Kinetic Selection in the Out‐of‐Equilibrium Autocatalytic Reaction Networks that Produce Macrocyclic Peptides

Miao, Xiaoming; Paikar, Arpita; Lerner, Benjamin; Diskin‐Posner, Yael; Shmul, Guy; Semenov, Sergey N.

doi:10.1002/ange.202105790

Cited by 4 publications

(4 citation statements)

References 63 publications

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“…Dynamic combinatorial chemistry has been used to discover a variety of functional molecules (78,79). Auto-catalytic synthesis has been used for selecting functional molecules (80,81). The majority of work on chemical evolution has taken place over the last 10 years; progress is accelerating.…”

Section: The Evolutionary Model Assumes the Line Between Chemistry An...mentioning

confidence: 99%

Origins of Life: Chemistry and Evolution

Matange,

Rajaei,

Schuster

et al. 2023

Preprint

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Progress in understanding the origins of life will be enhanced if models and their predictions are clearly understood and explicitly articulated. Two distinct models can be used to explain the genesis of biopolymers during the origins of life. In one model, which has been pursued for nearly 50 years, RNA is the result of inherent chemical reactivities of prebiotic chemical species. RNA invented evolution. This model enables the prediction that if the conditions of the ancient earth are sufficiently constrained, chemists will discover the direct synthetic pathways that produced RNA. In a fundamentally different model, which is more recent, RNA and other biopolymers are proposed to be the result of prolonged, creative, selection-based changes that occurred during chemical evolution and overlap with early biological evolution. Evolution invented RNA. In this evolutionary model, inherent chemical reactivities are not necessarily relevant to the origins of life and do not predict biosynthesis. These two models are fundamentally different from one another and guide design of very different experimental approaches to test their underlying assumptions. It is currently undetermined which model, or a hybrid of them, is closer to reality.

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Section: The Evolutionary Model Assumes the Line Between Chemistry An...mentioning

confidence: 99%

Origins of Life: Chemistry and Evolution

Matange,

Rajaei,

Schuster

et al. 2023

Preprint

View full text Add to dashboard Cite

show abstract

“…Dynamic combinatorial chemistry has been used to discover a variety of functional molecules (85,86). Auto-catalytic synthesis has been used for selecting functional molecules (87,88). The majority of work on chemical evolution has taken place over the last 10 years; progress is accelerating.…”

Section: Model 2 Origins By Chemical Evolutionmentioning

confidence: 99%

Origins of Life: Chemistry and Evolution

Matange,

Rajaei,

Schuster

et al. 2023

Preprint

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Our understanding of the origins of life will be enhanced if models and their predictions are clearly understood and explicitly articulated. Here we outline two distinct models that are currently used to explain the origins of life. In one model, which has been pursued for a half century, inherent chemical reactivities of prebiotic chemical species produced RNA, which then invented evolution. This direct synthesis model enables the prediction that if the conditions of the ancient earth are sufficiently constrained, chemists will discover the synthetic pathways that produced RNA. In a fundamentally different model, which is more recent and less mature, RNA in concert with other biopolymers arose from prolonged, selection-based changes that occurred during chemical evolution, which transitioned smoothly into biological evolution. This evolutionary model predicts common chemistry of linkage and amazing structures, assemblies and co-assemblies, as represented by double stranded DNA, tRNA, cellulose, collagen, globular proteins, ATP synthase, and the ribosome. This evolutionary model predicts profound integration of biological subsystems as represented by ATP, which is central to and inextricable from biopolymer structure and biosynthesis and metabolic systems. In the evolutionary model, inherent chemical reactivities of biological building blocks are not necessarily relevant to the origins of life and do not predict biosynthesis. The two models of the origins of life are fundamentally different from one another and guide design of very different experimental approaches to test their underlying assumptions. It is currently undetermined which model, or a hybrid of them, is closer to reality.

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“…Important advances in understanding chemical evolution have come from systems chemistry [24][25][26][27][28][29][30][31][32][33][34] , dynamic combinatorial chemistry (DCC) 35,36 , and models of self-organization 37 .…”

Section: Introductionmentioning

confidence: 99%

“…Mechanistic information on chemical evolution has been revealed by mutually catalytic systems 20 and reproducing catalytic micelles 42 . Auto-catalytic production of macrocycles has been used for selecting functional molecules 32,33 .…”

Section: Introductionmentioning

confidence: 99%

Evolution of Complex Chemical Mixtures Reveals Combinatorial Compression and Population Synchronicity

Matange,

Rajaei,

Capera-Aragonès

et al. 2023

Preprint

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Some of the most interesting open questions about the origins of life and molecular sciences center on chemical evolution and the spontaneous generation of complex and functional chemical species. The processes that generated the spectacular biopolymers that underlay biology demonstrate an untapped, by modern science, creative potential. We have established a robust, facile, and generally applicable platform for observing and analyzing chemical evolution using complex mixtures. While previous studies have characterized the formation of proto-polymers via chemical reactions, we systematically studied the process itself. We report empirical outcomes that were not foreseen or predicted. We have constructed an experimental platform to study the evolution of chemical systems that: (i) undergoes continuous recursive change with transitions to new chemical spaces while not converging throughout the course of the experiment, (ii) demonstrates chemical selection, during which combinatorial explosion is avoided, (iii) maintains synchronicity of molecular sub-populations, and (iv) harvests environmental energy that is stored in chemical energy. We have established some general guidelines for conducting chemical evolution. Our results suggest that chemical evolution can be adapted to produce a broad array of molecules with novel structures and functions.

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Kinetic Selection in the Out‐of‐Equilibrium Autocatalytic Reaction Networks that Produce Macrocyclic Peptides

Cited by 4 publications

References 63 publications

Origins of Life: Chemistry and Evolution

Origins of Life: Chemistry and Evolution

Origins of Life: Chemistry and Evolution

Evolution of Complex Chemical Mixtures Reveals Combinatorial Compression and Population Synchronicity

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