Early Selection of the Amino Acid Alphabet Was Adaptively Shaped by Biophysical Constraints of Foldability

The origins and evolution of translation factors

Translation is an ancient molecular information processing system found in all living organisms. Over the past decade, significant progress has been made in uncovering the origins of early translation. Yet, the evolution of translation factors - key regulators of protein synthesis - remains poorly understood. This review synthesizes recent findings on translation factors, highlighting their structural diversity, evolutionary history, and organism-specific adaptations across the tree of life. We examine conserved translation factors, their coevolution, and their roles in different steps in translation: initiation, elongation, and termination. The early evolution of translation factors serves as a natural link between modern genetics and the origins of life. Traditionally rooted in chemistry and geology, incorporating evolutionary molecular biology into the studies of life's emergence provides a complementary perspective on this complex question.

Designing single-polymer-chain nanoparticles to mimic biomolecular hydration frustration

Native folded proteins rely on sculpting the local chemical environment of their active or binding sites, as well as their shapes, to achieve functionality. In particular, proteins use hydration frustration-control over the dehydration of hydrophilic residues and the hydration of hydrophobic residues-to amplify their chemical or binding activity. Here we uncover that single-polymer-chain nanoparticles formed by random heteropolymers comprising four or more components can display similar levels of hydration frustration. We categorize these nanoparticles into three types based on whether either hydrophobic or hydrophilic residues, or both types, display frustrated states. We propose a series of physicochemical rules that determine the state of these nanoparticles. We demonstrate the generality of these rules in atomistic and simplified Monte Carlo models of single-polymer-chain nanoparticles with different backbones and residues. Our work provides insights into the design of single-chain nanoparticles, an emerging polymer modality that achieves the ease and cost of fabrication of polymeric material with the functionality of biological proteins.

Long-Range Electrostatics in Serine Proteases: Machine Learning-Driven Reaction Sampling Yields Insights for Enzyme Design

Computational enzyme design is a promising technique for producing novel enzymes for industrial and clinical needs. A key challenge that this technique faces is to consistently achieve the desired activity. Fundamental studies of natural enzymes revealed critical contributions from second-shell - and even more distant - residues to their remarkable efficiency. In particular, such residues organize the internal electrostatic field to promote the reaction. Engineering such fields computationally proved to be a promising strategy, which, however, has some limitations. Charged residues necessarily form specific patterns of local interactions that may be exploited for structural integrity. As a result, it is impossible to probe the electrostatic field alone by substituting amino acids. We hypothesize that an approach that isolates the influences of residues' charges from other influences could yield deeper insights. We use molecular modeling with AI-enhanced QM/MM reaction sampling to implement such an approach and apply it to a model serine protease subtilisin. We find that the negative charge 8 Å away from the catalytic site is crucial to achieving the enzyme's catalytic efficiency, contributing more than 2 kcal/mol to lowering the barrier. In contrast, a positive charge from the second-closest charged residue opposes the efficiency of the reaction by raising the barrier by 0.8 kcal/mol. This result invites discussion into the role of this residue and trade-offs that might have taken place in the evolution of such enzymes. Our approach is transferable and can help investigate the evolution of electrostatic preorganization in other enzymes. We believe that the study and engineering of electrostatic fields in enzymes is a promising direction to advance both fundamental and applied enzymology and lead to the design of new powerful biocatalysts.

Mg2+-driven selection of natural phosphatidic acids in primitive membranes

Biological membranes are composed exclusively of phospholipids comprising glycerol-1-phosphate or glycerol-3-phosphate. By contrast, primitive membranes would have likely been composed of heterogeneous mixtures of phospholipids, including non-natural analogues comprising glycerol-2-phosphate, as delivered by prebiotic synthesis. Thus, it is not clear how the selection of natural phospholipids could have come about. Here we show how differences in supramolecular properties, but not molecular properties, could have driven the selection of natural phosphatidic acids in primitive membranes. First, we demonstrate that at the molecular level it is unlikely that any prebiotic synthesis or hydrolysis pathway would have enabled the selection of natural phosphatidic acids. Second, we report that at the supramolecular level, natural phospholipids display a greater tendency to self-assemble in more packed and rigid membranes than non-natural analogues of the same chain length. Finally, taking advantage of these differences, we highlight that Mg2+, but not Na+, K+, Ca2+ or Zn2+, drives the selective precipitation of non-natural phosphatidic acids from heterogeneous mixtures obtained by prebiotic synthesis, leaving membranes proportionally enriched in natural phosphatidic acids. Our findings delineate a plausible pathway by which the transition towards biological membranes could have occurred under conditions compatible with prebiotic metal-driven processes, such as non-enzymatic RNA polymerization.

