiogenesis suggest that they may be useful biosignatures in the search for habitable extraterrestrial environments.

Prebiotic Peptide Synthesis: How Did Longest Peptide Appear?

The origin of proteins is a fundamental question in the study of the origin of life. Peptides, as the building blocks of proteins, necessarily preceded the first proteins in prebiotic chemical evolution. Prebiotic peptides may have also played crucial roles in early life's evolution, contributing to self-catalysis, interacting with nucleic acids, and stabilizing primitive cell compartments. Longer and more complicated prebiotic peptides often have greater structural flexibility and functional potential to support the emergence and evolution of early life. Since the Miller-Urey experiment demonstrated that amino acids can be synthesized in a prebiotic manner, the prebiotic synthesis route of peptides has garnered increasing attention from researchers. However, it is difficult for amino acids to condense into peptides in aqueous solutions spontaneously. Over the past few decades, researchers have explored various routes of prebiotic peptide synthesis in the plausible prebiotic Earth environment, such as thermal polymerization, clay mineral catalysis, wet-dry cycles, condensing agents, and lipid-mediated. This paper reviews advancements in prebiotic peptide synthesis research and discusses the conditions that may have facilitated the emergence of longer peptides.

Conformational versatility among crystalline solids of L-phenylalanine derivatives

In this study, we present a new N-derivative of L-phenylalanine with 2-naphthaldehyde (PN), obtained by the Schiff base formation procedure and its subsequent reduction. This compound was crystallized as a zwitterion {2-[(naphthalen-2-ylmethyl)azaniumyl]-3-phenylpropanoate, C20H19NO2}, as an anion in a sodium salt (catena-poly[[diaquasodium(I)-di-μ-aqua] 2-[(naphthalen-2-ylmethyl)amino]-3-phenylpropanoate monohydrate], {[Na(H2O)4](C20H18NO2)·H2O}n), as a cation in a chloride salt [(1-carboxy-2-phenylethyl)(naphthalen-2-ylmethyl)azanium chloride acetic acid monosolvate, C20H20NO2+·Cl-·CH3COOH], and additionally acting as a ligand in the pentacoordinated zinc compound aquabis{2-[(naphthalen-2-ylmethyl)amino]-3-phenylpropanoato-κO}zinc(II), [Zn(C20H18NO2)2(H2O)] or [Zn(PN)2(H2O)], denoted (PN-Zn), with the amino acid derivative in its carboxylate form. Interestingly, both enantiomers of the zinc complex co-exist within the crystalline structure, one constructed by the ligands with the L (or S) configuration and the other with the ligands having the D (or R) configuration, represented as L,L-PN-Zn and D,D-PN-Zn, respectively. Also, in the structure of the zwitterion, the racemate L,D is observed. These results imply that chirality inversion of the amino acid derivative synthesized from enantiomerically pure L-phenylalanine is taking place, a phenomenon known as oscillatory transenantiomerization. The analysis of these crystal structures reveals that they are primarily stabilized through electrostatic interactions assisted by hydrogen bonds. An interesting finding is that the conformation of PN varies along this family: it is unfolded in the zwitterionic and cationic forms, and folded in the anionic form. To evaluate such conformational differences, we propose the use of a dimensionless Shape Factor quantity defined as the Structural Aspect Ratio (SAR), computed from the geometrical features of the parallelepiped that tightly encloses a conformer constructed by rigid spheres. This parameter provides a simple but useful tool to distinguish conformational differences, providing insights that complement traditional structural analyses. The study of the structural features, conformational diversity, chirality and supramolecular properties of these compounds is also supported by density functional theory (DFT) calculations.

The Role of the CuCl Active Complex in the Stereoselectivity of the Salt-Induced Peptide Formation Reaction: Insights from Density Functional Theory Calculations

The salt-induced peptide formation (SIPF) reaction is a prebiotically plausible mechanism for the spontaneous polymerization of amino acids into peptides on early Earth. Experimental investigations of the SIPF reaction have found that in certain conditions, the l enantiomer is more reactive than the d enantiomer, indicating its potential role in the rise of biohomochirality. Previous work hypothesized that the distortion of the CuCl active complex toward a tetrahedral-like structure increases the central chirality on the Cu ion, which amplifies the inherent parity-violating energy differences between l- and d-amino acid enantiomers, leading to stereoselectivity. Computational evaluations of this theory have been limited to the protonated-neutral l + l forms of the CuCl active complex. Here, density functional theory methods were used to compare the energies and geometries of the homochiral (l + l and d + d) and heterochiral (l + d) CuCl-amino acid complexes for both the positive-neutral and neutral-neutral forms for alanine, valine, and proline. Significant energy differences were not observed between different chiral active complexes (i.e., d + d, l + l vs. l + d), and the distortions of active complexes between stereoselective systems and non-selective systems were not consistent, indicating that the geometry of the active complex is not the primary driver of the observed stereoselectivity of the SIPF reaction.

