The design of self-replicating helical peptides

Macromolecular Information Transfer

Macromolecular information transfer can be defined as the process by which a coded monomer sequence is communicated from one macromolecule to another. In such a transfer process, the information sequence can be kept identical, transformed into a complementary sequence or even translated into a different molecular language. Such mechanisms are crucial in biology and take place in DNA→DNA replication, DNA→RNA transcription and RNA→protein translation. In fact, there would be no life on Earth without macromolecular information transfer. Mimicking such processes with synthetic macromolecules would also be of major scientific relevance because it would open up new avenues for technological applications (e.g. data storage and processing) but also for the creation of artificial life. In this important context, this minireview summarizes recent research about information transfer in synthetic oligomers and polymers. Medium- and long-term perspectives are also discussed.

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.

From self-replication to replicator systems en route to de novo life

The process by which chemistry can give rise to biology remains one of the biggest mysteries in contemporary science. The de novo synthesis and origin of life both require the functional integration of three key characteristics - replication, metabolism and compartmentalization - into a system that is maintained out of equilibrium and is capable of open-ended Darwinian evolution. This Review takes systems of self-replicating molecules as starting points and describes the steps necessary to integrate additional characteristics of life. We analyse how far experimental self-replicators have come in terms of Darwinian evolution. We also cover models of replicator communities that attempt to solve Eigen's paradox, whereby accurate replication needs complex machinery yet obtaining such complex self-replicators through evolution requires accurate replication. Successful models rely on a collective metabolism and a way of (transient) compartmentalization, suggesting that the invention and integration of these two characteristics is driven by evolution. Despite our growing knowledge, there remain numerous key challenges that may be addressed by a combined theoretical and experimental approach.

Catalytic peptide assemblies

Self-assembly of molecules often results in new emerging properties. Even very short peptides can self-assemble into structures with a variety of physical and structural characteristics. Remarkably, many peptide assemblies show high catalytic activity in model reactions reaching efficiencies comparable to those found in natural enzymes by weight. In this review, we discuss different strategies used to rationally develop self-assembled peptide catalysts with natural and unnatural backbones as well as with metal-containing cofactors.

Native Chemical Ligation Directed by Photocleavable Peptide Nucleic Acid (PNA) Templates

A novel peptide-peptide ligation strategy is introduced that has the potential to provide peptide libraries of linearly or branched coupled fragments and will be suited to introduce simultaneous protein modifications at different ligation sites. Ligation is assisted by templating peptide nucleic acid (PNA) strands, and therefore, ligation specificity is solely encoded by the PNA sequence. PNA templating, in general, allows for various kinds of covalent ligation reactions. As a proof of principle, a native chemical ligation strategy was elaborated. This PNA-templated ligation includes easy on-resin procedures to couple linkers and PNA to the respective peptides, and a traceless photocleavage of the linker/PNA oligomer after the ligation step. A 4,5-dimethoxy-2-nitrobenzaldehyde-based linker that allowed the photocleavable linkage of two bio-oligomers was developed.

Towards open-ended evolution in self-replicating molecular systems

In this review we discuss systems of self-replicating molecules in the context of the origin of life and the synthesis of de novo life. One of the important aspects of life is the ability to reproduce and evolve continuously. In this review we consider some of the prerequisites for obtaining unbounded evolution of self-replicating molecules and describe some recent advances in this field. While evolution experiments involving self-replicating molecules have shown promising results, true open-ended evolution has not been realized so far. A full understanding of the requirements for open-ended evolution would provide a better understanding of how life could have emerged from molecular building blocks and what is needed to create a minimal form of life in the laboratory.

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.

