Catalyst: Can Systems Chemistry Unravel the Mysteries of the Chemical Origins of Life?

Abstract

Daniela Kroiss obtained her MSc degree in biotechnology at BOKU and is currently a PhD student in the biochemistry program at CUNY, where she works on a joint project between the Nanoscience Initiative and the University of Strathclyde.Gonen Ashkenasy is head of the Laboratory for Systems Chemistry at the Ben-Gurion University Chemistry Department. His research focuses on the design and analysis of synthetic replication networks.Adam Braunschweig earned his PhD in organic chemistry at the University of California and is an associate professor in the CUNY Nanoscience Initiative. His research focuses on the interface of organic chemistry with biology and material science.Tell Tuttle obtained his PhD in theoretical chemistry at Göteborg University and is a professor of theoretical chemistry at the University of Strathclyde. His research focuses on the directed discovery of peptide-based materials.Rein Ulijn gained his PhD in physical chemistry at the University of Strathclyde and is founding director of the Nanoscience Initiative at the CUNY Advanced Science Research Center. His research focuses on nanotechnology inspired by living systems. Daniela Kroiss obtained her MSc degree in biotechnology at BOKU and is currently a PhD student in the biochemistry program at CUNY, where she works on a joint project between the Nanoscience Initiative and the University of Strathclyde. Gonen Ashkenasy is head of the Laboratory for Systems Chemistry at the Ben-Gurion University Chemistry Department. His research focuses on the design and analysis of synthetic replication networks. Adam Braunschweig earned his PhD in organic chemistry at the University of California and is an associate professor in the CUNY Nanoscience Initiative. His research focuses on the interface of organic chemistry with biology and material science. Tell Tuttle obtained his PhD in theoretical chemistry at Göteborg University and is a professor of theoretical chemistry at the University of Strathclyde. His research focuses on the directed discovery of peptide-based materials. Rein Ulijn gained his PhD in physical chemistry at the University of Strathclyde and is founding director of the Nanoscience Initiative at the CUNY Advanced Science Research Center. His research focuses on nanotechnology inspired by living systems. How life originated on Earth remains one of the biggest unresolved questions of our time. Although no physical property is exclusive to living systems, several properties (including the abilities to self-replicate, to compartmentalize, to store and retrieve information, and to adapt in response to chemical and physical signals from the environment) are distinctive of life. These functions require continuous input of energy, they rely on the interplay of multiple components, and they take advantage of spatial and temporal separation of these chemical events. Hence, the most important hallmark of life is that it is underpinned by complex, heterogenous systems of molecular reactions and interactions, i.e., a metabolism, and operates in a steady state that is removed from the thermodynamic equilibrium. One striking characteristic of living organisms is that they perform tasks that exceed the functionality of their basic constituents. These emergent functions are enabled by the integration of complex chemical interactions and processes, where links between chemical properties and observed behavior are no longer obvious. Well-known biological examples include the circadian rhythm, the dynamic assembly and disassembly of microtubules to control motility, and transcription regulation in membrane-less organelles. The opportunity for the new field of systems chemistry is to systematically study how emergent function arises in synthetic, simplified mixtures obtained through bottom-up approaches with the ultimate objective of rationalizing emergent properties and integrating them to design novel systems that show life-like characteristics. Indeed, systems chemistry aims to develop experimental and theoretical frameworks to enable the systematic and holistic study of mixtures of components (inspired by concepts found in biology but with simpler building blocks) to understand how their interactions give rise to novel properties. Thus, although conventional (reductionist) chemistry approaches to characterizing individual building blocks utilized in living systems are unlikely to provide the information required to understand the guiding principles of emergent functions, a holistic approach is key to help unravel such systems and to experimentally address questions related to the chemical origins of life. Here, we discuss a trajectory relevant to understanding the emergence of the functions of living systems by moving from an initial selection of simple building blocks toward increasingly more complex and integrated molecular systems. This proposed evolution from molecules to ensembles to compartments and ultimately to artificial, life-like functional systems is discussed through selected recent experimental examples. As shown in Figure 1, the first step of the trajectory relies on the selection of suitable building blocks. We discuss different strategies for identifying modular building blocks that can subsequently be combined through supramolecular assembly, recognition, and reactivity to achieve additional properties. Moreover, we provide examples of how the subsequent interplay of such components can give rise to more complex function, such as catalysis, compartmentalization, replication, and adaptation (all dictated not only by chemical