Synthesis, structural and electrochemical properties of a new family of amino-acid-based coordination complexes

Metalloproteins involved in oxidation-reduction processes in metabolism are fundamental for the wellbeing of every organism. The use of amino-acid-based compounds as ligands for the construction of biomimetic coordination systems represents a promising alternative for the development of new catalysts. Herein is presented a new family of copper, zinc and nickel coordination compounds, which show four-, five- and six- coordination geometries, synthesized using Schiff base ligands obtained from the amino acids L-alanine and L-phenylalanine. Structural analysis and property studies were performed using single-crystal X-ray diffraction data, spectroscopic and electrochemical experiments and DFT calculations. The analysis of the molecular and supramolecular architectures showed that the non-covalent interactions developed in the systems, together with the identity of the metal and the amino acid backbone, are determinants for the formation of the complexes and the stabilization of the resultant geometries. The Cu^II complexes were tested as candidates for the electrochemical conversion reduction of nitrite to NO, finding that the five-coordinate L-phenylalanine complex is the most suitable. Finally, some insights into the rational design of ligands for the construction of biomimetic complexes are suggested.

Chirality and the Origin of Life

The origin of life, based on the homochirality of biomolecules, is a persistent mystery. Did life begin by using both forms of chirality, and then one of the forms disappeared? Or did the choice of homochirality precede the formation of biomolecules that could ensure replication and information transfer? Is the natural choice of L-amino acids and D-sugars on which life is based deterministic or random? Is the handedness present in/of the Universe from its beginning? The whole biosystem on the Earth, all living creatures are chiral. Many theories try to explain the origin of life and chirality on the Earth: e.g., the panspermia hypothesis, the primordial soup hypothesis, theory of parity violation in weak interactions. Additionally, heavy neutrinos and the impact of the fact that only left-handed particles decay, and even dark matter, all have to be considered.

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.

Formation of activated biomolecules by condensation on mineral surfaces--a comparison of peptide bond formation and phosphate condensation

Many studies have reported condensation reactions of prebiotic molecules, such as the formation of peptide bonds between amino acids, to occur to some degree on mineral surfaces. We have studied several such reactions on the same divided silica. When drying steps are applied, the equilibria of peptide formation from glycine, and polyphosphate formation from monophosphate, are displaced to the right because these reactions are dehydrating condensations, accompanied by the emission of water. In contrast, the equilibrium of AMP dismutation is not significantly favored by drying. The silica surface plays little role (if any) in the thermochemistry of the condensation reactions, but is does play a significant kinetic role by acting as a catalyst, lowering the condensation temperatures with respect to bulk solids. Of course, the surface also catalyzes the inverse hydrolysis reactions.

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?

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

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

The catalytic effect of L- and D-histidine on alanine and lysine peptide formation

A starting phase of chemical evolution on our ancient Earth around 4 billion years ago was the formation of amino acids and their combination to peptides and proteins. The salt-induced peptide formation (SIPF) reaction has been shown to be appropriate for this condensation reaction under moderate and plausible primitive Earth conditions, forming short peptides from amino acids in aqueous solution containing sodium chloride and Cu(II) ions. In this paper we report results about the formation of dialanine and dilysine from their monomers in this reaction. The catalytic influence of l- and d-histidine dramatically increases dialanine yields when starting from lower alanine concentrations, but also dilysine formation is markedly boosted by these catalysts. Attention is paid to measurable preferences for one enantiomeric form of alanine and lysine in the SIPF reaction. Alanine, especially, shows stereospecific behaviour, mostly in favour of the l-form.

Methionine peptide formation under primordial earth conditions

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

Emergence of homochirality in far-from-equilibrium systems: mechanisms and role in prebiotic chemistry

Since the model proposed by Frank (Frank FC, Biochem Biophys Acta 1953;11:459-463), several alternative models have been developed to explain how an asymmetric non-racemic steady state can be reached by a chirally symmetric chemical reactive system. This paper explains how a stable non-racemic regime can be obtained as a symmetry breaking occurring in a far-from-equilibrium reactive system initiated with an initial imbalance. Departing from the variations around the original Frank's model that are commonly described in the literature, i.e. open-flow systems of direct autocatalytic reactions, we discuss recent developments emphasizing both an active recycling of components and an autocatalytic network of simple reactions. We will present our APED model as the most natural realization of such thermodynamic openness and non-equilibrium, of recycling and of network autocatalysis, each of these in prebiotic conditions. The different experimental and theoretical models in the literature will be classified according to mechanism. The place and role of such self-structured networks responsible for the presence of homochirality in the primitive Earth will be detailed.

