The Influence of Modularity, Seeding, and Product Inhibition on Peptide Autocatalytic Network Dynamics

Self-generating autocatalytic networks: structural results, algorithms and their relevance to early biochemistry

The concept of an autocatalytic network of reactions that can form and persist, starting from just an available food source, has been formalized by the notion of a reflexively autocatalytic and food-generated (RAF) set. The theory and algorithmic results concerning RAFs have been applied to a range of settings, from metabolic questions arising at the origin of life, to ecological networks, and cognitive models in cultural evolution. In this article, we present new structural and algorithmic results concerning RAF sets, by studying more complex modes of catalysis that allow certain reactions to require multiple catalysts (or to not require catalysis at all), and discuss the differing ways catalysis has been viewed in the literature. We also focus on the structure and analysis of minimal RAFs and derive structural results and polynomial-time algorithms. We then apply these new methods to a large metabolic network to gain insights into possible biochemical scenarios near the origin of life.

Self-reproducing catalytic micelles as nanoscopic protocell precursors

Protocells at life's origin are often conceived as bilayer-enclosed precursors of life, whose self-reproduction rests on the early advent of replicating catalytic biopolymers. This Perspective describes an alternative scenario, wherein reproducing nanoscopic lipid micelles with catalytic capabilities were forerunners of biopolymer-containing protocells. This postulate gains considerable support from experiments describing micellar catalysis and autocatalytic proliferation, and, more recently, from reports on cross-catalysis in mixed micelles that lead to life-like steady-state dynamics. Such results, along with evidence for micellar prebiotic compatibility, synergize with predictions of our chemically stringent computer-simulated model, illustrating how mutually catalytic lipid networks may enable micellar compositional reproduction that could underlie primal selection and evolution. Finally, we highlight studies on how endogenously catalysed lipid modifications could guide further protocellular complexification, including micelle to vesicle transition and monomer to biopolymer progression. These portrayals substantiate the possibility that protocellular evolution could have been seeded by pre-RNA lipid assemblies.

Chemical control of peptide material phase transitions

Progressive solute-rich polymer phase transitions provide pathways for achieving ordered supramolecular assemblies. Intrinsically disordered protein domains specifically regulate information in biological networks via conformational ordering. Here we consider a molecular tagging strategy to control ordering transitions in polymeric materials and provide a proof-of-principle minimal peptide phase network captured with a dynamic chemical network.

Substrate initiated assembly of a dynamic chemical network.

Autocatalytic networks in biology: structural theory and algorithms

Self-sustaining autocatalytic networks play a central role in living systems, from metabolism at the origin of life, simple RNA networks and the modern cell, to ecology and cognition. A collectively autocatalytic network that can be sustained from an ambient food set is also referred to more formally as a 'reflexively autocatalytic food-generated' (RAF) set. In this paper, we first investigate a simplified setting for studying RAFs, which is nevertheless relevant to real biochemistry and which allows an exact mathematical analysis based on graph-theoretic concepts. This, in turn, allows for the development of efficient (polynomial-time) algorithms for questions that are computationally intractable (NP-hard) in the general RAF setting. We then show how this simplified setting for RAF systems leads naturally to a more general notion of RAFs that are 'generative' (they can be built up from simpler RAFs) and for which efficient algorithms carry over to this more general setting. Finally, we show how classical RAF theory can be extended to deal with ensembles of catalysts as well as the assignment of rates to reactions according to which catalysts (or combinations of catalysts) are available.

Molecular Diversity Required for the Formation of Autocatalytic Sets

Systems chemistry deals with the design and study of complex chemical systems. However, such systems are often difficult to investigate experimentally. We provide an example of how theoretical and simulation-based studies can provide useful insights into the properties and dynamics of complex chemical systems, in particular of autocatalytic sets. We investigate the issue of the required molecular diversity for autocatalytic sets to exist in random polymer libraries. Given a fixed probability that an arbitrary polymer catalyzes the formation of other polymers, we calculate this required molecular diversity theoretically for two particular models of chemical reaction systems, and then verify these calculations by computer simulations. We also argue that these results could be relevant to an origin of life scenario proposed recently by Damer and Deamer.

Autocatalytic Networks at the Basis of Life's Origin and Organization

Life is more than the sum of its constituent molecules. Living systems depend on a particular chemical organization, i.e., the ways in which their constituent molecules interact and cooperate with each other through catalyzed chemical reactions. Several abstract models of minimal life, based on this idea of chemical organization and also in the context of the origin of life, were developed independently in the 1960s and 1970s. These models include hypercycles, chemotons, autopoietic systems, (M,R)-systems, and autocatalytic sets. We briefly compare these various models, and then focus more specifically on the concept of autocatalytic sets and their mathematical formalization, RAF theory. We argue that autocatalytic sets are a necessary (although not sufficient) condition for life-like behavior. We then elaborate on the suggestion that simple inorganic molecules like metals and minerals may have been the earliest catalysts in the formation of prebiotic autocatalytic sets, and how RAF theory may also be applied to systems beyond chemistry, such as ecology, economics, and cognition.