composition but also by their underlying artificial metabolism of reactivity and interaction networks), and ultimately give rise to active materials that change and adapt to external stimuli from their environment while consuming fuels. In systems chemistry, building blocks are often deliberately simplified; they contain only the essential features of the reaction and interaction in a minimal scaffold. This approach enables chemists to systematically investigate how the molecular properties of the individual components govern the behavior and function of complex mixtures. In order to identify building blocks with desired characteristics, computational and experimental methods can be used to screen large molecular spaces to identify building blocks that are suited to design mixtures with specific functions. Coarse-grained molecular-dynamics simulations, for example, provide a powerful tool for studying the assembly of such building blocks as short peptides, (poly)nucleotides, and (oligo)saccharides. Recently, such simulations have been applied to screen the entire tripeptide sequence space (8,000 peptides) for aggregation propensity.1Frederix P.W.J.M. Scott G.G. Abul-Haija Y.M. Kalafatovic D. Pappas C.G. Javid N. Hunt N.T. Ulijn R.V. Tuttle T. Exploring the sequence space for (tri-)peptide self-assembly to design and discover new hydrogels.Nat. Chem. 2015; 7: 30-37Crossref PubMed Scopus (467) Google Scholar From the extensive dataset that this mapping exercise produced, a set of design rules that revealed the propensity of peptides to assemble was established. These design rules can be applied not only to establish the stable (deep thermodynamic wells) structures but also to predict order and disorder in shallow thermodynamic minima, which is critical for designing dynamic assembly and disassembly systems. Another important aspect for the design of life-like systems is the ability to mimic natural binding modes with ligands of interest. In biology, ligand-substrate recognition typically involves an “induced-fit” mechanism, where structures rearrange upon binding and often employ cooperativity and multivalency to increase affinity and specificity. Designing receptors to access these biologically inspired recognition modes challenges the conventional preorganization design principles that have dominated supramolecular chemistry. However, the use of simple, flexible building blocks has recently led to the discovery of several carbohydrate receptors that access multivalency and cooperativity to achieve specificity.2Palanichamy K. Bravo M.F. Shlain M.A. Schiro F. Naeem Y. Marianski M. Braunschweig A.B. Binding studies on a library of induced-fit synthetic carbohydrate receptors with mannoside selectivity.Chemistry. 2018; 24: 13971-13982Crossref PubMed Scopus (12) Google Scholar Recently, the phage-display in vitro screening method was applied to search a large library of peptide heptamers to identify dynamic ATP-complexing sequences.3Kroiss D. Aramini J. McPhee S. Tuttle T. Ulijn R.V. Unbiased discovery of dynamic peptide-ATP complexes.ChemSystemsChem. 2019; https://doi.org/10.1002/syst.201900013Crossref Google Scholar The discovered heptapeptide is unrelated to any known nucleotide-binding motif, demonstrating that phage display is a powerful method for identifying novel functional sequences. Importantly, the selected peptide takes on a set of dynamic conformations that adapt to the presence of ATP, a feature that is not easily obtained through rational design. Efforts have been made to study synthetic systems in which simple precursors interact and react to form novel, more complex (supra-) molecules, leading to properties and structures that are not observed in the components. Autonomous selection of structures that connect building blocks in ways that lead to overall thermodynamic stabilization can be observed in such systems. For example, a dynamic combinatorial library based on a hybrid molecule consisting of an amino acid and a nucleobase subunit was studied for the identification of macrocycles that form via dynamic covalent bonds and subsequently fold into three-dimensional structures.4Liu B. Pappas C.G. Zangrando E. Demitri N. Chmielewski P.J. Otto S. Complex molecules that fold like proteins can emerge spontaneously.J. Am. Chem. Soc. 2019; 141: 1685-1689Crossref PubMed Scopus (39) Google Scholar Importantly, it was observed that residues that are not close in the primary sequence of the polymer interact with each other in the folded structure, which mimics key features of protein folding. Stepwise condensation of amino acids (and other organic precursors) through repeated hydration-dehydration cycles has also been applied, leading to the formation of ensembles of polymeric structures, the composition of which is complex and has hints of sequence enrichment.5Surman A.J. Rodriguez-Garcia M. Abul-Haija Y.M. Cooper G.J.T. Gromski P.S. Turk-MacLeod R. Mullin M. Mathis C. Walker S.I. Cronin L. Environmental control programs the emergence of distinct functional ensembles from unconstrained chemical reactions.Proc. Natl. Acad. Sci. USA. 2019; 116: 5387-5392Crossref PubMed Scopus (29) Google Scholar Importantly, these dynamic library-based approaches are receptive to changes in the environmental conditions during this process, thus allowing control of the selection of different sequences and nanoscale morphologies through environmental pressures. These examples demonstrate that combinatorial libraries are powerful tools for identifying novel folding motifs, sequence enrichment, and supramolecular structures. A current drawback of these systems, however, is that they are typically driven by