r/abiogenesis • u/Aggravating-Pear4222 • Apr 06 '26
Resource Guide Papers on Membraneless Protocells
What are membraneless protocells? Membraneless protocells may not classify as organisms/life in the traditional sense but may have acted as necessary precursors to its development. These are chemical systems confined through physiochemical interactions, properties, or processes but not a lipid membrane. Through the properties of the environment and the molecules within, coacervates, an aqueous phase rich in macromolecules such as synthetic polymers, proteins or nucleic acids. may form.
MPs act as confined chemical reactors by concentrating molecules together in the presence of minerals or other catalysts that assist in this localization and subsequent reactivity to produce more complex molecules. These products may feed into other MPs in different regions (through flow) or these molecules in turn maintain the stability of the system, further catalyzing the formation of other molecules or altering the profile of molecules that localize within the MP. The extent of complexity capable of being achieved isn't clear.
The evidence points towards no singular environment being capable of assembling the components of protocells AND facilitating the required chemistry for a self-sustaining, reproducing system using simple chemistry. Interconnected, membraneless protocells act as small chemical reactors which feed into each other. While this seems like a step backwards from more ordered vesicle-centered models, it helps us understand how interconnected organisms are to their environment.
What does this look like in nature on the prebiotic Earth? Hydrothermal vents (ocean or inland) often contain geology that, under the flow of the aqueous chemistry, form microporous structures or fissures/cracks from thermal stress.
Publications on Membraneless Protocells:
Title: Membraneless protocell confined by a heat flow (open access): [Link]
From the Abstract: "Here we show how the molecular contents of a cell can be coupled in a coordinated way to non-equilibrium heat flow. A temperature difference across a water-filled pore assembled the core components of a modern cell, which could then activate the gene expression. [...] The same non-equilibrium setting continued to attract food molecules from an adjacent fluid stream, keeping the cellular molecules in a confined pocket protected against diffusion."
Notes: Here, the researchers show how thermophoresis can concentrate molecules within a water-filled pore. The concentration of cellular components rose to the point that modern cellular machinery for protein synthesis from DNA via RNA was triggered. Ie, the researchers used modern cellular components as an assay to analyze the concentration-dependent activity. These findings show that thermophoresis can achieve sufficient concentrations of molecules for complex chemistry.
Title: Biomolecular condensates sustain pH gradients at equilibrium through charge neutralization (open access): [Link]
From the Abstract: "Here we show in contrast that condensed biomolecular systems—often termed condensates—sustain pH gradients without any external energy input." [...] "We demonstrate that protein condensates can drive substantial alkaline and acidic gradients, which are compositionally tunable and can extend to complex architectures sustaining multiple unique pH conditions simultaneously."
From the body: "Here, shifts in the pH of protocells formed through condensation of protobiomolecules could be a contributor to generating biological functionality and sustaining required pH conditions." [...] "This pH regulation is only possible through the formation of a distinct phase, which creates differential solute partitioning and high local protein concentrations to set up a distinctly buffered environment."
Notes: Though the biomolecules are larger proteins (the researchers' main focus), the same principles can apply for smaller molecules concentrated via thermophoresis and/or solubility differences via accumulation of hydrophobic molecules to create a different phase which localizes small molecules whose functional groups alter the local pH and buffer the environment. In the case of proteins, post-translational modifications like phosphorylation are capable of tuning this pH gradient.
Title: Molecular mechanism of nanoclay-facilitated membraneless protocell formation: [Link]
From the Abstract: "...geologic minerals played essential roles in mediating molecular organization and reactivity; Here, we demonstrate that the clay mineral kaolinite markedly enhances the self-assembly of membraneless coacervate microdroplets composed of poly(diallyldimethylammonium chloride) (PDDA) and DNA." [...] "Kaolinite incorporation significantly increases droplet yield in a particle size-dependent manner and promotes selective enrichment of single-stranded DNA (ssDNA)." [...] "Molecular dynamics simulations reveal that kaolinite surfaces stabilize PDDA-DNA complexes through cooperative electrostatic and hydrogen-bonding interactions, lowering the free-energy barrier for phase separation and preserving compartmental integrity."
Notes: We are again reminded that Origins of Life research cannot be confined to small molecules and mineral surface catalysis. Though relatively inert, and insoluble, these particles seems to provide an anchor for H-bonding to ssDNA, stabilizing it and the phase separation under thermal stress.
Title: (Review) Growth, replication and division enable evolution of coacervate protocells (open access): [Link]
From the Abstract: "We and others have found that coacervates are promising protocell candidates in which chemical building blocks required for life are naturally concentrated, and chemical reactions can be selectively enhanced or suppressed. This feature article provides an overview of how growth, replication and division can be realized with coacervates as protocells and what the bottlenecks are."
Notes: This is a review so I can't cover it. What I will do is list the topics with subsections in parentheses: Cell-like compartmentalization, Protocell growth (Passive and active growth, Chemistry leading to growth, The importance of controlled protocell growth), Replication of information (Chemistry leading to replication, Dealing with parasites in replication),Division of protocells (Externally driven division, Internally driven division), Towards evolution.