Chemical evolution toward the origin of life

Numerous hypotheses about how life on earth could have started can be found in the literature. In this article, we give an overview about the most widespread ones and try to point out which of them might have occurred on the primordial earth with highest probability from a chemical point of view. The idea that a very early stage of life was the "RNA world" encounters crucial problems concerning the formation of its building blocks and their stability in a prebiotic environment. Instead, it seems much more likely that a "peptide world" originated first and that RNA and DNA took up their part at a much later stage. It is shown that amino acids and peptides can be easily formed in a realistic primordial scenario and that these biomolecules can start chemical evolution without the help of RNA. The origin of biohomochirality seems strongly related to the most probable formation of the first peptides via the salt-induced peptide formation (SIPF) reaction.

The Possible Influence ofL-Histidine on the Origin of the First Peptides on the Primordial Earth

One of the most unsettled problems of prebiotic evolution and the origin of life is the explanation why one enantiomeric form of biomolecules prevailed. In the experiments presented in this paper, the influence of L-histidine on the peptide formation in the Salt-Induced Peptide Formation (SIPF) reaction of the enantiomeric forms of valine, proline, serine, lysine, and tryptophan, and the catalytic effects in this first step toward the first building blocks of proteins on the primordial earth were investigated. In the majority of the produced dipeptides, a remarkable increase of yields was shown, and the preference of the L-amino acids in the peptide formation in most cases cannot be denied. In summary, our data provide further experimental evidence for the plausibility of the SIPF reaction and point at a possible important role of L-histidine in the chemical evolution on the primordial Earth.

Catalytically increased prebiotic peptide formation: ditryptophan, dilysine, and diserine

"Mutual" amino acid catalysis of glycine on the formation of ditryptophan, dilysine, and diserine in the prebiotically relevant Salt-Induced Peptide Formation (SIPF) Reaction was investigated varying the starting concentration and chirality of the educt amino acid, and analyzing the increase of yield resulting from this catalytic effect. Our results show the possibility of an amplified diverse pool of peptides being available for chemical evolution of larger peptides and proteins using also these more complicated amino acids for the evolution of more complex functions in future biochemical cycles and thus for the emergence of life. Catalytic effects are especially high in the case of serine, the most basic amino acid of the three, but are also significant for the other two examples investigated in the present work. Besides that, especially for serine, but also in the case of tryptophan, differences in catalytic yield increase according to the chiral form of the amino acid used could be observed.

Catalytic effects of glycine on prebiotic divaline and diproline formation

The catalytic effects of the simple amino acid glycine on the formation of diproline and divaline in the prebiotically relevant salt-induced peptide formation (SIPF) reaction was investigated in systems of different amino acid starting concentrations and using the two enantiomeric forms of the respective amino acid. Results show an improved applicability of the SIPF reaction to prebiotic conditions, especially at low amino acid concentrations, as presumably present in a primordial scenario, and indicate excellent conditions and resources for chemical evolution of peptides and proteins on the early earth. For valine, furthermore differences in catalytic yield increase are found indicating a chiral selectivity of the active copper complex of the reaction and showing a connection to previously found enantiomeric differences in complex formation constants with amino acids.

Stereoselective differentiation in the Salt-induced Peptide Formation reaction and its relevance for the origin of life

All living organisms on earth are almost totally made up of biomolecules of only one chiral form. For example, proteins are built almost exclusively of L-amino acids, and sugars are composed of D-saccharides, a fact that is usually referred to as biohomochirality. Its origin is the center of numerous investigations and theories but is not really elucidated yet. The results of experimental investigations of peptide formation in a prebiotically relevant scenario, as described in this paper, give indications on a possible pathway for the synthesis of homochiral L-peptides in the course of the Salt-induced Peptide Formation (SIPF) reaction.

Recycling Frank: Spontaneous emergence of homochirality in noncatalytic systems

In this work, we introduce a prebiotically relevant protometabolic pattern corresponding to an engine of deracemization by using an external energy source. The spontaneous formation of a nonracemic mixture of chiral compounds can be observed in out-of-equilibrium systems via a symmetry-breaking phenomenon. This observation is possible thanks to chirally selective autocatalytic reactions (Frank's model) [Frank, F. C. (1953) Biochim. Biophys. Acta 11, 459-463]. We show that the use of a Frank-like model in a recycled system composed of reversible chemical reactions, rather than the classical irreversible system, allows for the emergence of a synergetic autoinduction from simple reactions, without any autocatalytic or even catalytic reaction. This model is described as a theoretical framework, based on the stereoselective reactivity of preexisting chiral monomeric building blocks (polymerization, epimerization, and depolymerization) maintained out of equilibrium by a continuous energy income, via an activation reaction. It permits the self-conversion of all monomeric subunits into a single chiral configuration. Real prebiotic systems of amino acid derivatives can be described on this basis. They are shown to be able to spontaneously reach a stable nonracemic state in a few centuries. In such systems, the presence of epimerization reactions is no more destructive, but in contrast is the central driving force of the unstabilization of the racemic state.