Kinetic analysis of artificial peptide self-replication. Part II: the heterochiral case

A kinetic model has been designed to describe and to analyze the stereoselective behavior of a recently discovered heterochiral template-directed peptide self-replicator by Ghadiri and co-workers [Nature 409 (2001) 797-801]. It turned out that previous assumptions stating that exclusively homochiral species participate in a stereoselective and autocatalytic pathway and that heterochiral species originate only from uncatalyzed background reactions could not be validated by our model. On the contrary, excellent fitting of experimental data indicated that the whole combinatorial variety of possible cross-catalytic processes involving L- and D- peptide species play an important role and need to be taken into account. The system shows no net creation of chiral matter but only a redistribution of the initially present chiral material. Both, the separation of an optically inactive meso-type template dimer and a slight chiroselective autocatalytic effect, contribute to a predicted amplification of enantiomeric excess that, in some cases, can simultaneously result in a substantial amount of optically active matter.     

Chiral symmetry breaking: Experimental results and computer analysis of a liquid-phase autoxidation

The autoxidation of tetralin is treated as a model reaction system to define the applicability of stereospecific autocatalysis. This concept, predicting a spontaneous amplification of enantiomeric excess generated by an autocatalytic chemical reaction, is used in several theoretical models as an explanation for the origin of natural optical activity. The reaction system investigated obeys the basic criteria of these models: a chiral intermediate (tetralin hydroperoxide) is produced from an achiral substrate (tetralin) via an autocatalytic pathway where the feedback mechanism is expected to generate a state of broken chiral symmetry. In order to test the amplification capacity of this reaction a computer analysis of the kinetic scheme is performed. This simulation is derived from the known kinetic scheme of autoxidation and is validated by fitting the experimentally observed data of hydroperoxide evolution. Calculations show that this model allows powerful amplification of enantiomeric excess and a transient amplification of the optical rotation. It is also demonstrated that the model system exhibits pronounced sensitivity toward any loss of absolute configuration of the involved chiral species. Since an amplification effect results exclusively at a high degree of stereoselectivity, it is concluded that stereospecific autocatalysis is possible in systems which show template reactions, crystallization, or colloidal effects. © 1993 Wiley-Liss, Inc.     

Conditions for chiral asymmetry generation in the preparation of the chiral octahedral cobalt complex

We have reported that the random chiral asymmetry generation, which is a spontaneous preferential generation of one enantiomer, was observed in the synthesis of a chiral octahedral cobalt complex, cis-[CoBr(NH(3))(en)(2)]Br(2). In this article, we review our studies to explain in this system the autocatalytic growth of small enantiomeric excess that arises due to statistical fluctuations. One important experimental finding was that the rate of chiral autocatalysis increased with increasing the degree of supersaturation. Furthermore, our numerical simulation indicates that even small inhomogeneities in the reaction system may play a significant role because their effect is amplified by the autocatalytic reaction under appropriate conditions. In a small volume, fluctuations in concentration can grow if the autocatalytic growth overcomes the diffusional loss of the excess concentration from this volume. This may makes the enantiomeric excess of the chiral complex randomly fluctuate from run to run.     

Analysis of the mechanism of asymmetric amplification by chiral auxiliary trans-1,2-diaminocyclohexane bistriflamide

Asymmetric amplification is a phenomenon in which the enantiomeric excess (ee) of a product is higher than that of a chiral auxiliary for a catalyst. We analyzed the mechanism of asymmetric amplification observed in the addition of diethylzinc (Et(2)Zn) to benzaldehyde (PhCHO) to synthesize 1-phenyl-1-propanol in the presence of trans-1,2-diaminocyclohexane bistriflamide (DCBF) and titanium tetraisopropoxide (TIOP). In a manner similar to the reaction in which 1-piperidino-3,3-dimethyl-2-butanol is a chiral auxiliary for the catalyst, when asymmetric amplification was observed, the ee of the product varied as the reaction progressed. The mechanisms of variation in ee in the two reactions, however, were different. No asymmetric amplification was observed when TIOP and PhCHO were added to a mixture of DCBF and Et(2)Zn, while the ee of the product was always higher than that of DCBF when PhCHO and Et(2)Zn were added to a mixture of DCBF and TIOP. In the latter case, the product ee decreased as the reaction progressed. The results indicate that DCBF forms inactive heterochiral complex causing an increase in the ee of DCBF in the solution, which is the chiral auxiliary for the catalyst. But the complex is not very stable and gradually dissociates due to the reaction with Et(2)Zn. As a result, the asymmetric amplification decreases as the reaction progresses.     