The minimotif synthesis hypothesis for the origin of life

Several theories for the origin of life have gained widespread acceptance, led by primordial soup, chemical evolution, metabolism first, and the RNA world. However, while new and existing theories often address a key step, there is less focus on a comprehensive abiogenic continuum leading to the last universal common ancestor. Herein, I present the "minimotif synthesis" hypothesis unifying select origin of life theories with new and revised steps. The hypothesis is based on first principles, on the concept of selection over long time scales, and on a stepwise progression toward complexity. The major steps are the thermodynamically-driven origination of extant molecular specificity emerging from primordial soup leading to the rise of peptide catalysts, and a cyclic feed-forward catalytic diversification of compound and peptides in the primordial soup. This is followed by degenerate, semi-partially conservative peptide replication to pass on catalytic knowledge to progeny protocells. At some point during this progression, the emergence of RNA and selection could drive the separation of catalytic and genetic functions, allowing peptides and proteins to permeate the catalytic space, and RNA to encode higher fidelity information transfer. Translation may have emerged from RNA template driven organization and successive ligation of activated amino acids as a predecessor to translation.

Supramolecular catalysis. Part 2: artificial enzyme mimics

The design of artificial catalysts able to compete with the catalytic proficiency of enzymes is an intense subject of research. Non-covalent interactions are thought to be involved in several properties of enzymatic catalysis, notably (i) the confinement of the substrates and the active site within a catalytic pocket, (ii) the creation of a hydrophobic pocket in water, (iii) self-replication properties and (iv) allosteric properties. The origins of the enhanced rates and high catalytic selectivities associated with these properties are still a matter of debate. Stabilisation of the transition state and favourable conformations of the active site and the product(s) are probably part of the answer. We present here artificial catalysts and biomacromolecule hybrid catalysts which constitute good models towards the development of truly competitive artificial enzymes.

Self-assembly of coiled coils in synthetic biology: inspiration and progress

Biological self-assembly is very complex and results in highly functional materials. In effect, it takes a bottom-up approach using biomolecular building blocks of precisely defined shape, size, hydrophobicity, and spatial distribution of functionality. Inspired by, and drawing lessons from self-assembly processes in nature, scientists are learning how to control the balance of many small forces to increase the complexity and functionality of self-assembled nanomaterials. The coiled-coil motif, a multipurpose building block commonly found in nature, has great potential in synthetic biology. In this review we examine the roles that the coiled-coil peptide motif plays in self-assembly in nature, and then summarize the advances that this has inspired in the creation of functional units, assemblies, and systems.

Self-propagating beta-sheet polypeptide structures as prebiotic informational molecular entities: the amyloid world

The idea is advanced that under the extreme earth conditions for ~3.9 billions years ago, protein-based beta-sheet molecular structures were the first self-propagating and information-processing biomolecules that evolved. The amyloid structure of these aggregates provided an effective protection against the harsh conditions known to decompose both polyribonucleotides and natively folded polypeptides. In the prebiotic amyloid world, both the replicative and informational functions were carried out by structurally stable beta-sheet protein aggregates in a prion-like mode involving templated self-propagation and storage of information in the beta-sheet conformation. In this amyloid (protein)-first, hybrid replication-metabolism view, the synthesis of RNA, and the evolvement of an RNA-protein world, were later, but necessary events for further biomolecular evolution to occur. I further argue that in our contemporary DNA<-->RNA-->protein world, the primordial beta-conformation-based information system is preserved in the form of a cytoplasmic epigenetic memory.

Systems chemistry: logic gates, arithmetic units, and network motifs in small networks

A mixture of molecules can be regarded as a network if all the molecular components participate in some kind of interaction with other molecules--either physical or functional interactions. Template-assisted ligation reactions that direct replication processes can serve as the functional elements that connect two members of a chemical network. In such a process, the template does not necessarily catalyze its own formation, but rather the formation of another molecule, which in turn can operate as a template for reactions within the network medium. It was postulated that even networks made up of small numbers of molecules possess a wealth of molecular information sufficient to perform rather complex behavior. To probe this assumption, we have constructed virtual arrays consisting of three replicating molecules, in which dimer templates are capable of catalyzing reactants to form additional templates. By using realistic parameters from peptides or DNA replication experiments, we simulate the construction of various functional motifs within the networks. Specifically, we have designed and implemented each of the three-element Boolean logic gates, and show how these networks are assembled from four basic "building blocks". We also show how the catalytic pathways can be wired together to perform more complex arithmetic units and network motifs, such as the half adder and half subtractor computational modules, and the coherent feed-forward loop network motifs under different sets of parameters. As in previous studies of chemical networks, some of the systems described display behavior that would be difficult to predict without the numerical simulations. Furthermore, the simulations reveal trends and characteristics that should be useful as "recipes" for future design of experimental functional motifs and for potential integration into modular circuits and molecular computation devices.