Similarity Analysis of Computer-Generated and Commercial Libraries for Targeted Biocompatible Coded Amino Acid Replacement

Many non-natural amino acids can be incorporated by biological systems into coded functional peptides and proteins. For such incorporations to be effective, they must not only be compatible with the desired function but also evade various biochemical error-checking mechanisms. The underlying molecular mechanisms are complex, and this problem has been approached previously largely by expert perception of isomer compatibility, followed by empirical study. However, the number of amino acids that might be incorporable by the biological coding machinery may be too large to survey efficiently using such an intuitive approach. We introduce here a workflow for searching real and computed non-natural amino acid libraries for biosimilar amino acids which may be incorporable into coded proteins with minimal unintended disturbance of function. This workflow was also applied to molecules which have been previously benchmarked for their compatibility with the biological translation apparatus, as well as commercial catalogs. We report the results of scoring their contents based on fingerprint similarity via Tanimoto coefficients. These similarity scoring methods reveal candidate amino acids which could be substitutable into modern proteins. Our analysis discovers some already-implemented substitutions, but also suggests many novel ones.

The interplay between peptides and RNA is critical for protoribosome compartmentalization and stability

The ribosome, owing to its exceptional conservation, harbours a remarkable molecular fossil known as the protoribosome. It surrounds the peptidyl transferase center (PTC), responsible for peptide bond formation. While previous studies have demonstrated the PTC activity in RNA alone, our investigation reveals the intricate roles of the ribosomal protein fragments (rPeptides) within the ribosomal core. This research highlights the significance of rPeptides in stability and coacervation of two distinct protoribosomal evolutionary stages. The 617nt 'big' protoribosome model, which associates with rPeptides specifically, exhibits a structurally defined and rigid nature, further stabilized by the peptides. In contrast, the 136nt 'small' model, previously linked to peptidyltransferase activity, displays greater structural flexibility. While this construct interacts with rPeptides with lower specificity, they induce coacervation of the 'small' protoribosome across a wide concentration range, which is concomitantly dependent on the RNA sequence and structure. Moreover, these conditions protect RNA from degradation. This phenomenon suggests a significant evolutionary advantage in the RNA-protein interaction at the early stages of ribosome evolution. The distinct properties of the two protoribosomal stages suggest that rPeptides initially provided compartmentalization and prevented RNA degradation, preceding the emergence of specific RNA-protein interactions crucial for the ribosomal structural integrity.

Alkylation of Complex Glycine Precursor (CGP) as a Prebiotic Route to 20 Proteinogenic Amino Acids Synthesis

It is not known why the number of proteinogenic amino acids is limited to 20. Since Miller's experiment, many studies have shown that amino acids could have been generated under prebiotic conditions. However, the amino acid compositions obtained from simulated experiments and exogenous origins are different from those of life. We hypothesized that some simple precursor compounds generated by high-energy reactions were selectively combined by organic reactions to afford a limited number of amino acids. To this direction, we propose two scenarios. One is the reaction of HCN with each side-chain precursor (the aminomalononitrile scenario), and the other is alkylation of the "complex glycine precursor", which is the main product of proton irradiation of the primordial atmosphere (the new polyglycine scenario). Here, selective formation of the 20 amino acids is described focusing on the latter scenario. The structural features of proteinogenic amino acids can be described systematically. The scenario consists of three stages: a high-energy reaction stage (Gly, Ala, Asn, and Asp were established); an alkylation stage (Gln, Glu, Ser, Thr, Val, Ile, Leu, and Pro were generated in considerable amounts); and a peptide formation stage (Phe, Tyr, Trp, His, Lys, Arg, Cys, and Met were selected due to their structural advantages). This scenario is a part of the evolution of Garakuta World, in which many prebiotic materials are contained.