Enantioselective Autocatalysis. V. The Spontaneous Resolution of Tri-o-Thymotide

We have attempted to appraise experimentally the allegation that minute chemical and physical differences due to the parity violating energy difference (PVED) between enantiomers are, after suitable autocatalytic amplification, ultimately responsible for the homochirality of contemporary biomolecules. The autocatalytic amplification technique employed involved the spontaneous resolution under racemizing conditions (SRURC) of a conglomerate during crystallization, and the system studied was the known crystallization of P(+)- or M(–)-tri-o-thymotide (TOT) as its optically active inclusion compound (clathrate) with benzene. Our premise was that if a PVED effect were operative, there should be a strong and consistent bias favoring the crystallization of one enantiomer of the TOT-benzene clathrate. Repetitive preparations of the clathrate, however, yielded crystalline products showing random optical activity. These results thus afford no evidence whatsoever for stereoselective bias due to a PVED, and are in accord with earlier statistical studies demonstrating random SRURC in other conglomerate crystallizations, again indicating the inefficacy of PVEDs to promote a preferred chirality in such systems.     

An Auto-Catalytic Surface for Conformational Replication of Amyloid Fibrils—Genesis of an Amyloid World?

Amyloid fibrils are composed of self assembled stacked peptide or protein molecules folded and trapped in a stable cross-beta-sheet conformation. The amyloid fibrillation mechanism represents an intriguing self-catalyzed process rendering replication of a molecular conformational memory of interest for prebiotic chemistry. Herein we describe how a solid surface can be rendered auto-catalytic for fibrillation of a protein solution. We have discovered that a hydrophobic silicon or glass surface can be made to continuously fibrillate solutions of insulin monomers under stressed conditions (pH 1.6, 65°C). It was found that the surface acts as a platform for the formation of nascent seeds that induce fibril replication on and at the surface. This autocatalytic effect stems from a layer a few insulin molecules thick representing an oligomeric layer of misfolded, conformationally trapped, insulin molecules that rapidly through epitaxial growth catalyze the rate determining step (nucleation) during fibril replication. This autocatalytic layer is generated by the protein-solid surface interaction and conformational changes of the adsorbed protein during exposure at the air-water interface. The resulting autocatalytic surface thus both initiates local conformational molecular self-replication and acts as a reservoir for fibril seeds budding off into solution spreading fibril replication entities to the surrounding medium. The possibility of catalysis of the conformational replication process by minute amounts of nucleation sites located on a recruiting surface can evade the issue of dramatic concentration dependence of amyloidogenesis.     

The role of glycophosphatidylinositol anchor in the amplification of the scrapie isoform of prion protein in vitro

Transmissible spongiform encephalopathies are associated with an autocatalytic conversion of normal prion protein, PrP^C, to a protease-resistant form, PrPres. This autocatalytic reaction can be reproduced in vitro using a procedure called protein misfolding cyclic amplification (PMCA). Here we show that, unlike brain-derived PrP^C, bacterially-expressed recombinant prion protein (rPrP) is a poor substrate for PrPres amplification in a standard PMCA reaction. The differences between PrP^C and rPrP appear to be due to the lack of the glycophosphatidylinositol anchor in the recombinant protein. These findings shed a new light on prion protein conversion process and have important implications for the efforts to generate synthetic prions for structural and biophysical studies.     

