Prebiotic alternatives to proteins: structure and function of hyperbranched polyesters

Reactions Driven by Primitive Nonbiological Polyesters

ConspectusAll life on Earth is composed of cells, which are built from and run by biological reactions and structures. These reactions and structures are generally the result of action by cellular biomolecules, which are indispensable for the function and survival of all living organisms. Specifically, biological catalysis, namely by protein enzymes, but also by other biomolecules including nucleic acids, is an essential component of life. How the biomolecules themselves that perform biological catalysis came to exist in the first place is a major unanswered question that plagues researchers to this day, which is generally the focus of the origins of life (OoL) research field. Based on current knowledge, it is generally postulated that early Earth was full of a myriad of different chemicals, and that these chemicals reacted in specific ways that led to the emergence of biochemistry, cells, and later, life. In particular, a significant part of OoL research focuses on the synthesis, evolution, and function of biomolecules potentially present under early Earth conditions, as a way to understand their eventual transition into modern life. However, this narrative overlooks possibilities that other molecules contributed to the OoL, as while biomolecules that led to life were certainly present on early Earth, at the same time, other molecules that may not have strict, direct biological lineage were also widely and abundantly present. For example, hydroxy acids, although playing a role in metabolism or as parts of certain biological structures, are not generally considered to be as essential to modern biology as amino acids (a chemically similar monomer), and thus research in the OoL field tends to perhaps focus more on amino acids than hydroxy acids. However, their likely abundance on early Earth coupled with their ability to spontaneously condense into polymers (i.e., polyesters) make hydroxy acids, and their subsequent products, functions, and reactions, a reasonable target of investigation for prebiotic chemists. Whether "non-biological" hydroxy acids or polyesters can contribute to the emergence of life on early Earth is an inquiry that deserves attention within the OoL community, as this knowledge can also contribute to our understanding of the plausibility of extraterrestrial life that does not exactly use the biochemical set found in terrestrial organisms. While some demonstrations have been made with respect to compartment assembly, compartmentalization, and growth of primitive polyester-based systems, whether these "non-biological" polymers can contribute any catalytic function and/or drive primitive reactions is still an important step toward the development of early life. Here, we review research both from the OoL field as well as from industry and applied sciences regarding potential catalysis or reaction driven by "non-biological" polyesters in various forms: as linear polymers, as hyperbranched polyesters, and as membraneless microdroplets.

Thermoplastic starch/polyvinyl alcohol blends modification by citric acid-glycerol polyesters

Thermoplastic starch/polyvinyl alcohol (TPS/PVA) films have limitations for being used in long-term applications due to starch retrogradation. This leads to plasticizer migration, especially when low molecular weight plasticizers such as glycerol, are used. In this work, we employed mixtures of oligomers based on glycerol citrates with higher molecular weight than glycerol as plasticizers for potato-based TPS/PVA blends obtained by melt-mixing. This constitutes an alternative to reduce plasticizer migration while keeping high swelling degree, and to provide high mechanical performance. The novelty lies in the usage of these oligomers by melt-mixing technique, aspect not deeply explored previously and that represents the first step towards industrial scalability. Prior to the blending process, oligomers mixtures were prepared with different molar ratios of citric acid (0-40 mol%) and added them. This minimizes the undesirable hydrolysis effect of free carboxylic groups on starch chains. The results demonstrated that the migration of plasticizers in TPS/PVA blends decreased by up to 70 % when the citric acid content increased. This reduction was attributed to the higher molecular weight (the majority in the range 764-2060 Da) and the 3D structure of the oligomers compared to using raw glycerol. Furthermore, the films exhibited a 150 % increase in Young's modulus and tensile strength without a reduction in elongation at break, while maintaining a high gel content, due to a moderate crosslinking.

Geoelectrochemistry-driven alteration of amino acids to derivative organics in carbonaceous chondrite parent bodies

A long-standing question regarding carbonaceous chondrites (CCs) is how the CCs' organics were sourced and converted before and after the accretion of their parent bodies. Growing evidence shows that amino acid abundances in CCs decrease with an elongated aqueous alteration. However, the underlying chemical processes are unclear. If CCs' parent bodies were water-rock differentiated, pH and redox gradients can drive electrochemical reactions by using H2 as an electron source. Here, we simulate such redox conditions and demonstrate that α-amino acids are electrochemically altered to monoamines and α-hydroxy acids on FeS and NiS catalysts at 25 °C. This conversion is consistent with their enrichment compared to amino acid analogs in heavily altered CCs. Our results thus suggest that H2 can be an important driver for organic evolution in water-rock differentiated CC parent bodies as well as the Solar System icy bodies that might possess similar pH and redox gradients.

