Browse
Submit Data
Databases
API
Help

Dataset Information

43 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Dissipative self-assembly, competition and inhibition in a self-reproducing protocell model.

ABSTRACT: The bottom-up synthesis of artificial, life-like systems promises to enable the study of emergent properties distinctive to life. Here, we report protocell systems generated from phase-separated building blocks. Vesicle protocells self-reproduce through a phase-transfer mechanism, catalysing their own formation. Dissipative self-assembly by the protocells is achieved when a hydrolysis step to destroy the surfactant is introduced. Competition between micelle and vesicle based replicators for a common feedstock shows that environmental conditions can control what species predominates: under basic conditions vesicles predominate, but in a neutral medium micelles are selected for via a mechanism which inhibits vesicle formation. Finally, the protocells enable orthogonal reactivity by catalysing in situ formation of an amphiphilic organocatalyst, which after incorporation into the vesicle bilayer enantioselectively forms a secondary product.

SUBMITTER: Post EAJ

PROVIDER: S-EPMC8162124 | biostudies-literature | 2020 Aug

REPOSITORIES: biostudies-literature

ACCESS DATA

Json Xml

Publications

Dissipative self-assembly, competition and inhibition in a self-reproducing protocell model.

Post Elias A J EAJ Fletcher Stephen P SP

Chemical science 20200812 35

The bottom-up synthesis of artificial, life-like systems promises to enable the study of emergent properties distinctive to life. Here, we report protocell systems generated from phase-separated building blocks. Vesicle protocells self-reproduce through a phase-transfer mechanism, catalysing their own formation. Dissipative self-assembly by the protocells is achieved when a hydrolysis step to destroy the surfactant is introduced. Competition between micelle and vesicle based replicators for a co ...[more]

PMID: 34094210

Similar Datasets

Hierarchical Self-Assembly of a Copolymer-Stabilized Coacervate Protocell.

Project description:Complex coacervate microdroplets are finding increased utility in synthetic cell applications due to their cytomimetic properties. However, their intrinsic membrane-free nature results in instability that limits their application in protocell research. Herein, we present the development of a new protocell model through the spontaneous interfacial self-assembly of copolymer molecules on biopolymer coacervate microdroplets. This hierarchical protocell model not only incorporates the favorable properties of coacervates (such as spontaneous assembly and macromolecular condensation) but also assimilates the essential features of a semipermeable copolymeric membrane (such as discretization and stabilization). This was accomplished by engineering an asymmetric, biodegradable triblock copolymer molecule comprising hydrophilic, hydrophobic, and polyanionic components capable of direct coacervate membranization via electrostatic surface anchoring and chain self-association. The resulting hierarchical protocell demonstrated striking integrity as a result of membrane formation, successfully stabilizing enzymatic cargo against coalescence and fusion in discrete protocellular populations. The semipermeable nature of the copolymeric membrane enabled the incorporation of a simple enzymatic cascade, demonstrating chemical communication between discrete populations of neighboring protocells. In this way, we pave the way for the development of new synthetic cell constructs.

| S-EPMC5724030 | biostudies-literature

The fabrication of a supra-amphiphile for dissipative self-assembly.

Project description:Dissipative self-assembly is a challenging but attractive field of supramolecular science, because it generally concerns complex systems but is more close to the self-assembly of living bodies. In this article, we realized dissipative self-assembly by coupling a supra-amphiphile with a chemical oscillator. The supra-amphiphile was fabricated with iodine and a double hydrophilic block copolymer containing PEG segments, as the non-covalent interaction between PEG and iodine could turn PEG hydrophobic, leading to the formation of the supra-amphiphile. The self-assembly and disassembly of the supra-amphiphile could be controlled by varying the concentration of iodine. Therefore, the dissipative self-assembly of the supra-amphiphile was realized when it was coupled with the IO3--NH3OH+-OH- chemical oscillator, which was able to produce iodine periodically. Meanwhile, the kinetic data of the self-assembly and disassembly of the supra-amphiphile could be estimated by the theoretical simulation of the chemical oscillations. This line of research promotes the self-assembly of supra-amphiphiles one step forward from thermodynamic statics to a dissipative system, and also suggests a new strategy to investigate the kinetics of stimuli-responsive molecular self-assembly.

| S-EPMC5975747 | biostudies-literature

Dissipative self-assembly of particles interacting through time-oscillatory potentials.

Project description:Dissipative self-assembly is the emergence of order within a system due to the continuous input of energy. This form of nonequilibrium self-organization allows the creation of structures that are inaccessible in equilibrium self-assembly. However, design strategies for dissipative self-assembly are limited by a lack of fundamental understanding of the process. This work proposes a novel route for dissipative self-assembly via the oscillation of interparticle potentials. It is demonstrated that in the limit of fast potential oscillations the structure of the system is exactly described by an effective potential that is the time average of the oscillatory potential. This effective potential depends on the shape of the oscillations and can lead to effective interactions that are physically inaccessible in equilibrium. As a proof of concept, Brownian dynamics simulations were performed on a binary mixture of particles coated by weak acids and weak bases under externally controlled oscillations of pH. Dissipative steady-state structures were formed when the period of the pH oscillations was smaller than the diffusional timescale of the particles, whereas disordered oscillating structures were observed for longer oscillation periods. Some of the dissipative structures (dimers, fibers, and honeycombs) cannot be obtained in equilibrium (fixed pH) simulations for the same system of particles. The transition from dissipative self-assembled structures for fast oscillations to disordered oscillating structures for slow oscillations is characterized by a maximum in the energy dissipated per oscillation cycle. The generality of the concept is demonstrated in a second system with oscillating particle sizes.

| S-EPMC4103377 | biostudies-literature

Modelling lipid competition dynamics in heterogeneous protocell populations.