Dendritic crystal growth, differential circular scattering, and the origin of biomolecular homochirality

Phthalic acid rapidly crystallizing in thin aqueous films is deposited radially and rhythmically as dendritic banded spherulites that have heterochiral meso-textures in hemi-circles. The chiral fields differentially scatter left and right circularly polarized light. A scenario for chiral amplification and the origin of biomolecular homochirality is thus proposed that combines the influences of crystals and light.     

Organocatalytic aza-Michael/retro-aza-Michael reaction: pronounced chirality amplification in aza-Michael reaction and racemization via retro-aza-Michael reaction

A detailed experimental investigation of an aza-Michael reaction of aniline and chalcone is presented. A series of Cinchona alkaloid-derived organocatalysts with different functional groups were prepared and used in the aza-Michael and retro-aza-Michael reaction. There was an interesting finding that a complete reversal of stereoselectivity when a benzoyl group was introduced to the cinchonine and cinchonidine. The chirality amplification vs. time proceeds in the quinine-derived organocatalyst containing silicon-based bulky group, QN-TBS, -catalyzed aza-Michael reaction under solvent-free conditions. In addition, we have demonstrated for the first time that racemization was occurred in suitable solvents under mild conditions due to retro-aza-Michael reaction of the Michael adduct of aniline with chalcone. These indicate the equilibrium of retro-aza-Michael reaction and aza-Michael reaction produce the happening of chirality amplification in aza-Michael reaction and racemization via retro-aza-Michael reaction under different conditions, which would be beneficial to the development of novel chiral catalysts for the aza-Michael reactions.     

Chiral memory: induction, amplification, and switching in porphyrin assemblies

The interaction between the tetra-anionic porphyrin H2TPPS and its copper derivative, CuTPPS, with the tetra-cationic porphyrin H2T4 and its copper derivative, CuT4, leads, in aqueous solution, to the formation of remarkably stable and kinetically inert heteroaggregates. The aggregation process is under hierarchic control and, in the presence of a suitable chiral mold, leads to the formation of chiral porphyrin heteroassemblies as stable and inert as the achiral ones. Because of these properties, the chirality of the porphyrin "imprinted" heteroaggregates not only survives the disruption of the template, but also to its complete removal from the solution. Notably, the template-free chiral porphyrin system is an excellent mold for its own self-replication. The relevant characteristics of these chiral heteroaggregates together with the knowledge of the forces that guide the aggregation processes permitted us to design a new but similar system. This system not only is able to store chiral information, but also is capable to release and restore it reversibly, in a cyclic manner. This has been achieved by modulating the charges carried by one of the two coupled porphyrins through protonation under various pH conditions. The role of the central metal ion and the template-free chiral structure of the CuT4-H2TPPS heteroaggregate, determined through EDXD analysis, are also presented.     

Observation of hyperpositive non-linear effect in catalytic asymmetric organozinc additions to aldehydes

Asymmetric amplification is a phenomenon that is believed to play a key role in the emergence of homochirality in life. In asymmetric catalysis, theoretical and experimental models have been investigated to provide an understanding of how chiral amplification is possible, in particular based on non-linear effects. Interestingly, it has been proposed a quarter century ago that chiral catalysts, when not enantiopure might even be more enantioselective than their enantiopure counterparts. We show here that such hyperpositive non-linear effect in asymmetric catalysis is indeed possible. An in-depth study into the underlying mechanism was carried out, and the scheme we derive differs from the previous proposed models.     