Protoenzymes: The Case of Hyperbranched Polymer-Scaffolded ZnS Nanocrystals

Enzymes are biological catalysts that are comprised of small-molecule, metal, or cluster catalysts augmented by biopolymeric scaffolds. It is conceivable that early in chemical evolution, ancestral enzymes opted for simpler, easier to assemble scaffolds. Herein, we describe such possible protoenzymes: hyperbranched polymer-scaffolded metal-sulfide nanocrystals. Hyperbranched polyethyleneimine (HyPEI) and glycerol citrate polymer-supported ZnS nanocrystals (NCs) are formed in a simple process. Transmission electron microscopy (TEM) analyses of HyPEI-supported NCs reveal spherical particles with an average size of 10 nm that undergo only a modest aggregation over a 14-day incubation. The polymer-supported ZnS NCs are shown to possess a high photocatalytic activity in an eosin B photodegradation assay, making them an attractive model for the study of the origin of life under the “Zn world” theory dominated by a photocatalytic proto-metabolic redox reaction network. The catalyst, however, could be easily adapted to apply broadly to different protoenzymatic systems.

Polyesters as a Model System for Building Primitive Biologies from Non-Biological Prebiotic Chemistry

A variety of organic chemicals were likely available on prebiotic Earth. These derived from diverse processes including atmospheric and geochemical synthesis and extraterrestrial input, and were delivered to environments including oceans, lakes, and subaerial hot springs. Prebiotic chemistry generates both molecules used by modern organisms, such as proteinaceous amino acids, as well as many molecule types not used in biochemistry. As prebiotic chemical diversity was likely high, and the core of biochemistry uses a rather small set of common building blocks, the majority of prebiotically available organic compounds may not have been those used in modern biochemistry. Chemical evolution was unlikely to have been able to discriminate which molecules would eventually be used in biology, and instead, interactions among compounds were governed simply by abundance and chemical reactivity. Previous work has shown that likely prebiotically available α-hydroxy acids can combinatorially polymerize into polyesters that self-assemble to create new phases which are able to compartmentalize other molecule types. The unexpectedly rich complexity of hydroxy acid chemistry and the likely enormous structural diversity of prebiotic organic chemistry suggests chemical evolution could have been heavily influenced by molecules not used in contemporary biochemistry, and that there is a considerable amount of prebiotic chemistry which remains unexplored.

Water vapor permeable polyurethane films based on the hyperbranched aminoethers of boric acid

The hyperbranched polymers have drawn intensive attention in the design of macromolecules and functional materials because of their unique physical and chemical properties resulting from the branched architecture and the high number of functional groups. In the present study, by means of light scattering, viscosimetry, thermomechanical analysis, tensile stress–strain, mechanical loss tangent and water vapor permeability measurements, we demonstrate the hierarchical macromolecular organization of organoboron polyurethanes synthesized using sterically hindered amino ethers (AEBA) of boric acid. It is shown that the water vapor permeability of polyurethanes obtained on the basis of sterically hindered aminoethers of boric acid is due to the peculiarities of the chemical structure of AEBA, which can exhibit an ionomeric nature and the presence of steric hindrances created in the hyperbranched structure of AEBA, which can lead to an increase in free volume in such polyurethanes.

It is shown that the water vapor permeability of polyurethanes obtained on the basis of sterically hindered aminoethers of boric acid is due to the peculiarities of the chemical structure of AEBA.

Membraneless polyester microdroplets as primordial compartments at the origins of life