Project description:Recent experimental work in the field of synthetic protocell biology has shown that prebiotic vesicles are able to 'steal' lipids from each other. This phenomenon is driven purely by asymmetries in the physical state or composition of the vesicle membranes, and, when lipid resource is limited, translates directly into competition amongst the vesicles. Such a scenario is interesting from an origins of life perspective because a rudimentary form of cell-level selection emerges. To sharpen intuition about possible mechanisms underlying this behaviour, experimental work must be complemented with theoretical modelling. The aim of this paper is to provide a coarse-grain mathematical model of protocell lipid competition. Our model is capable of reproducing, often quantitatively, results from core experimental papers that reported distinct types vesicle competition. Additionally, we make some predictions untested in the lab, and develop a general numerical method for quickly solving the equilibrium point of a model vesicle population.

| S-EPMC4097352 | biostudies-literature

Dissipative Self-Assembly of Patchy Particles under Nonequilibrium Drive: A Computational Study.

Project description:Inspired by biology and implemented using nanotechnology, the self-assembly of patchy particles has emerged as a pivotal mechanism for constructing complex structures that mimic natural systems with diverse functionalities. Here, we explore the dissipative self-assembly of patchy particles under nonequilibrium conditions, with the aim of overcoming the constraints imposed by equilibrium assembly. Utilizing extensive Monte Carlo (MC) and Molecular Dynamics (MD) simulations, we provide insight into the effects of external forces that mirror natural and chemical processes on the assembly rates and the stability of the resulting assemblies comprising 8, 10, and 13 patchy particles. Implemented by a favorable bond-promoting drive in MC or a pulsed square wave potential in MD, our simulations reveal the role these external drives play in accelerating assembly kinetics and enhancing structural stability, evidenced by a decrease in the time to first assembly and an increase in the duration the system remains in an assembled state. Through the analysis of an order parameter, entropy production, bond dynamics, and interparticle forces, we unravel the underlying mechanisms driving these advancements. We also validated our key findings by simulating a larger system of 100 patchy particles. Our comprehensive results not only shed light on the impact of external stimuli on self-assembly processes but also open a promising pathway for expanding the application by leveraging patchy particles for novel nanostructures.

| S-EPMC11500309 | biostudies-literature

Dissipative Particle Dynamics Simulations of a Protein-Directed Self-Assembly of Nanoparticles.

Project description:Design and fabrication of multifunctional porous structures play key roles in the development of high-performance energy storage devices. Our experiments demonstrated that nanostructured porous components, such as electrodes and interlayers, generated from the protein-directed self-assembly of nanoparticles can significantly improve the battery performances. The protein-directed assembly of nanoparticles in solution is a complex process involving the complicated interactions among proteins, particles, and solvent molecules. In this paper, we investigate the effects of coating proteins and specific solvent environments on the assembled porous structures. Comprehensive dissipative particle dynamics (DPD) simulations have been implemented to explore the molecular interactions and uncover the fundamental mechanisms in a gelatin-directed self-assembly of carbon black particles under different solvent conditions. Our simulations show that compact triple-strand "rod-like" structures are formed in water while loose curved "sheet-like" structures are formed in an acetic acid/water mixture. The structural difference is mainly due to the redistribution of the charges on the gelatin side chains under specific acid-solvent conditions. The strong and flexible "sheet-like" structures lead to a homogenous porous structure with high porosity and with large functionalized surfaces. Our simulations results can reasonably explain the experimental observations; this work demonstrates the great potential of DPD as a powerful tool in guiding future experimental design and optimization.

| S-EPMC6648767 | biostudies-literature

Translation of Chemical Structure into Dissipative Particle Dynamics Parameters for Simulation of Surfactant Self-Assembly.

Project description:Dissipative particle dynamics (DPD) can be used to simulate the self-assembly properties of surfactants in aqueous solutions, but in order to simulate a new compound, a large number of new parameters are required. New methods for the calculation of reliable DPD parameters directly from chemical structure are described, allowing the DPD approach to be applied to a much wider range of organic compounds. The parameters required to describe the bonded interactions between DPD beads were calculated from molecular mechanics structures. The parameters required to describe the nonbonded interactions were calculated from surface site interaction point (SSIP) descriptions of molecular fragments that represent individual beads. The SSIPs were obtained from molecular electrostatic potential surfaces calculated using density functional theory and used in the SSIMPLE algorithm to calculate transfer free energies between different bead liquids. This approach was used to calculate DPD parameters for a range of different types of surfactants, which include ester, amide, and sugar moieties. The parameters were used to simulate the self-assembly properties in aqueous solutions, and comparison of the results for 27 surfactants with the available experimental data shows that these DPD simulations accurately predict critical micelle concentrations, aggregation numbers, and the shapes of the supramolecular assemblies formed. The methods described here provide a general approach to determining DPD parameters for neutral organic compounds of arbitrary structure.

| S-EPMC8154614 | biostudies-literature

RNA catalysis in model protocell vesicles.