Chiral Polymerization in Open Systems From Chiral-Selective Reaction Rates

We investigate the possibility that prebiotic homochirality can be achieved exclusively through chiral-selective reaction rate parameters without any other explicit mechanism for chiral bias. Specifically, we examine an open network of polymerization reactions, where the reaction rates can have chiral-selective values. The reactions are neither autocatalytic nor do they contain explicit enantiomeric cross-inhibition terms. We are thus investigating how rare a set of chiral-selective reaction rates needs to be in order to generate a reasonable amount of chiral bias. We quantify our results adopting a statistical approach: varying both the mean value and the rms dispersion of the relevant reaction rates, we show that moderate to high levels of chiral excess can be achieved with fairly small chiral bias, below 10%. Considering the various unknowns related to prebiotic chemical networks in early Earth and the dependence of reaction rates to environmental properties such as temperature and pressure variations, we argue that homochirality could have been achieved from moderate amounts of chiral selectivity in the reaction rates.     

Autocatalytic sets of proteins

This article investigates the possibility that the emergence of reflexively autocatalytic sets of peptides and polypeptides may be an essentially inevitable collective property of any sufficiently complex set of polypeptides. The central idea is based on the connectivity properties of random directed graphs. In the set of amino acid monomer and polymer species up to some maximum length, M, the number of possible polypeptides is large, but, for specifiable "legitimate" end condensation, cleavage and transpeptidation exchange reactions, the number of potential reactions by which the possible polypeptides can interconvert is very much larger. A directed graph in which arrows from smaller fragments to larger condensation products depict potential synthesis reactions, while arrows from the larger peptide to the smaller fragments depict the reverse cleavage reactions, comprises the reaction graph for such a system. Polypeptide protoenzymes are able to catalyze such reactions. The distribution of catalytic capacities in peptide space is a fundamental problem in its own right, and in its bearing on the existence of autocatalytic sets of proteins. Using an initial idealized hypothesis that an arbitrary polypeptide has a fixed a priori probability of catalyzing any arbitrary legitimate reaction to assign to each polypeptide those reactions, if any, which it catalyzes, the probability that the set of polypeptides up to length M contains a reflexively autocatalytic subset can be calculated and is a percolation problem on such reaction graphs. Because, as M increases, the ratio of reactions among the possible polypeptides to polypeptides rises rapidly, the existence of such autocatalytic subsets is assured for any fixed probability of catalysis. The main conclusions of this analysis appear independent of the idealizations of the initial model, introduce a novel kind of parallel selection for peptides catalyzing connected sequences of reactions, depend upon a new kind of minimal critical complexity whose properties are definable, and suggest that the emergence of self replicating systems may be a self organizing collective property of critically complex protein systems in prebiotic evolution. Similar principles may apply to the emergence of a primitive connected metabolism. Recombinant DNA procedures, cloning random DNA coding sequences into expression vectors, afford a direct avenue to test the distribution of catalytic capacities in peptide space, may provide a new means to select or screen for peptides with useful properties, and may ultimately lead toward the actual construction of autocatalytic peptide sets.     

Kinetic relationship in parallel autocatalytic amplifications of pyridyl alkanol and chiral trigger pyrimidyl alkanol

Experimental and kinetic analysis of a chemical system combines autocatalytic amplification of 2-alkynyl-5-pyrimidyl alkanol 2 and 6-alkynyl-3-pyridyl akanol 4 in which 2 acts as a chiral trigger and 4 being the subsequent autocatalyst. Starting from a very low initial ee, both alkanols are produced with high enantiopurity in one single cycle. This provides insight into a dual nonlinear amplification of chirality observed with amplifying trigger 2 and accelerated amplification of autocatalyst 4 . These kinetic studies reveal a five-fold magnitude superior amplification rates of 4 associated with trigger's enantiopurity at the outset.     

Demonstration of spontaneous chiral symmetry breaking in asymmetric Mannich and Aldol reactions

Spontaneous symmetry breaking in reactive systems, known as a rare physical phenomenon and for the Soai autocatalytic irreversible reaction, might in principle also occur in other, more common asymmetric reactions when the chiral product is capable to promote its formation and an element of "nonlinearity" is involved in the reaction scheme. Such phenomena are long sought after in chemistry as a possible explanation for the biological homochirality of biomolecules. We have investigated homogeneous organic stereoselective Mannich and Aldol reactions, in which the product is capable to form H-bridged complexes with the prochiral educt, and found by applying NMR spectroscopy, HPLC analysis, and optical rotation measurements 0.3-50.8% of random product enantiomeric excess under essentially achiral reaction conditions. These findings imply a hitherto overlooked mechanism for spontaneous symmetry breaking and, hence, a novel approach to the problem of absolute asymmetric synthesis and could have also potential significance for the conundrum of homochirality.     