A Proposal for the RNAome at the Dawn of the Last Universal Common Ancestor

From the most ancient RNAs, which followed an RNY pattern and folded into small hairpins, modern RNA molecules evolved by two different pathways, dubbed Extended Genetic Code 1 and 2, finally conforming to the current standard genetic code. Herein, we describe the evolutionary path of the RNAome based on these evolutionary routes. In general, all the RNA molecules analysed contain portions encoded by both genetic codes, but crucial features seem to be better recovered by Extended 2 triplets. In particular, the whole Peptidyl Transferase Centre, anti-Shine-Dalgarno motif, and a characteristic quadruplet of the RNA moiety of RNAse-P are clearly unveiled. Differences between bacteria and archaea are also detected; in most cases, the biological sequences are more stable than their controls. We then describe an evolutionary trajectory of the RNAome formation, based on two complementary evolutionary routes: one leading to the formation of essentials, while the other complemented the molecules, with the cooperative assembly of their constituents giving rise to modern RNAs.

Phosphoric acid salts of amino acids as a source of oligopeptides on the early Earth

Because of their unique proton-conductivity, chains of phosphoric acid molecules are excellent proton-transfer catalysts. Here we demonstrate that this property could have been exploited for the prebiotic synthesis of the first oligopeptide sequences on our planet. Our results suggest that drying highly diluted solutions containing amino acids (like glycine, histidine and arginine) and phosphates in comparable concentrations at elevated temperatures (ca. 80 °C) in an acidic environment could lead to the accumulation of amino acid:phosphoric acid crystalline salts. Subsequent heating of these materials at 100 °C for 1-3 days results in the formation of oligoglycines consisting of up to 24 monomeric units, while arginine and histidine form shorter oligomers (up to trimers) only. Overall, our results suggest that combining the catalytic effect of phosphate chains with the crystalline order present in amino acid:phosphoric acid salts represents a viable solution that could be utilized to generate the first oligopeptide sequences in a mild acidic hydrothermal field scenario. Further, we propose that crystallization could help overcoming cyclic oligomer formation that is a generally known bottleneck of prebiotic polymerization processes preventing further chain growth.

Origins of Life: The Protein Folding Problem all over again?

How did specific useful protein sequences arise from simpler molecules at the origin of life? This seemingly needle-in-a-haystack problem has remarkably close resemblance to the old Protein Folding Problem, for which the solution is now known from statistical physics. Based on the logic that Origins must have come only after there was an operative evolution mechanism-which selects on phenotype, not genotype-we give a perspective that proteins and their folding processes are likely to have been the primary driver of the early stages of the origin of life.

Does arginine aggregate formation in aqueous solutions follow a two-step mechanism?

The formation of aggregates was studied in arginine aqueous solutions using light scattering. The main driving force for aggregate formation is hydrogen bonding between the arginine (Arg) amino acids, which is partially verified using density functional theory calculations. The measurement of energy loss during this process, coupled with Cryo-EM morphology data, indicates that these aggregates are in the solid state. The aggregation occurs in two steps, with a liquid intermediate stage. The investigation of the effect of pH and solute concentration on aggregate formation for other amino acid aqueous solutions verifies that aggregate formation is amino-acid specific, while small-sized clusters formed by weak interactions lead to large-sized aggregation. The water structure around amino acid molecules sheds light on the prediction of their aggregate formation. Homochirality is observed in the aggregates; its existence sheds light on the origin of protein homochirality.

Peptides En Route from Prebiotic to Biotic Catalysis

In the quest to understand prebiotic catalysis, different molecular entities, mainly minerals, metal ions, organic cofactors, and ribozymes, have been implied as key players. Of these, inorganic and organic cofactors have gained attention for their ability to catalyze a wide array of reactions central to modern metabolism and frequently participate in these reactions within modern enzymes. Nevertheless, bridging the gap between prebiotic and modern metabolism remains a fundamental question in the origins of life. In this Account, peptides are investigated as a potential bridge linking prebiotic catalysis by minerals/cofactors to enzymes that dominate modern life's chemical reactions. Before ribosomal synthesis emerged, peptides of random sequences were plausible on early Earth. This was made possible by different sources of amino acid delivery and synthesis, as well as their condensation under a variety of conditions. Early peptides and proteins probably exhibited distinct compositions, enriched in small aliphatic and acidic residues. An increase in abundance of amino acids with larger side chains and canonical basic groups was most likely dependent on the emergence of their more challenging (bio)synthesis. Pressing questions thus arise: how did this composition influence the early peptide properties, and to what extent could they contribute to early metabolism? Recent research from our group and colleagues shows that highly acidic peptides/proteins comprising only the presumably "early" amino acids are in fact competent at secondary structure formation and even possess adaptive folding characteristics such as spontaneous refoldability and chaperone independence to achieve soluble structures. Moreover, we showed that highly acidic proteins of presumably "early" composition can still bind RNA by utilizing metal ions as cofactors to bridge carboxylate and phosphoester functional groups. And finally, ancient organic cofactors were shown to be capable of binding to sequences from amino acids considered prebiotically plausible, supporting their folding properties and providing functional groups, which would nominate them as catalytic hubs of great prebiotic relevance. These findings underscore the biochemical plausibility of an early peptide/protein world devoid of more complex amino acids yet collaborating with other catalytic species. Drawing from the mechanistic properties of protein-cofactor catalysis, it is speculated here that the early peptide/protein-cofactor ensemble could facilitate a similar range of chemical reactions, albeit with lower catalytic rates. This hypothesis invites a systematic experimental test. Nonetheless, this Account does not exclude other scenarios of prebiotic-to-biotic catalysis or prioritize any specific pathways of prebiotic syntheses. The objective is to examine peptide availability, composition, and functional potential among the various factors involved in the emergence of early life.

