Peptide-RNA Coacervates as a Cradle for the Evolution of Folded Domains

Formation of RNA lipid nanoparticles: an equilibrium process with a liquid intermediate stage

This paper presents evidence that RNA-lipid nanoparticles (LNPs) can be assembled using a slow, thermodynamically controlled process. The lipid mixture used in the Spikevax vaccine was dissolved in 52% (v/v) ethanol and titrated into a solution containing tRNA. The titration was conducted using an isothermal titration calorimeter (ITC) and consisted of 40 injections with enough time between each injection so that equilibrium was reached before the next injection. Liquid phase separation occurred where the RNA-lipid complex had a lipid amine to RNA phosphate (N/P) ratio around 1 : 1. The liquid droplets had a mean hydrodynamic diameter of 1020 ± 150 nm measured using dynamic light scattering (DLS) and were clearly observable by light microscopy. At a N/P ratio of 6 : 1 the LNPs were 109 ± 0 nm and LNPs were observed using transmission electron microscopy. The mechanism for conversion of the liquid intermediate into LNPs is likely to be spontaneous emulsification driven by negative surface tension. This equilibrium process for making RNA-LNPs is very different from current manufacture strategies using rapid single step mixing in a microfluidic device. This approach provides a low shear alternative process that could be adapted to a stirred tank.

Role of Electron Spin, Chirality, and Charge Dynamics in Promoting the Persistence of Nascent Nucleic Acid-Peptide Complexes

Primitive nucleic acids and peptides likely collaborated in early biochemistry. What forces drove their interactions and how did these forces shape the properties of primitive complexes? We investigated how two model primordial polypeptides associate with DNA. When peptides were coupled to a ferromagnetic substrate, DNA binding depended on the substrate's magnetic moment orientation. Reversing the magnetic field nearly abolished binding despite complementary charges. Inverting the peptide chirality or just the cysteine residue reversed this effect. These results are attributed to the chiral-induced spin selectivity (CISS) effect, where molecular chirality and electron spin alter a protein's electric polarizability. The presence of CISS in simple protein-DNA complexes suggests that it played a significant role in ancient biomolecular interactions. A major consequence of CISS is enhancement of the kinetic stability of protein-nucleic acid complexes. These findings reveal how chirality and spin influence bioassociation, offering insights into primitive biochemical evolution and shaping contemporary protein functions.

Redefining the Limits of Functional Continuity in the Early Evolution of P-Loop NTPases

At the heart of many nucleoside triphosphatases is a conserved phosphate-binding sequence motif. A current model of early enzyme evolution proposes that this six to eight residue motif could have sparked the emergence of the very first nucleoside triphosphatases-a striking example of evolutionary continuity from simple beginnings, if true. To test this provocative model, seven disembodied Walker A-derived peptides were extensively computationally characterized. Although dynamic flickers of nest-like conformations were observed, significant structural similarity between the situated peptide and its disembodied counterpart was not detected. Simulations suggest that phosphate binding is nonspecific, with a preference for GTP over orthophosphate. Control peptides with the same amino acid composition but different sequences and situated conformations behaved similarly to the Walker A peptides, revealing no indication that the Walker A sequence is privileged as a disembodied peptide. We conclude that the evolutionary history of the P-loop NTPase family is unlikely to have started with a disembodied Walker A peptide in an aqueous environment. The limits of evolutionary continuity for this protein family must be reconsidered. Finally, we argue that motifs such as the Walker A motif may represent incomplete or fragmentary molecular fossils-the true nature of which has been eroded by time.

Peptide-mediated liquid-liquid phase separation and biomolecular condensates

Liquid-liquid phase separation (LLPS) is a cornerstone of cellular organization, driving the formation of biomolecular condensates that regulate diverse biological processes and inspire innovative applications. This review explores the molecular mechanisms underlying peptide-mediated LLPS, emphasizing the roles of intermolecular interactions such as hydrophobic effects, electrostatic interactions, and π-π stacking in phase separation. The influence of environmental factors, such as pH, temperature, ionic strength, and molecular crowding on the stability and dynamics of peptide coacervates is examined, highlighting their tunable properties. Additionally, the unique physicochemical properties of peptide coacervates, including their viscoelastic behavior, interfacial dynamics, and stimuli-responsiveness, are discussed in the context of their biological relevance and engineering potential. Peptide coacervates are emerging as versatile platforms in biotechnology and medicine, particularly in drug delivery, tissue engineering, and synthetic biology. By integrating fundamental insights with practical applications, this review underscores the potential of peptide-mediated LLPS as a transformative tool for advancing science and healthcare.