Simulation of non-enzymatic template-directed synthesis of oligonucleotides and peptides

A simulation model is proposed for the template- and sequence-directed (TSD) condensation of two trideoxyribonucleotide 3'-phosphate molecules into a hexameric template with palindromic sequence studied experimentally by von Kiedrowski (1986;Angew. Int. Ed. Engl.25, 932--935). The model simulates reasonably well the kinetics of synthesis of both the template, and the pyrophosphate product which is not directly involved in the autocatalytic reaction. It offers quantitative approximation of the different rate constants of the processes involved in the reaction. The model simulates and gives predictions for the influence of factors such as the initial concentrations of the trimers and the template, and gives predictions for the effect of temperature on the dynamics of the autocatalytic reaction. The model also simulates well the production rate of a different self-replicating system (coiled coil peptide) used in the experiments of Lee et al. (1997;Nature390, 591--594). Comparing the different rate constants, it seems that chain elongation occurs at higher rates in the peptide system (at 23 degrees C) than in the nucleotide one (at 0 degrees C), but that the relative contribution of template-directed synthesis is significantly larger with the nucleotides.     

The Sugar Model: Autocatalytic Activity of the Triose–Ammonia Reaction

Reaction of triose sugars with ammonia under anaerobic conditions yielded autocatalytic products. The autocatalytic behavior of the products was examined by measuring the effect of the crude triose–ammonia reaction product on the kinetics of a second identical triose–ammonia reaction. The reaction product showed autocatalytic activity by increasing both the rate of disappearance of triose and the rate of formation of pyruvaldehyde, the product of triose dehydration. This synthetic process is considered a reasonable model of origin-of-life chemistry because it uses plausible prebiotic substrates, and resembles modern biosynthesis by employing the energized carbon groups of sugars to drive the synthesis of autocatalytic molecules.     

Luminescent probing of the simplest chiral α‐amino acid–alanine in an enantiopure and racemic state

Luminescent spectroscopy combined with the technique of luminescent probing with rare earth ions (europium, gadolinium, terbium) and an actinide ion (uranyl) was used to differentiate enantiopure and racemic alanine, the simplest chiral proteinogenic amino acid. Using the achiral luminescent probes, small differences between pure L and DL alanine in the solid state were strongly amplified. Based on the observed electronic transitions of the probes, the position of the triplet level of the coordinated alanine was estimated. Formation of homo‐ and heterochiral complexes between enantiomers of alanine and the metal ions is discussed as a possible mechanism of chiral self‐discrimination.     

Challenging the concept of "recycling" as a mechanism for the evolution of homochirality in chemical reactions

The concept that "recycling" of reactants may be key to the spontaneous generation of a homochiral state in closed autocatalytic reaction networks has recently been introduced and has been supported by computer simulations of such reaction networks. It has been suggested that unidirectional cycles maintained away from equilibrium may avoid the inevitable establishment of a racemic state, and under such conditions the explicit reverse reactions dictated by microscopic reversibility may be all be treated as having negligible rates. We show here that because the equilibrium constants in a recycled network are interdependent, it is not valid to neglect all reverse reactions simultaneously; a very low value for the rate constant of one reverse reaction in the network dictates that another reverse reaction in the same network will exhibit a large rate constant. This conclusion is general and applies to any closed mass system where the energy input is subject to microscopic reversibility. Therefore, chemical reversibility cannot be invoked as a mechanism for the evolution of a single chiral molecular state in thermally activated reactions.     

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.