Primordial aminoacyl-tRNA synthetases preferred minihelices to full-length tRNA

Aminoacyl-tRNA synthetases (AARS) and tRNAs translate the genetic code in all living cells. Little is known about how their molecular ancestors began to enforce the coding rules for the expression of their own genes. Schimmel et al. proposed in 1993 that AARS catalytic domains began by reading an 'operational' code in the acceptor stems of tRNA minihelices. We show here that the enzymology of an AARS urzyme•TΨC-minihelix cognate pair is a rich in vitro realization of that idea. The TΨC-minihelixLeu is a very poor substrate for full-length Leucyl-tRNA synthetase. It is a superior RNA substrate for the corresponding urzyme, LeuAC. LeuAC active-site mutations shift the choice of both amino acid and RNA substrates. AARS urzyme•minihelix cognate pairs are thus small, pliant models for the ancestral decoding hardware. They are thus an ideal platform for detailed experimental study of the operational RNA code.

The prebiotic emergence of biological evolution

The origin of life must have been preceded by Darwin-like evolutionary dynamics that could propagate it. How did that adaptive dynamics arise? And from what prebiotic molecules? Using evolutionary invasion analysis, we develop a universal framework for describing any origin story for evolutionary dynamics. We find that cooperative autocatalysts, i.e. autocatalysts whose per-unit reproductive rate grows as their population increases, have the special property of being able to cross a barrier that separates their initial degradation-dominated state from a growth-dominated state with evolutionary dynamics. For some model parameters, this leap to persistent propagation is likely, not rare. We apply this analysis to the Foldcat Mechanism, wherein peptides fold and help catalyse the elongation of each other. Foldcats are found to have cooperative autocatalysis and be capable of emergent evolutionary dynamics.

Genetic Encoding of Phosphorylated Amino Acids into Proteins

Reversible phosphorylation is a fundamental mechanism for controlling protein function. Despite the critical roles phosphorylated proteins play in physiology and disease, our ability to study individual phospho-proteoforms has been hindered by a lack of versatile methods to efficiently generate homogeneous proteins with site-specific phosphoamino acids or with functional mimics that are resistant to phosphatases. Genetic code expansion (GCE) is emerging as a transformative approach to tackle this challenge, allowing direct incorporation of phosphoamino acids into proteins during translation in response to amber stop codons. This genetic programming of phospho-protein synthesis eliminates the reliance on kinase-based or chemical semisynthesis approaches, making it broadly applicable to diverse phospho-proteoforms. In this comprehensive review, we provide a brief introduction to GCE and trace the development of existing GCE technologies for installing phosphoserine, phosphothreonine, phosphotyrosine, and their mimics, discussing both their advantages as well as their limitations. While some of the technologies are still early in their development, others are already robust enough to greatly expand the range of biologically relevant questions that can be addressed. We highlight new discoveries enabled by these GCE approaches, provide practical considerations for the application of technologies by non-GCE experts, and also identify avenues ripe for further development.

