Primordial Radioactivity and Prebiotic Chemical Evolution: Effect of γ Radiation on Formamide-Based Synthesis

In the Beginning: Let Hydration Be Coded in Proteins for Manifestation and Modulation by Salts and Adenosine Triphosphate

Water exists in the beginning and hydrates all matter. Life emerged in water, requiring three essential components in compartmentalized spaces: (1) universal energy sources driving biochemical reactions and processes, (2) molecules that store, encode, and transmit information, and (3) functional players carrying out biological activities and structural organization. Phosphorus has been selected to create adenosine triphosphate (ATP) as the universal energy currency, nucleic acids for genetic information storage and transmission, and phospholipids for cellular compartmentalization. Meanwhile, proteins composed of 20 α-amino acids have evolved into extremely diverse three-dimensional forms, including folded domains, intrinsically disordered regions (IDRs), and membrane-bound forms, to fulfill functional and structural roles. This review examines several unique findings: (1) insoluble proteins, including membrane proteins, can become solubilized in unsalted water, while folded cytosolic proteins can acquire membrane-inserting capacity; (2) Hofmeister salts affect protein stability by targeting hydration; (3) ATP biphasically modulates liquid-liquid phase separation (LLPS) of IDRs; (4) ATP antagonizes crowding-induced protein destabilization; and (5) ATP and triphosphates have the highest efficiency in inducing protein folding. These findings imply the following: (1) hydration might be encoded in protein sequences, central to manifestation and modulation of protein structures, dynamics, and functionalities; (2) phosphate anions have a unique capacity in enhancing μs-ms protein dynamics, likely through ionic state exchanges in the hydration shell, underpinning ATP, polyphosphate, and nucleic acids as molecular chaperones for protein folding; and (3) ATP, by linking triphosphate with adenosine, has acquired the capacity to spacetime-specifically release energy and modulate protein hydration, thus possessing myriad energy-dependent and -independent functions. In light of the success of AlphaFolds in accurately predicting protein structures by neural networks that store information as distributed patterns across nodes, a fundamental question arises: Could cellular networks also handle information similarly but with more intricate coding, diverse topological architectures, and spacetime-specific ATP energy supply in membrane-compartmentalized aqueous environments?

An experimental and numerical model of the behavior of cytosine in aqueous solution under gamma radiation. Relevance in prebiotic chemistry

Cytosine is an essential chemical molecule in living systems, such as DNA and RNA, it is essential in astrobiology to study how it behaves under probable primitive conditions. We looked at how cytosine broke down in aqueous solutions exposed to high radiation levels to learn more about how stable it might have been on the early Earth. We conducted various types of analysis, such as ultraviolet-visible spectroscopy and high-pressure liquid chromatography. We also developed a computer model to describe the kinetic processes and learn more about the molecules involved in the system. This model fits the results of experiments and lets us study cytosine's stability when it is exposed to gamma radiation. It enables researchers to theorize processes that are hard to test in the laboratory and is essential for studying how stable cytosine behaves in high-radiation settings.

UV Transmission in Prebiotic Environments on Early Earth

Ultraviolet (UV) light is likely to have played important roles in surficial origins of life scenarios, potentially as a productive source of energy and molecular activation, as a selective means to remove unwanted side products, or as a destructive mechanism resulting in loss of molecules/biomolecules over time. The transmission of UV light through prebiotic waters depends upon the chemical constituents of such waters, but constraints on this transmission are limited. Here, we experimentally measure the molar decadic extinction coefficients for a number of small molecules used in various prebiotic synthetic schemes. We find that many small feedstock molecules absorb most at short (∼200 nm) wavelengths, with decreasing UV absorption at longer wavelengths. For comparison, we also measured the nucleobase adenine and found that adenine absorbs significantly more than the simpler molecules often invoked in prebiotic synthesis. Our results enable the calculation of UV photon penetration under varying chemical scenarios and allow further constraints on plausibility and self-consistency of such scenarios. While the precise path that prebiotic chemistry took remains elusive, improved understanding of the UV environment in prebiotically plausible waters can help constrain both the chemistry and the environmental conditions that may allow such chemistry to occur.