A Combined Approach to Extract Rotational Dynamics of Globular Proteins Undergoing Liquid-Liquid Phase Separation

The formation of protein condensates (droplets) via liquid-liquid phase separation (LLPS) is a commonly observed phenomenon in vitro. Changing the environmental properties with cosolutes, molecular crowders, protein partners, temperature, pressure, etc. has been shown to favor or disfavor the formation of protein droplets by fine-tuning the water-water, water-protein, and protein-protein interactions. Therefore, these environmental properties and their spatiotemporal fine-tuning are likely to be important also in a cellular context at the existing protein expression levels. One of the key physicochemical properties of biomolecules impacted by molecular crowding is diffusion, which determines the viscoelastic behavior of the condensates. Here, we investigate the change in the rotational diffusion of γD-crystallin, undergoing LLPS in vitro in aqueous solutions in the absence and presence of cosolutes. We studied its rotational dynamics using molecular dynamics simulations (MD), electron paramagnetic resonance (EPR) spectroscopy, and fluorescence spectroscopy. MD simulations performed under dilute and crowded conditions show that the rotational diffusion of crystallin in water is retarded by 1 to 2 orders of magnitude in the condensed phase. To obtain the rotational dynamics in the dilute phase, we used fluorescence anisotropy and to extract the retardation factor in the condensed phase, we used spin-labeled γD-crystallin proteins as EPR viscosity nanoprobes. Aided by a viscosity nanoruler calibrated with solutions at increasing sucrose concentrations, we validated the rotational diffusion retardation predicted by MD simulations. This study underlines the predictive power of MD simulations and showcases the use of a sensitive EPR nanoprobe to extract the viscosity of biomolecular condensates.

Form Equals Function: Influence of Coacervate Architecture on Drug Delivery Applications

Complex coacervates, formed through electrostatic interactions between oppositely charged polymers, present a versatile platform for drug delivery, providing rapid assembly, selective encapsulation, and responsiveness to environmental stimuli. The architecture and properties of coacervates can be tuned by controlling structural and environmental design factors, which significantly impact the stability and delivery efficiency of the drugs. While environmental design factors such as salt, pH, and temperature play a crucial role in coacervate formation, structural design factors such as polymer concentration, polymer structure, mixing ratio, and chain length serve as the core framework that shapes coacervate architecture. These elements modulate the phase behavior and material properties of coacervates, allowing for a highly tunable system. In this review, we primarily analyze how these structural design factors contribute to the formation of diverse coacervate architecture, ranging from bulk coacervates to polyion complex micelles, vesicles, and cross-linked gels, though environmental design factors are considered. We then examine the effectiveness of these architectures in enhancing the delivery and efficacy of drugs across various administration routes, such as noninvasive (e.g., oral and transdermal) and invasive delivery. This review aims to provide foundational insights into the design of advanced drug delivery systems by examining how the origin and chemical structure of polymers influence coacervate architecture, which in turn defines their material properties. We then explore how the architecture can be tailored to optimize drug delivery for specific administration routes. This approach leverages the intrinsic properties derived from the coacervate architecture to enable targeted, controlled, and efficient drug release, ultimately enhancing therapeutic outcomes in precision medicine.

Optical Control over Liquid–Liquid Phase Separation

Liquid-liquid phase separation (LLPS) is responsible for the emergence of intracellular membrane-less organelles and the development of coacervate protocells. Benefitting from the advantages of simplicity, precision, programmability, and noninvasiveness, light has become an effective tool to regulate the assembly dynamics of LLPS, and mediate various biochemical processes associated with LLPS. In this review, recent advances in optically controlling membrane-less organelles within living organisms are summarized, thereby modulating a series of biological processes including irreversible protein aggregation pathologies, transcription activation, metabolic flux, genomic rearrangements, and enzymatic reactions. Among these, the intracellular systems (i.e., optoDroplet, Corelet, PixELL, CasDrop, and other optogenetic systems) that enable the photo-mediated control over biomolecular condensation are highlighted. The design of photoactive complex coacervate protocells in laboratory settings by utilizing photochromic molecules such as azobenzene and diarylethene is further discussed. This review is expected to provide in-depth insights into phase separation-associated biochemical processes, bio-metabolism, and diseases.

Peptide-Based Biomimetic Condensates via Liquid-Liquid Phase Separation as Biomedical Delivery Vehicles

Biomolecular condensates are dynamic liquid droplets through intracellular liquid-liquid phase separation that function as membraneless organelles, which are highly involved in various complex cellular processes and functions. Artificial analogs formed via similar pathways that can be integrated with biological complexity and advanced functions have received tremendous research interest in the field of synthetic biology. The coacervate droplet-based compartments can partition and concentrate a wide range of solutes, which are regarded as attractive candidates for mimicking phase-separation behaviors and biophysical features of biomolecular condensates. The use of peptide-based materials as phase-separating components has advantages such as the diversity of amino acid residues and customized sequence design, which allows for programming their phase-separation behaviors and the physicochemical properties of the resulting compartments. In this Perspective, we highlight the recent advancements in the design and construction of biomimicry condensates from synthetic peptides relevant to intracellular phase-separating protein, with specific reference to their molecular design, self-assembly via phase separation, and biorelated applications, to envisage the use of peptide-based droplets as emerging biomedical delivery vehicles.