Project description:We are engaged in a long-term effort to synthesize chemical systems capable of Darwinian evolution, based on the encapsulation of self-replicating nucleic acids in self-replicating membrane vesicles. Here, we address the issue of the compatibility of these two replicating systems. Fatty acids form vesicles that are able to grow and divide, but vesicles composed solely of fatty acids are incompatible with the folding and activity of most ribozymes, because low concentrations of divalent cations (e.g., Mg(2+)) cause fatty acids to precipitate. Furthermore, vesicles that grow and divide must be permeable to the cations and substrates required for internal metabolism. We used a mixture of myristoleic acid and its glycerol monoester to construct vesicles that were Mg(2+)-tolerant and found that Mg(2+) cations can permeate the membrane and equilibrate within a few minutes. In vesicles encapsulating a hammerhead ribozyme, the addition of external Mg(2+) led to the activation and self-cleavage of the ribozyme molecules. Vesicles composed of these amphiphiles grew spontaneously through osmotically driven competition between vesicles, and further modification of the membrane composition allowed growth following mixed micelle addition. Our results show that membranes made from simple amphiphiles can form vesicles that are stable enough to retain encapsulated RNAs in the presence of divalent cations, yet dynamic enough to grow spontaneously and allow the passage of Mg(2+) and mononucleotides without specific macromolecular transporters. This combination of stability and dynamics is critical for building model protocells in the laboratory and may have been important for early cellular evolution.

| S-EPMC5072289 | biostudies-literature

Dissipative Particle Dynamics Simulation for the Self-Assembly of Symmetric Pentablock Terpolymers Melts under 1D Confinements.

Project description:The phase behavior of CBABC pentablock terpolymers confined in thin films is investigated using the Dissipative Particle Dynamic method. Phase diagrams are constructed and used to reveal how chain length (i-block length), block composition and wall selectivity influence the self-assembly structures. Under neutral walls, four categories of morphologies, i.e., perpendicular lamellae, core-shell types of microstructures, complex networks, and half-domain morphologies, are identified with the change in i-block length. Ordered structures are more common at weak polymer-polymer interaction strengths. For polymers of a consistent chain length, when one of the three components has a relatively smaller length, the morphologies transition is sensitive to block composition. With selective walls, parallel lamellae structures are prevalent. Wall selectivity also impacts chain conformations. While a large portion of chains form loop conformations under A-selective walls, more chains adopt bridge conformation when the wall prefers C-blocks. These findings offer insights for designing nanopatterns using symmetric pentablock terpolymers.

| S-EPMC10575399 | biostudies-literature

Concentration-driven growth of model protocell membranes.

Project description:The first protocell membranes may have assembled from fatty acids and related single-chain lipids available in the prebiotic environment. Prior to the evolution of complex cellular machinery, spontaneous protocell membrane growth and division had to result from the intrinsic physicochemical properties of these molecules, in the context of specific environmental conditions. Depending on the nature of the chemical and physical environment, fatty acids can partition between several different phases, including soluble monomers, micelles, and lamellar vesicles. Here we address the concentration dependence of fatty acid aggregation, which is dominated by entropic considerations. We quantitatively distinguish between fatty acid phases using a combination of physical and spectroscopic techniques, including the use of the fluorescent fatty acid analogue Laurdan, whose emission spectrum is sensitive to structural differences between micellar and lamellar aggregates. We find that the monomer-aggregate transition largely follows a characteristic pseudophase model of molecular aggregation but that the composition of the aggregate phase is also concentration dependent. At low amphiphile concentrations above the critical aggregate concentration, vesicles coexist with a significant proportion of micelles, while more concentrated solutions favor the lamellar vesicle phase. We subsequently show that the micelle-vesicle equilibrium can be used to drive the growth of pre-existing vesicles upon an increase in amphiphile concentration either through solvent evaporation or following the addition of excess lipids. We propose a simple model for a primitive environmentally driven cell cycle, in which protocell membrane growth results from evaporative concentration, followed by shear force or photochemically induced division.

| S-EPMC3530389 | biostudies-literature

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

Tweets

OmicsDI Databases

PRIDE
PeptideAtlas
MassIVE
JPOST Repository
Physiome Model Repository

EGA
EVA
ENA
LINCS
PAXDB
Cell Collective

MetaboLights
Metabolomics Workbench
MetabolomeExpress
GNPS
BioModels
FAIRDOMHub

ArrayExpress
dbGaP
ExpressionAtlas
GEO
NODE

Information

Databases
Help
API
Contact us
Code on GitHub
Terms of use
Submit Data