Self‐Replicating Amphiphilic β‐Sheet Peptides

Rubinov, Boris; Wagner, Nathaniel; Rapaport, Hanna; Ashkenasy, Gonen

doi:10.1002/ange.200902790

Cited by 62 publications

(32 citation statements)

References 49 publications

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“…Enzyme-free autocatalytic systems, which are generally simpler than those with enzymes, are known to exponentially replicate one or a small set of species (1)(2)(3)(4)(5), but none of these systems replicate an arrangement of subunits defining a combinatorial sequence of information. Without the capacity for combinatorial information replication, open-ended evolution, in which complexity increases without bound (6), cannot occur.…”

mentioning

confidence: 99%

Robust self-replication of combinatorial information via crystal growth and scission

Schulman

Yurke²,

Winfree³

2012

Proc. Natl. Acad. Sci. U.S.A.

118

110

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Understanding how a simple chemical system can accurately replicate combinatorial information, such as a sequence, is an important question for both the study of life in the universe and for the development of evolutionary molecular design techniques. During biological sequence replication, a nucleic acid polymer serves as a template for the enzyme-catalyzed assembly of a complementary sequence. Enzymes then separate the template and complement before the next round of replication. Attempts to understand how replication could occur more simply, such as without enzymes, have largely focused on developing minimal versions of this replication process. Here we describe how a different mechanism, crystal growth and scission, can accurately replicate chemical sequences without enzymes. Crystal growth propagates a sequence of bits while mechanically-induced scission creates new growth fronts. Together, these processes exponentially increase the number of crystal sequences. In the system we describe, sequences are arrangements of DNA tile monomers within ribbon-shaped crystals. 99.98% of bits are copied correctly and 78% of 4-bit sequences are correct after two generations; roughly 40 sequence copies are made per growth front per generation. In principle, this process is accurate enough for 1,000-fold replication of 4-bit sequences with 50% yield, replication of longer sequences, and Darwinian evolution. We thus demonstrate that neither enzymes nor covalent bond formation are required for robust chemical sequence replication. The form of the replicated information is also compatible with the replication and evolution of a wide class of materials with precise nanoscale geometry such as plasmonic nanostructures or heterogeneous protein assemblies.algorithmic self-assembly | DNA nanotechnology | self-assembly I n cells, long genomes are accurately replicated via a complex replication process involving tens or sometimes hundreds of enzymes. Nearer to life's origins, a much simpler system must have been responsible for genome replication; evolution of this information then produced more and more complex forms. How a chemical system could be capable of sustained replication and evolution and yet be simple enough to arise spontaneously is an open question.Enzyme-free autocatalytic systems, which are generally simpler than those with enzymes, are known to exponentially replicate one or a small set of species (1-5), but none of these systems replicate an arrangement of subunits defining a combinatorial sequence of information. Without the capacity for combinatorial information replication, open-ended evolution, in which complexity increases without bound (6), cannot occur. Some RNA sequences have been shown to act as RNA polymerases that can assemble a general RNA sequence given a template (7). If such an RNA sequence polymerized a copy of itself, the required enzyme would be produced by the replication process, making it self-sustaining. However, fidelity sufficient for RNA-mediated RNA self-replication has not yet been observe...

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mentioning

confidence: 99%

Robust self-replication of combinatorial information via crystal growth and scission

Schulman

Yurke²,

Winfree³

2012

Proc. Natl. Acad. Sci. U.S.A.

118

110

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“…A related model asserts that autocatalytic chain elongation arises from template-assisted ligation and random breakage (13). Autocatalytic templating of the self-replication of peptides has also been shown (14,15). These are models of the "preinformational" world before heteropolymers begin to encode biological sequence-structure relationships.…”

Section: Ctb Requires An Autocatalytic Processmentioning

confidence: 99%

Foldamer hypothesis for the growth and sequence differentiation of prebiotic polymers

Guseva

Zuckermann

Dill

2017

Proc. Natl. Acad. Sci. U.S.A.

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It is not known how life originated. It is thought that prebiotic processes were able to synthesize short random polymers. However, then, how do short-chain molecules spontaneously grow longer? Also, how would random chains grow more informational and become autocatalytic (i.e., increasing their own concentrations)? We study the folding and binding of random sequences of hydrophobic (H) and polar (P) monomers in a computational model. We find that even short hydrophobic polar (HP) chains can collapse into relatively compact structures, exposing hydrophobic surfaces. In this way, they act as primitive versions of today's protein catalysts, elongating other such HP polymers as ribosomes would now do. Such foldamer catalysts are shown to form an autocatalytic set, through which short chains grow into longer chains that have particular sequences. An attractive feature of this model is that it does not overconverge to a single solution; it gives ensembles that could further evolve under selection. This mechanism describes how specific sequences and conformations could contribute to the chemistry-to-biology (CTB) transition.origin of life | HP model | biopolymers | autocatalytic sets A mong the most mysterious processes in chemistry is how the spontaneous transition occurred more than 3 billion years ago from a soup of prebiotic molecules to living cells. What was the mechanism of the chemistry-to-biology (CTB) transition? In this paper, we develop a model to explore how prebiotic polymerization processes might have produced long chains of proteinlike or nucleic acid-like molecules (1, 2). What polymerization processes are autocatalytic? How could they have produced long chains? Also, how might random chain sequences have become informational and self-serving? Our questions here are about physical spontaneous mechanisms, not about specific monomer or polymer chemistries. CTB Requires an Autocatalytic ProcessEarly on, it was recognized that the transition from simple chemistry to self-supporting biological behavior requires autocatalysis (i.e., some form of positive feedback or bootstrapping, in which the concentrations of some molecules become amplified and selfsustaining relative to other molecules) (3-8). That work has led to the idea of an autocatalytic set, a collection of entities in which any one entity can catalyze another.We first review some of the key results. A class of models called Graded Autocatalysis Replication Domain (GARD) (9-11) predicts that artificial autocatalytic chemical kinetic networks can lead to self-replication, with a corresponding amplification of some chemicals over others. Such systems display some degree of inheritance and adaptability. GARD model is a subset of metabolism first models, which envision that small molecule chemical processes precede information transfer and precede the first biopolymers. Focusing on polymers, Wu and Higgs (12) developed a model of RNA chain-length autocatalysis. They envision that some of the RNA chains can spontaneously serve as polymerase ribozymes, l...

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“…Challenged by Menger et al [12,13], who argued that the rate enhancement is due to amide-catalysis and not due to templateautocatalysis, Rebek's interpretation of self-replication has been vindicated by Reinhoudt's group later [14]. Since then, a few other scattered reports about selfreplicating molecules have appeared in the literature [15][16][17][18].…”

Section: Reviewmentioning

confidence: 99%

Organoautocatalysis: Challenges for experiment and theory

Tsogoeva

2010

J Syst Chem

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Recent reports about enantioselective organoautocatalytic systems, in which small organic molecules assist in their own formation and under conservation of their absolute configuration, are discussed. This process, appearing as a natural extension to non-covalent enantioselective organocatalysis, seems analogous to template-directed self-replication, previously observed in simple organic molecules and holds implications for models on the origin of life.

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Self‐Replicating Amphiphilic β‐Sheet Peptides

Cited by 62 publications

References 49 publications

Robust self-replication of combinatorial information via crystal growth and scission

Robust self-replication of combinatorial information via crystal growth and scission

Foldamer hypothesis for the growth and sequence differentiation of prebiotic polymers

Organoautocatalysis: Challenges for experiment and theory

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