Core-shell model of the clusters of CPEB4 isoforms preceding liquid-liquid phase separation

Protein solutions can undergo liquid-liquid phase separation (LLPS), where a dispersed phase with a low protein concentration coexists with coacervates with a high protein concentration. We focus on the low complexity N-terminal domain of cytoplasmic polyadenylation element binding-4 protein, CPEB4NTD, and its isoform depleted of the Exon4, CPEB4Δ4NTD. They both exhibit LLPS, but in contrast to most systems undergoing LLPS, the single-phase regime preceding LLPS consists mainly of soluble protein clusters. We combine experimental and theoretical approaches to resolve the internal structure of the clusters and the basis for their formation. Dynamic light scattering and atomic force microscopy show that both isoforms exhibit clusters with diameters ranging from 35 to 80 nm. Electron paramagnetic resonance spectroscopy of spin-labeled CPEB4NTD and CPEB4Δ4NTD revealed that these proteins have two distinct dynamical properties in both the clusters and coacervates. Based on the experimental results, we propose a core-shell structure for the clusters, which is supported by the agreement of the dynamic light scattering data on cluster size distribution with a statistical model developed to describe the structure of clusters. This model treats clusters as swollen micelles (microemulsions) where the core and the shell regions comprise different protein conformations, in agreement with the electron paramagnetic resonance detection of two protein populations. The effects of ionic strength and the addition of 1,6-hexanediol were used to probe the interactions responsible for cluster formation. While both CPEB4NTD and CPEB4Δ4NTD showed phase separation with increasing temperature and formed clusters, differences were found in the properties of the clusters and the coacervates. The data also suggested that the coacervates may consist of aggregates of clusters.

Sequence, Structure, and Functional Space of Drosophila De Novo Proteins

During de novo emergence, new protein coding genes emerge from previously nongenic sequences. The de novo proteins they encode are dissimilar in composition and predicted biochemical properties to conserved proteins. However, functional de novo proteins indeed exist. Both identification of functional de novo proteins and their structural characterization are experimentally laborious. To identify functional and structured de novo proteins in silico, we applied recently developed machine learning based tools and found that most de novo proteins are indeed different from conserved proteins both in their structure and sequence. However, some de novo proteins are predicted to adopt known protein folds, participate in cellular reactions, and to form biomolecular condensates. Apart from broadening our understanding of de novo protein evolution, our study also provides a large set of testable hypotheses for focused experimental studies on structure and function of de novo proteins in Drosophila.

Primitive purine biosynthesis connects ancient geochemistry to modern metabolism

An unresolved question in the origin and evolution of life is whether a continuous path from geochemical precursors to the majority of molecules in the biosphere can be reconstructed from modern-day biochemistry. Here we identified a feasible path by simulating the evolution of biosphere-scale metabolism, using only known biochemical reactions and models of primitive coenzymes. We find that purine synthesis constitutes a bottleneck for metabolic expansion, which can be alleviated by non-autocatalytic phosphoryl coupling agents. Early phases of the expansion are enriched with enzymes that are metal dependent and structurally symmetric, supporting models of early biochemical evolution. This expansion trajectory suggests distinct hypotheses regarding the tempo, mode and timing of metabolic pathway evolution, including a late appearance of methane metabolisms and oxygenic photosynthesis consistent with the geochemical record. The concordance between biological and geological analyses suggests that this trajectory provides a plausible evolutionary history for the vast majority of core biochemistry.

Back in time to the Gly-rich prototype of the phosphate binding elementary function

Binding of nucleotides and their derivatives is one of the most ancient elementary functions dating back to the Origin of Life. We review here the works considering one of the key elements in binding of (di)nucleotide-containing ligands - phosphate binding. We start from a brief discussion of major participants, conditions, and events in prebiotic evolution that resulted in the Origin of Life. Tracing back to the basic functions, including metal and phosphate binding, and, potentially, formation of primitive protein-protein interactions, we focus here on the phosphate binding. Critically assessing works on the structural, functional, and evolutionary aspects of phosphate binding, we perform a simple computational experiment reconstructing its most ancient and generic sequence prototype. The profiles of the phosphate binding signatures have been derived in form of position-specific scoring matrices (PSSMs), their peculiarities depending on the type of the ligands have been analyzed, and evolutionary connections between them have been delineated. Then, the apparent prototype that gave rise to all relevant phosphate-binding signatures had also been reconstructed. We show that two major signatures of the phosphate binding that discriminate between the binding of dinucleotide- and nucleotide-containing ligands are GxGxxG and GxxGxG, respectively. It appears that the signature archetypal for dinucleotide-containing ligands is more generic, and it can frequently bind phosphate groups in nucleotide-containing ligands as well. The reconstructed prototype's key signature GxGGxG underlies the role of glycine residues in providing flexibility and interactions necessary for binding the phosphate groups. The prototype also contains other ancient amino acids, valine, and alanine, showing versatility towards evolutionary design and functional diversification.