thermodynamics and thus reach low-energy states. Consequently, there is a need for systems that are more adaptive and explore a shallower free-energy landscape, including ways to access out-of-equilibrium structures by exploring library response under continuous energy input. A hallmark of living cells, compared with conventional chemistry, is that chemistry-of-life processes are spatially heterogeneous and involve compartments to enable multiple reactions to occur in concert but without direct interference. Noncovalent interactions between fatty acids form membranes, whereas biopolymer mixtures containing, for example, proteins and RNA govern the formation of membrane-less compartments. The molecular principles governing the latter as liquid coacervates are currently a significant focus of investigation given their importance in biology and in relation to the chemical origins of life. A number of synthetic systems have been designed for studying the recruitment, concentration, and activation of biomolecules within these phase-separated compartments. Recently, it has been shown that the activity of a hammerhead ribozyme inside fatty-acid vesicles can be controlled through compartmentalization.6Engelhart A.E. Adamala K.P. Szostak J.W. A simple physical mechanism enables homeostasis in primitive cells.Nat. Chem. 2016; 8: 448-453Crossref PubMed Scopus (60) Google Scholar Vesicles containing the ribozyme and small amounts of a phospholipid grow at the expense of phospholipid-free vesicles. This can be exploited to overcome the inhibiting effect of polynucleotide sequences that bind to the ribozyme inside these vesicles. Thus, the specific activity of the ribozyme is maintained at a constant level, thereby mimicking homeostatic behavior. Another study that applied this compartmentalization approach used the formation of complex coacervates (formed in dynamic equilibrium through competing kinase and phosphatase activities) between cationic peptides and poly-U RNA.7Aumiller Jr., W.M. Keating C.D. Phosphorylation-mediated RNA/peptide complex coacervation as a model for intracellular liquid organelles.Nat. Chem. 2016; 8: 129-137Crossref PubMed Scopus (291) Google Scholar These results demonstrate that compartmentalization can be achieved with simple building blocks and, when combined with the catalytic formation or breakdown of structural components, provides an effective and dynamic approach to concentrating biomolecules and controlling their activity. Moreover, these examples show that kinetics, and not just thermodynamics, can be exploited for the design of adaptive systems comprising dynamic structures whose formation and breakdown can be controlled. This interplay of kinetics and thermodynamics in heterogeneous systems poses significant challenges for theoretical treatment. In living systems, continuously adapting to the environment is a key process that ensures fitness and survival. Equally important is the ability to pass on information to offspring, which allows for the evolution of increasingly complex and specialized species. Hence, the emergence of a simple mechanism by which functional biopolymers could replicate is considered a crucial step in the origin of life. Mimicking these processes by using minimalistic components is challenging; nevertheless, the design of adaptive and self-replicating systems has been an area of extensive research. A recent example demonstrated the template-directed replication of macrocycles that were formed from simple building blocks upon oxidation.8Sadownik J.W. Mattia E. Nowak P. Otto S. Diversification of self-replicating molecules.Nat. Chem. 2016; 8: 264-269Crossref PubMed Scopus (135) Google Scholar Initially, two compounds both consisting of an aromatic core, two thiol groups, and a peptide chain were mixed. This resulted in the formation of two distinct sets of replicators that competed for the remaining building blocks. Each replicator set preferred one of the two supplied building blocks, which is comparable to a system with different “food niches.” Remarkably, one replicator was found to be a descendant of the other. Consequently, the product of the reaction was dependent not only on the availability of precursor molecules but also on the history of the sample. Template-assisted replication has also been studied through investigation of the evolution of a network that originates from β sheet peptides.9Nanda J. Rubinov B. Ivnitski D. Mukherjee R. Shtelman E. Motro Y. Miller Y. Wagner N. Cohen-Luria R. Ashkenasy G. Emergence of native peptide sequences in prebiotic replication networks.Nat. Commun. 2017; 8: 434-441Crossref PubMed Scopus (35) Google Scholar Two precursor peptides were ligated to form the main building block; spontaneous epimerization and non-canonical connectivity during this process gave rise to structural isomers that differed from the original peptide in their hydrophobicity and self-assembly propensity. Initially, reaction networks that were seeded with isomers of the peptide precursors showed only slow amplification of the native peptide; however, over time, its amplification progressed in a non-linear fashion, suggesting the presence of an error-correction mechanism. Consequently, this artificial system was capable of sustaining the concentration of the native peptide in a complex mixture, a characteristic that was crucial in the origin of life for selecting and subsequently amplifying functional molecules. Next steps will require the integration of several of these functions. As an important first step in this direction, the design of a chemical reaction network that can direct a phase change and control chemical reactions in a microfluidic