A Surface Hydrothermal Source of Nitriles and Isonitriles

Giant impacts can generate transient hydrogen-rich atmospheres, reducing atmospheric carbon. The reduced carbon will form hazes that rain out onto the surface and can become incorporated into the crust. Once heated, a large fraction of the carbon is converted into graphite. The result is that local regions of the Hadean crust were plausibly saturated with graphite. We explore the consequences of such a crust for a prebiotic surface hydrothermal vent scenario. We model a surface vent fed by nitrogen-rich volcanic gas from high-temperature magmas passing through graphite-saturated crust. We consider this occurring at pressures of 1-1000bar and temperatures of 1500-1700 ∘C. The equilibrium with graphite purifies the leftover gas, resulting in substantial quantities of nitriles (0.1% HCN and 1ppm HC3N) and isonitriles (0.01% HNC) relevant for prebiotic chemistry. We use these results to predict gas-phase concentrations of methyl isocyanide of ∼1 ppm. Methyl isocyanide can participate in the non-enzymatic activation and ligation of the monomeric building blocks of life, and surface or shallow hydrothermal environments provide its only known equilibrium geochemical source.

An inorganic mineral-based protocell with prebiotic radiation fitness

Protocell fitness under extreme prebiotic conditions is critical in understanding the origin of life. However, little is known about protocell's survival and fitness under prebiotic radiations. Here we present a radioresistant protocell model based on assembly of two types of coacervate droplets, which are formed through interactions of inorganic polyphosphate (polyP) with divalent metal cation and cationic tripeptide, respectively. Among the coacervate droplets, only the polyP-Mn droplet is radiotolerant and provides strong protection for recruited proteins. The radiosensitive polyP-tripeptide droplet sequestered with both proteins and DNA could be encapsulated inside the polyP-Mn droplet, and form into a compartmentalized protocell. The protocell protects the inner nucleoid-like condensate through efficient reactive oxygen species' scavenging capacity of intracellular nonenzymic antioxidants including Mn-phosphate and Mn-peptide. Our results demonstrate a radioresistant protocell model with redox reaction system in response to ionizing radiation, which might enable the protocell fitness to prebiotic radiation on the primitive Earth preceding the emergence of enzyme-based fitness. This protocell might also provide applications in synthetic biology as bioreactor or drug delivery system.

Gamma irradiation of adenine and guanine adsorbed into hectorite and attapulgite

This study focuses on the radiolysis (up to 36 kGy) of guanine and adenine (nitrogenous bases) adsorbed in hectorite and attapulgite to highlight the potential role of clays as protective agents against ionizing radiation in prebiotic processes. In this framework, the study investigated the nitrogenous bases' behavior in two types of systems: a) aqueous suspension of adenine-clay systems and b) guanine-clay systems in the solid state. This research utilized spectroscopic and chromatographic techniques for its analytical purposes. Regardless of the reaction medium conditions, the results reveal that nitrogenous bases are stable under ionizing irradiation when adsorbed on both clays.

New physical insights: Formamide discharge decomposition and the role of fragments in the formation of large biomolecules

In this work we present a time-resolved FTIR spectroscopic study on kinetics of atomic and molecular species, specifically CO, CN radical, N₂, HCN and CO₂ generated in a glow discharge of formamide-nitrogen-water mixture in a helium buffer gas. Radicals such as NH, CH and OH have been proven to be fundamental stones of subsequent chemical reactions having a crucial role in a prebiotic synthesis of large organic molecules. This work contains three main goals. Firstly, we present our time-resolved spectra of formamide decomposition products and discuss the mechanism of collisional excitations between specific species. Secondly, according to our time resolution, we demonstrate and explain the band shape of CO's first overtone and the energy transfer between excited nitrogen and CO, present in our spectra. Lastly, we present theoretical results for the non-LTE modelling of the spectra using bi-temperature approach and a 1D harmonic Franck-Condon approach for the multi-molecule spectra of the formamide decomposition process in the 1800-5600 cm^-1 spectral range.

Automated Exploration of Prebiotic Chemical Reaction Space: Progress and Perspectives

Prebiotic chemistry often involves the study of complex systems of chemical reactions that form large networks with a large number of diverse species. Such complex systems may have given rise to emergent phenomena that ultimately led to the origin of life on Earth. The environmental conditions and processes involved in this emergence may not be fully recapitulable, making it difficult for experimentalists to study prebiotic systems in laboratory simulations. Computational chemistry offers efficient ways to study such chemical systems and identify the ones most likely to display complex properties associated with life. Here, we review tools and techniques for modelling prebiotic chemical reaction networks and outline possible ways to identify self-replicating features that are central to many origin-of-life models.