Amorphous Silica-Promoted Lysine Dimerization: a Thermodynamic Prediction

Amino Acid Polymerization on Silica Surfaces

The polymerization of unactivated amino acids (AAs) is an important topic because of its applications in various fields including industrial medicinal chemistry and prebiotic chemistry. Silica as a promoter for this reaction, is of great interest owing to its large abundance and low cost. The amide/peptide bond synthesis on silica has been largely demonstrated but suffers from a lack of knowledge regarding its reaction mechanism, the key parameters, and surface features that influence AA adsorption and reactivity, the selectivity of the reaction product, the role of water in the reaction, etc. The present review addresses these problems by summarizing experimental and modeling results from the literature and attempts to rationalize some apparent divergences in published results. After briefly presenting the main types of silica surface sites and other relevant macroscopic features, we discuss the different deposition procedures of AAs, whose importance is often neglected. We address the possible AA adsorption mechanisms including covalent grafting and H-bonding and show that they are highly dependent on silanol types and density. We then consider how the adsorption mechanisms determine the occurrence and outcome of AA condensation (formation of cyclic dimers or of long linear chains), and outline some recent results that suggest significant polymerization selectivity in systems containing several AAs, as well as the formation of specific elements of secondary structure in the growing polypeptide chains.

Why we are made of proteins and nucleic acids: Structural biology views on extraterrestrial life

Is it a miracle that life exists on the Earth, or is it a common phenomenon in the universe? If extraterrestrial organisms exist, what are they like? To answer these questions, we must understand what kinds of molecules could evolve into life, or in other words, what properties are generally required to perform biological functions and store genetic information. This review summarizes recent findings on simple ancestral proteins, outlines the basic knowledge in textbooks, and discusses the generally required properties for biological molecules from structural biology viewpoints (e.g., restriction of shapes, and types of intra- and intermolecular interactions), leading to the conclusion that proteins and nucleic acids are at least one of the simplest (and perhaps very common) forms of catalytic and genetic biopolymers in the universe. This review article is an extended version of the Japanese article, On the Origin of Life: Coevolution between RNA and Peptide, published in SEIBUTSU BUTSURI Vol. 61, p. 232-235 (2021).

Hydrophobic-cationic peptides modulate RNA polymerase ribozyme activity by accretion

Accretion and the resulting increase in local concentration is a widespread mechanism in biology to enhance biomolecular functions (for example, in liquid-liquid demixing phases). Such macromolecular aggregation phases (e.g., coacervates, amyloids) may also have played a role in the origin of life. Here, we report that a hydrophobic-cationic RNA binding peptide selected by phage display (P43: AKKVWIIMGGS) forms insoluble amyloid-containing aggregates, which reversibly accrete RNA on their surfaces in an RNA-length and Mg²⁺-concentration dependent manner. The aggregates formed by P43 or its sequence-simplified version (K₂V₆: KKVVVVVV) inhibited RNA polymerase ribozyme (RPR) activity at 25 mM MgCl₂, while enhancing it significantly at 400 mM MgCl₂. Our work shows that such hydrophobic-cationic peptide aggregates can reversibly concentrate RNA and enhance the RPR activity, and suggests that they could have aided the emergence and evolution of longer and functional RNAs in the fluctuating environments of the prebiotic earth.

Thermodynamic Impact of Mineral Surfaces on Amino Acid Polymerization: Aspartate Dimerization on Goethite

This article presents a thermodynamic predictive scheme for amino acid polymerization in the presence of minerals as a function of various environmental parameters (pH, ionic strength, amino acid concentration, and the solid/water ratio) using l-aspartate (Asp) and goethite as a model combination. This prediction is enabled by the combination of the surface adsorption constants of amino acid and its polymer, determined from the extended triple layer model characterization of the corresponding experimental results, with the thermodynamic data of these organic compounds in water reported in the literature. Calculations for the Asp-goethite system showed that the goethite surface drastically shifts the Asp monomer-dipeptide equilibrium toward the dipeptide side; when the dimerization of 0.1 mM Asp was considered in the presence of 10 m² L^-1 of goethite, an Asp dipeptide concentration around 10⁵ times larger was computed to be thermodynamically attainable compared with that in the absence of goethite at acidic pH (4-5) and low ionic strength (0.1 mM NaCl). Under this condition, the dipeptide-to-monomer molecular ratio in the adsorbed state reached 20%. In contrast, no significant enhancement by goethite was predicted at alkaline pH (>8), where the electrostatic interactions of the goethite surface with Asp and Asp dipeptide are weak. Thus, mineral surfaces should have had a significant impact on the thermodynamics of prebiotic peptide bond formation on the early Earth, although the influences likely depended largely on the environmental conditions. Future experimental studies for various amino acid-mineral interactions using our proposed methodology will provide a quantitative constraint on favorable geochemical settings for the chemical evolution on Earth. This approach can also offer important clues for future exploration of extraterrestrial life.

Geochemistry and the Origin of Life: From Extraterrestrial Processes, Chemical Evolution on Earth, Fossilized Life's Records, to Natures of the Extant Life

In 2001, the first author (S.N.) led the publication of a book entitled "Geochemistry and the origin of life" in collaboration with Dr. Andre Brack aiming to figure out geo- and astro-chemical processes essential for the emergence of life. Since then, a great number of research progress has been achieved in the relevant topics from our group and others, ranging from the extraterrestrial inputs of life's building blocks, the chemical evolution on Earth with the aid of mineral catalysts, to the fossilized records of ancient microorganisms. Here, in addition to summarizing these findings for the origin and early evolution of life, we propose a new hypothesis for the generation and co-evolution of photosynthesis with the redox and photochemical conditions on the Earth's surface. Besides these bottom-up approaches, we introduce an experimental study on the role of water molecules in the life's function, focusing on the transition from live, dormant, and dead states through dehydration/hydration. Further spectroscopic studies on the hydrogen bonding behaviors of water molecules in living cells will provide important clues to solve the complex nature of life.

Origin of the Reductive Tricarboxylic Acid (rTCA) Cycle-Type CO2 Fixation: A Perspective

The reductive tricarboxylic acid (rTCA) cycle is among the most plausible candidates for the first autotrophic metabolism in the earliest life. Extant enzymes fixing CO₂ in this cycle contain cofactors at the catalytic centers, but it is unlikely that the protein/cofactor system emerged at once in a prebiotic process. Here, we discuss the feasibility of non-enzymatic cofactor-assisted drive of the rTCA reactions in the primitive Earth environments, particularly focusing on the acetyl-CoA conversion to pyruvate. Based on the energetic and mechanistic aspects of this reaction, we propose that the deep-sea hydrothermal vent environments with active electricity generation in the presence of various sulfide catalysts are a promising setting for it to progress. Our view supports the theory of an autotrophic origin of life from primordial carbon assimilation within a sulfide-rich hydrothermal vent.