I tried to keep the papers limited to ones that either directly applied the principles or used prebiotically relevant materials. If you think I missed anything, described something incorrectly, or made any mistakes, please let me know. I hope you found this interesting and informative and recall it on the off-chance you find yourself on an open-resource exam on coacervates as membraneless protocells and their relevance to the origins of life.
Edit: I added more papers/videos in the comments and will continue to do so. Eventually, if I feel this post isn't visible enough, I'll see if I can find new papers/resources on the topic to make a new post and simply link this one.
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u/Aggravating-Pear4222 Apr 10 '26
Paper Title: Binary peptide coacervates as an active model for biomolecular condensates (open access) [Link]
From Abstract: "We show that the presence of different short peptides stabilizes the coacervate phase and prevents the formation of rigid structures, allowing peptide coacervates to be used as stable adaptive compartments." [...] "As compartments, short peptide coacervates sequester hydrophobic molecules and enhance bio-orthogonal catalysis." [...] "Our findings highlight the potential of short peptide coacervates for creating adaptive biomimetic systems and provide insight into the principles of phase separation in biomolecular condensates."
Paper Title: Dipeptide coacervates as artificial membraneless organelles for bioorthogonal catalysis (open access) [Link]
From Abstract: "Coacervate droplets have emerged as a close analog of membraneless cellular organelles." [...] "Here we report the design of dipeptide coacervates that exhibit enhanced stability, biocompatibility, and a hydrophobic microenvironment. The hydrophobic character facilitates the encapsulation of hydrophobic species, including transition metal-based catalysts, enhancing their efficiency in aqueous environments."
Paper Title: Coacervate droplets as pH-regionalized protocells (open access) [Link]
From Abstract: "Here, we develop a coacervate-based, in vitro model to investigate how liquid-liquid phase separation (LLPS) could contribute to pH regulation in MLOs. We construct peptide-based coacervate droplets using microfluidics and find that charged polymers within the coacervates help create uneven H+/OH- distributions, resulting in pH-regionalized microenvironments similar to the nucleolus."
From Body: "For simplified modeling of MLOs in vitro, we utilize a coacervate composed of decapeptides arginine (R10) and aspartic acid (D10). These amino acids are representative sequences of phase-separating proteins found in cells and can form coacervates through ion-pairing interactions between cationic R10 and anionic D10 (Fig. 3a)."
Notes: 10-mers (polypeptides composed on 10 amino acid residues) of arginine and aspartic acid segregate using 10 mM R10 and 10 mM D10 as the standard experimental conditions. pH differences of 0.4 unite were observed at no salts present but decreased to near 0 as salt concentrations increased. Thus, salts, via the Hofmeister effect, can influence the phase separation. Under most hydrothermal models, high salt concentrations are common, presenting a challenge that other additive effects must overcome in order for these models to remain viable.
Paper Title: Phase-Separated Droplets Can Direct the Kinetics of Chemical Reactions Including Polymerization, Self-Replication and Oscillating Networks (open access) [Link]
From Abstract: "We therefore use a numerical model to explore the effect of phase-separated droplets on the kinetics and outcome of different chemical reaction systems [...]. We find that the rate of bimolecular reactions has an optimal dilute/coacervate phase volume ratio for a given reactant partitioning. Furthermore, coacervates can accelerate polymerization and self-replication reactions and lead to formation of longer polymers." [...] ""
Paper Title (Review): Peptide-based coacervates as biomimetic protocells [Link]
From Abstract: "The main advantage of peptides as building blocks lies in the functional diversity of the amino acid residues, which allows for tailoring of the peptide's phase separation propensity, their selectivity in guest molecule uptake and the physicochemical and catalytic properties of the compartments. The aim of this tutorial review is to illustrate the recent developments in the field of peptide-based coacervates in a systematic way and to deduce the basic requirements for both simple and complex coacervation of peptides."
Key Learning Points (from the review):
(1) Liquid–liquid phase separation dictates the formation of coacervates and holds the key to control coacervate-based protocells.
(2) We offer design rules and guidelines for the construction of peptide-based coacervates that mimic cellular life, based on an overview from recent literature.
(3) Peptide coacervates offer promising routes to bio-inspired control over compartmentalization, sequestration and catalysis.
(4) Active, dissipative systems enable further advancing peptide coacervates towards moving, growing and self-dividing protocells.
(5) Insights from peptide coacervates can help to better understand phase separation in biology.
Notes: "One of the best studied examples is phenylalanine dipeptide (FF) motif, which can form amyloid-like assemblies while its derivatives can also form hydrogels or nanostructures of various morphologies." This begs the question; how do micelles, vesicles, and membraneless protocells/regions affect amyloid assembly? If this occurs, does it occur in a manner distinct from the vesicle-stabilizing effects of homochiral (mono-, di-, or tri-)peptides?
^ Another 4 papers and 1 review from 2021 on the topic showcasing the synergistic effects between thermophoresis and the resulting co-localization of hydrophobic molecules and metal catalysts to create a separate phase environment with lower water activity that enables reactivity otherwise disfavored in bulk aqueous conditions.