How hydrophobicity, side chains, and salt affect the dimensions of disordered proteins

Despite the generally accepted role of the hydrophobic effect as the driving force for folding, many intrinsically disordered proteins (IDPs), including those with hydrophobic content typical of foldable proteins, behave nearly as self-avoiding random walks (SARWs) under physiological conditions. Here, we tested how temperature and ionic conditions influence the dimensions of the N-terminal domain of pertactin (PNt), an IDP with an amino acid composition typical of folded proteins. While PNt contracts somewhat with temperature, it nevertheless remains expanded over 10-58°C, with a Flory exponent, ν, >0.50. Both low and high ionic strength also produce contraction in PNt, but this contraction is mitigated by reducing charge segregation. With 46% glycine and low hydrophobicity, the reduced form of snow flea anti-freeze protein (red-sfAFP) is unaffected by temperature and ionic strength and persists as a near-SARW, ν ~ 0.54, arguing that the thermal contraction of PNt is due to stronger interactions between hydrophobic side chains. Additionally, red-sfAFP is a proxy for the polypeptide backbone, which has been thought to collapse in water. Increasing the glycine segregation in red-sfAFP had minimal effect on ν. Water remained a good solvent even with 21 consecutive glycine residues (ν > 0.5), and red-sfAFP variants lacked stable backbone hydrogen bonds according to hydrogen exchange. Similarly, changing glycine segregation has little impact on ν in other glycine-rich proteins. These findings underscore the generality that many disordered states can be expanded and unstructured, and that the hydrophobic effect alone is insufficient to drive significant chain collapse for typical protein sequences.

Assembly-driven protection from hydrolysis as key selective force during chemical evolution

The origins of biopolymers pose fascinating questions in prebiotic chemistry. The marvelous assembly proficiencies of biopolymers suggest they are winners of a competitive evolutionary process. Sophisticated molecular assembly is ubiquitous in life where it is often emergent upon polymerization. We focus on the influence of molecular assembly on hydrolysis rates in aqueous media and suggest that assembly was crucial for biopolymer selection. In this model, incremental enrichment of some molecular species during chemical evolution was partially driven by the interplay of kinetics of synthesis and hydrolysis. We document a general attenuation of hydrolysis by assembly (i.e., recalcitrance) for all universal biopolymers and highlight the likely role of assembly in the survival of the 'fittest' molecules during chemical evolution.

Xeno Amino Acids: A Look into Biochemistry as We Do Not Know It

Would another origin of life resemble Earth's biochemical use of amino acids? Here, we review current knowledge at three levels: (1) Could other classes of chemical structure serve as building blocks for biopolymer structure and catalysis? Amino acids now seem both readily available to, and a plausible chemical attractor for, life as we do not know it. Amino acids thus remain important and tractable targets for astrobiological research. (2) If amino acids are used, would we expect the same L-alpha-structural subclass used by life? Despite numerous ideas, it is not clear why life favors L-enantiomers. It seems clearer, however, why life on Earth uses the shortest possible (alpha-) amino acid backbone, and why each carries only one side chain. However, assertions that other backbones are physicochemically impossible have relaxed into arguments that they are disadvantageous. (3) Would we expect a similar set of side chains to those within the genetic code? Many plausible alternatives exist. Furthermore, evidence exists for both evolutionary advantage and physicochemical constraint as explanatory factors for those encoded by life. Overall, as focus shifts from amino acids as a chemical class to specific side chains used by post-LUCA biology, the probable role of physicochemical constraint diminishes relative to that of biological evolution. Exciting opportunities now present themselves for laboratory work and computing to explore how changing the amino acid alphabet alters the universe of protein folds. Near-term milestones include: (a) expanding evidence about amino acids as attractors within chemical evolution; (b) extending characterization of other backbones relative to biological proteins; and (c) merging computing and laboratory explorations of structures and functions unlocked by xeno peptides.

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).

Impact of non-proteinogenic amino acid norvaline and proteinogenic valine misincorporation on a secondary structure of a model peptide

Norvaline is a straight-chain, hydrophobic, non-proteinogenic amino acid, isomeric with valine. Both amino acids can be misincorporated into proteins at isoleucine positions by isoleucyl-tRNA synthetase when the mechanisms of translation fidelity are impaired. Our previous study showed that the proteome-wide substitution of isoleucine with norvaline resulted in higher toxicity in comparison to the proteome-wide substitution of isoleucine with valine. Although mistranslated proteins/peptides are considered to have non-native structures responsible for their toxicity, the observed difference in protein stability between norvaline and valine misincorporation has not yet been fully understood. To examine the observed effect, we chose the model peptide with three isoleucines in the native structure, introduced selected amino acids at isoleucine positions and applied molecular dynamics simulations at different temperatures. The obtained results showed that norvaline has the highest destructive effect on the β-sheet structure and suggested that the higher toxicity of norvaline over valine is predominantly due to the misincorporation within the β-sheet secondary elements.