Complex dynamics in a cross-catalytic self-replication mechanism

The authors consider a minimal cross-catalytic self-replicating system of only two cross-catalytic templates that mimics the R3C ligase ribozyme system of Dong-Eu and Joyce [Chem. Biol. 11, 1505 (2004)]. This system displays considerably more complex dynamics than its self-replicating counterpart. In particular, the authors discuss the Poincare-Andronov-Hopf bifurcation, canard transitions, excitability, and hysteresis that yield birhythmicity between simple and complex oscillations.

Probing Structural Effects on Replication Efficiency through Comparative Analyses of Families of Potential Self-Replicators

A formidable synthetic apparatus for the creation of nanoscale molecular structures and supramolecular assemblies through molecular structures can potentially be created from systems that are capable of parallel automultiplication (self-replication). In order to achieve this goal, a detailed understanding of the relationship between molecular structure and replication efficiency is necessary. Diastereoisomeric templates that are capable of specific and simultaneous autocatalysis have been synthesised. A systematic experimental and theoretical evaluation of their behaviour and that of structurally-related systems reveals the key determinants that dictate the emergence of self-replicative function and defines the structural space within which this behaviour is observed.

Chemical oscillations and Turing patterns in a generalized two-variable model of chemical self-replication

Chemical self-replication of oligonucleotides and helical peptides show the so-called square root rate law. Based on this rate we extend our previous work on ideal replicators to include the square root rate and other possible nonlinearities, which we couple with an enzimatic sink. Although the nonlinearity is necessary for complex dynamics, the nature of the sink is the essential feature in the mechanism that allows temporal and spatial patterns. We obtain exact general relations for the Poincare-Adronov-Hopf and Turing bifurcations, and our generalized results include the Higgins, autocatalator, and templator models as specific cases.

Reciprocal template effects in a simple synthetic system

Two mutually-complementary templates are capable of catalysing the formation of each other, creating a framework for their reciprocal replication.

Minimal self-replicating systems

Minimal self-replicating systems typically consist of three components: a product molecule, and two substrate molecules that become joined to form another product molecule. An important characteristic of self-replicating systems is the ability of the product to catalyze the formation of additional product, resulting in autocatalytic behavior. Recent advances in the area of self-replication have led to improved efficiency of autocatalysis, both by increasing the fraction of product molecules that can participate in further rounds of replication, and by improving the efficiency of the catalysts themselves. This review analyzes chemical self-replicating systems that have been developed to date and discusses ongoing challenges in this area of research.

Peptide self-assembly as a model of proteins in the pre-genomic world

Excellent catalytic efficiency has been obtained within a series of self replicating peptides, and nucleobase inclusion into a salt-switchable self replicating peptide is found to override the switch. Interestingly, cross-catalytic formation of an RNA aptamer is reported with a cationic peptide, and novel, amide-based biopolymers have been designed to self assemble.

Self-replication vs. reactive binary complexes--manipulating recognition-mediated cycloadditions by simple structural modifications

The rate of reaction and the selectivity of a Diels-Alder cycloaddition between a furan and a maleimide can be enhanced by the introduction of complementary recognition sites on the reactant species. Subtle manipulation of other structural elements allows the generation of the observed rate enhancements and selectivities through either self-replication or formation of a pre-reactive binary complex.