reactor has recently been reported.10Semenov S.N. Wong A.S.Y. van der Made R.M. Postma S.G.J. Groen J. van Roekel H.W.H. de Greef T.F.A. Huck W.T.S. Rational design of functional and tunable oscillating enzymatic networks.Nat. Chem. 2015; 7: 160-165Crossref PubMed Scopus (157) Google Scholar The chemical system is based on the biocatalytic activation of inhibitors, thus creating feedback loops. Specifically, the enzyme trypsin was applied to establish a positive feedback loop through cleavage of its precursor trypsinogen. Concurrently, trypsin activated a trypsin inhibitor via a two-step reaction, thereby introducing a time delay in the system, which is crucial for stable oscillation. Although the provided examples illustrate that significant progress has been made toward mimicking individual features of life, we still have far to go, especially in understanding how the chemically simple, passive parts become the functioning, dynamic whole. Systems chemistry offers the opportunity to systematically study how simple biomolecules interact to give rise to novel functions and might ultimately enable the design of artificial cells in the future. Although the traditional top-down approach aims to understand the working principles of an existing system through stepwise simplification, systems chemistry follows a bottom-up strategy, by which complex systems are assembled from simple components. In contrast to synthetic biology, which is focused on engineering existing biological components and modules, the field of systems chemistry aims to design systems with specific properties and functions from novel, minimalistic building blocks. Even though this approach is undoubtedly challenging with respect to design and synthesis, the process is worth pursuing because the resulting systems often provide superior control over a desired function and give rise to properties that are simply not accessible via conventional chemistry approaches. We note that the approaches to building-block selection, beyond adaptions of known molecules, typically take advantage of combinatorial screening or search methods that can be either computational or experimental. Artificial intelligence (AI) is becoming important in this context and is especially attractive for integrating computational and experimental search steps. As systems become more complex, a disadvantage of using AI is the black-box nature of it, in that correlations between structure and function can be found, but these connections might not be easily rationalized. It is important that these approaches remain closely integrated with chemical understanding. In the future, it could be possible to design self-regulating and highly adaptive chemical systems to address the critical needs in process engineering, biomedicine, and material science. To achieve this, it will be crucial to embrace more complex networks that are heterogeneous and yield multiple products through the dynamic exchange of building blocks and the formation of out-of-equilibrium structures fueled by the consumption of an energy source, in other words to create materials and nanostructures whose function is underpinned by a designed metabolic network. To reach these goals, it will be necessary to improve tools to identify components that can co-assemble into dynamic complexes that sample a shallow energy landscape, as well as to further develop feedback mechanisms and integrate several reactions into a complex network. One crucial requirement for this undertaking will be to improve available techniques to analyze complex reaction mixtures in detail. Moreover, computational prediction tools will continue to be used alongside experimental studies to elucidate the principles guiding the behavior of these systems on the molecular level. D.K. is grateful for funding from the City University of New York (CUNY)-Strathclyde partnership. G.A. thanks the CUNY Advanced Science Research Center for hosting him for a sabbatical period. A.B.B. and R.V.U. acknowledge the Air Force Office of Scientific Research (FA9550-17-1-0356 and FA9550-19-1-0111) for financial support and the research infrastructure support of the National Science Foundation Centers of Research Excellence in Science and Technology (CREST) Center for Interface Design and Engineered Assembly of Low Dimensional Systems (IDEALS). Reaction: Life Is MessyIrving R. EpsteinChemJuly 15, 2019In BriefSystems chemistry provides potential insights into the origin of life, but a full understanding of how life might arise requires understanding heterogeneous mixtures subject to temporally changing influences, such as light, temperature, and mechanical forces. Such complex systems are best studied by interdisciplinary teams with a range of expertise. One such effort involves the quest to build “reflexively autocatalytic and food-generated sets,” collections of molecules interacting on mineral grains and capable of catalyzing the reproduction of the entire set. Full-Text PDF Open ArchiveReaction: A Plea for Hypothesis-Driven Research in Prebiotic Systems ChemistryKepa Ruiz-MirazoChemJuly 15, 2019In BriefOne of the deepest frontiers of human knowledge has to do with life’s inherent complexity and how it came about. Despite the magnitude of the challenge, current prospects for making scientific progress in the question of origins of life are encouraging. However, the conversion of this promising situation into actual progress requires scientific breakthroughs that open new ground for prebiotic systems investigations. Careful, hypothesis-driven, specific proposals ought to be favored—over more extensive explorations—in this context. Full-Text PDF Open Archive