Compartmentalization was likely essential for primitive chemical systems during the emergence of life, both for preventing leakage of important components, i.e., genetic materials, and for enhancing chemical reactions. Although life as we know it uses lipid bilayer-based compartments, the diversity of prebiotic chemistry may have enabled primitive living systems to start from other types of boundary systems. Here, we demonstrate membraneless compartmentalization based on prebiotically available organic compounds, α-hydroxy acids (αHAs), which are generally coproduced along with α-amino acids in prebiotic settings. Facile polymerization of αHAs provides a model pathway for the assembly of combinatorially diverse primitive compartments on early Earth. We characterized membraneless microdroplets generated from homo- and heteropolyesters synthesized from drying solutions of αHAs endowed with various side chains. These compartments can preferentially and differentially segregate and compartmentalize fluorescent dyes and fluorescently tagged RNA, providing readily available compartments that could have facilitated chemical evolution by protecting, exchanging, and encapsulating primitive components. Protein function within and RNA function in the presence of certain droplets is also preserved, suggesting the potential relevance of such droplets to various origins of life models. As a lipid amphiphile can also assemble around certain droplets, this further shows the droplets' potential compatibility with and scaffolding ability for nascent biomolecular systems that could have coexisted in complex chemical systems. These model compartments could have been more accessible in a "messy" prebiotic environment, enabling the localization of a variety of protometabolic and replication processes that could be subjected to further chemical evolution before the advent of the Last Universal Common Ancestor.

Wet-Dry Cycling Delays the Gelation of Hyperbranched Polyesters: Implications to the Origin of Life

In extant biology, biopolymers perform multiple crucial functions. The biopolymers are synthesized by enzyme-controlled biosystems that would not have been available at the earliest stages of chemical evolution and consist of correctly sequenced and/or linked monomers. Some of the abiotic "messy" polymers approximate some functions of biopolymers. Condensation polymers are an attractive search target for abiotic functional polymers since principal polymers of life are produced by condensation and since condensation allows for the accurate construction of high polymers. Herein the formation of hyperbranched polyesters that have been previously used in the construction of enzyme-like catalytic complexes is explored. The experimental setup compares between the branched polyesters prepared under mild continuous heating and the wet-dry cycling associated with environmental conditions, such as dew formation or tidal activities. The results reveal that periodic wetting during which partial hydrolysis of the polyester occurs, helps to control the chain growth and delays the gel transition, a mechanism contributing to the tar formation. Moreover, the NMR and mass spec analyses indicate that continuously dried samples contain higher quantities of crosslinked and macrocyclic products, whereas cycled systems are enriched in branched structures. Ostensibly, environmental conditions have the ability to exert a rudimentary pressure to selectively enrich the polyesterification products in polymers of different structures and properties. At the early stages of chemical evolution, in the absence of biological machinery, this example of environmental control could have been for selectivity in chemical systems. As expected in marginally controlled systems, the identification of each component of the heterogeneous system has proved challenging, but it is not crucial for drawing the conclusions.

Re-conceptualizing the origins of life

Over the last several hundred years of scientific progress, we have arrived at a deep understanding of the non-living world. We have not yet achieved an analogous, deep understanding of the living world. The origins of life is our best chance at discovering scientific laws governing life, because it marks the point of departure from the predictable physical and chemical world to the novel, history-dependent living world. This theme issue aims to explore ways to build a deeper understanding of the nature of biology, by modelling the origins of life on a sufficiently abstract level, starting from prebiotic conditions on Earth and possibly on other planets and bridging quantitative frameworks approaching universal aspects of life. The aim of the editors is to stimulate new directions for solving the origins of life. The present introduction represents the point of view of the editors on some of the most promising future directions.This article is part of the themed issue 'Reconceptualizing the origins of life'.

Protoenzymes: the case of hyperbranched polyesters

Enzymes are biopolymeric complexes that catalyse biochemical reactions and shape metabolic pathways. Enzymes usually work with small molecule cofactors that actively participate in reaction mechanisms and complex, usually globular, polymeric structures capable of specific substrate binding, encapsulation and orientation. Moreover, the globular structures of enzymes possess cavities with modulated microenvironments, facilitating the progression of reaction(s). The globular structure is ensured by long folded protein or RNA strands. Synthesis of such elaborate complexes has proven difficult under prebiotically plausible conditions. We explore here that catalysis may have been performed by alternative polymeric structures, namely hyperbranched polymers. Hyperbranched polymers are relatively complex structures that can be synthesized under prebiotically plausible conditions; their globular structure is ensured by virtue of their architecture rather than folding. In this study, we probe the ability of tertiary amine-bearing hyperbranched polyesters to form hydrophobic pockets as a reaction-promoting medium for the Kemp elimination reaction. Our results show that polyesters formed upon reaction between glycerol, triethanolamine and organic acid containing hydrophobic groups, i.e. adipic and methylsuccinic acid, are capable of increasing the rate of Kemp elimination by a factor of up to 3 over monomeric triethanolamine.This article is part of the themed issue 'Reconceptualizing the origins of life'.