Peptide self-replication enhanced by a proline kink

The effect of a proline substitution within a self-replicating coiled-coil peptide was investigated. Substitutions at either the d (hydrophobic, XL-1) or e (hydrophilic, XL-2) positions within the coiled-coil led to remarkable self-replication differences. The fragments of XL-1 showed little propensity for ligation even in the presence of template, whereas XL-2 demonstrated a high catalytic efficiency for self-replication. These results may be due to intrinsic differences in the bend of the helical axis within the two peptides away from the side with the proline residue, resulting in the loss of the continuous hydrophobic interface within XL-1.

Kinetic analysis of artificial peptide self-replication. Part I: the homochiral case

Computational kinetic analysis of a lately discovered homochiral peptide self-replicator is presented. A 6-step kinetic model was designed that addresses the main reactions and hydrophobic interactions involved in this template-directed, autocatalytic system and that gave rise to excellent fitting of 4 previously published independent experimental series. The model sheds light on the mechanistic principle of the reaction system and illustrates directly a number of dynamic properties such as the observed autocatalytic efficiency. It was found that the dynamics are basically governed by two reversible hydrophobic interactions: between the template and a peptide fragment and between two template species. The later association was determined to be considerably more favored, which leads to the predominant presence of the catalytically inactive template dimer in the reaction system. Our results show that the involvement of a template trimer is not necessary to obtain the observed fittings.

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.

Approaching exponential growth with a self-replicating peptide

Self-replicating peptide systems hold great promise for a wide range of technological applications, as well as to address fundamental questions pertaining to the molecular origins of life. The development of self-replicating compounds capable of high efficiency, however, has remained elusive. Here we disclose a successful strategy whereby modulation of coiled-coil stability results in remarkable catalytic efficiency for self-replication. By shortening the peptide to the minimum length necessary for coiled-coil formation a highly efficient self-replicating system was obtained due to very low background reaction rates, bringing the efficiency close to naturally occurring enzymes.

Product-conformation-driven ligation of peptides by V8 protease

Organic co-solvent-induced secondary conformation of alpha(17-40) of human hemoglobin facilitates the splicing of E30-R31 in a mixture of its complementary segments by V8 protease. The amino acid sequence of alpha(17-40) has been conceptualized by the general structure FR(I)-EALER-FR(II) and the pentapeptide sequence EALER playing a major role in inducing the alpha-helical conformation. The primary structure of alpha(17-40) has been engineered in multiple ways to perturb one, two, or all three regions and the influence of the organic co-solvent-induced conformation and the concomitant resistance of E30-R31 peptide bond to V8 protease digestion has been investigated. The central pentapeptide (EALER), referred to here as splicedon,(3) appears to dictate a primary role in facilitating the splicing reaction. When the same flanking regions are used, (1) splicedons that carry amino acid residues of low alpha-helical potential, for example G at position 2 or 3 of the splicedon, generate a conformational trap of very low thermodynamic stability, giving an equilibrium yield of only 3%-5%; (2) splicedons with amino acid residues of good alpha-helical potential generate a conformational trap of medium thermodynamic stability and give an equilibrium yield of 20%-25%; (3) the splicedons with amino residues of good alpha-helical potential and also an amino acid that can generate an i, i + 4 side-chain carboxylate-guanidino (amino) interaction, a conformational trap of maximum thermodynamic stability is generated, giving an equilibrium yield of 45%-50%; and (4) the thermodynamic stability of the conformational trap of the spliced peptide is also influenced by the amino acid composition of the flanking regions. The V8 protease resistance of the spliced peptide bond is not a direct correlate of the amount of alpha-helical conformation induced into the product. The results of this study reflect the unique role of the splicedon in translating the organic co-solvent-induced product conformation as a site-specific stabilization of the spliced peptide bond. It is speculated that the splicedon with higher alpha-helical potential as compared to either one of the flanking regions achieves this by integrating its potential with that of the flanking region(s). Exchange of flanking regions with the products of other V8 protease-catalyzed splicing reactions will help to establish the general primary structural requirements of this class of splicing reactions and facilitate their application in modular construction of proteins.