C-terminal domain dimerization in yeast Hsp90 is moderately modulated by the other domains

Heat shock protein 90 (Hsp90) serves as a crucial regulator of cellular proteostasis by stabilizing and regulating the activity of numerous substrates, many of which are oncogenic proteins. Therefore, Hsp90 is a drug target for cancer therapy. Hsp90 comprises three structural domains, a highly conserved amino-terminal domain (NTD), a middle domain (MD), and a carboxyl-terminal domain (CTD). The CTD is responsible for protein dimerization, is crucial for Hsp90's activity, and has therefore been targeted for inhibiting Hsp90. Here we addressed the question of whether the CTD dimerization in Hsp90, in the absence of bound nucleotides, is modulated by allosteric effects from the other domains. We studied full length (FL) and isolated CTD (isoC) yeast Hsp90 spin-labeled with a Gd(III) tag by double electron-electron resonance measurements to track structural differences and to determine the apparent dissociation constant (Kd). We found the distance distributions for both the FL and isoC to be similar, indicating that the removal of the NTD and MD does not significantly affect the structure of the CTD dimer. The low-temperature double electron-electron resonance-derived Kd values, as well as those obtained at room temperature using microscale thermophoresis and native mass spectrometry, collectively suggested the presence of some allosteric effects from the NTDs and MDs on the CTD dimerization stability in the apo state. This was evidenced by a moderate increase in the Kd for the isoC compared with the FL mutants. Our results reveal a fine regulation of the CTD dimerization by allosteric modulation, which may have implications for drug targeting strategies in cancer therapy.

Enhanced sensitivity for pulse dipolar EPR spectroscopy using variable-time RIDME

Pulse dipolar EPR spectroscopy (PDS) measurements are an important complementary tool in structural biology and are increasingly applied to macromolecular assemblies implicated in human health and disease at physiological concentrations. This requires ever higher sensitivity, and recent advances have driven PDS measurements into the mid-nanomolar concentration regime, though optimization and acquisition of such measurements remains experimentally demanding and time expensive. One important consideration is that constant-time acquisition represents a hard limit for measurement sensitivity, depending on the maximum measured distance. Determining this distance a priori has been facilitated by machine-learning structure prediction (AlphaFold2 and RoseTTAFold) but is often confounded by non-representative behaviour in frozen solution that may mandate multiple rounds of optimization and acquisition. Herein, we endeavour to simultaneously enhance sensitivity and streamline PDS measurement optimization to one-step by benchmarking a variable-time acquisition RIDME experiment applied to CuII-nitroxide and CuII-CuII model systems. Results demonstrate marked sensitivity improvements of both 5- and 6-pulse variable-time RIDME of between 2- and 5-fold over the constant-time analogues.

Protein salvage and repurposing in evolution: Phospholipase D toxins are stabilized by a remodeled scrap of a membrane association domain

The glycerophosphodiester phosphodiesterase (GDPD)-like SMaseD/PLD domain family, which includes phospholipase D (PLD) toxins in recluse spiders and actinobacteria, evolved anciently in bacteria from the GDPD. The PLD enzymes retained the core (β/α)8 barrel fold of GDPD, while gaining a signature C-terminal expansion motif and losing a small insertion domain. Using sequence alignments and phylogenetic analysis, we infer that the C-terminal motif derives from a segment of an ancient bacterial PLAT domain. Formally, part of a protein containing a PLAT domain repeat underwent fusion to the C terminus of a GDPD barrel, leading to attachment of a segment of a PLAT domain, followed by a second complete PLAT domain. The complete domain was retained only in some basal homologs, but the PLAT segment was conserved and repurposed as the expansion motif. The PLAT segment corresponds to strands β7-β8 of a β-sandwich, while the expansion motif as represented in spider PLD toxins has been remodeled as an α-helix, a β-strand, and an ordered loop. The GDPD-PLAT fusion led to two acquisitions in founding the GDPD-like SMaseD/PLD family: (1) a PLAT domain that presumably supported early lipase activity by mediating membrane association, and (2) an expansion motif that putatively stabilized the catalytic domain, possibly compensating for, or permitting, loss of the insertion domain. Of wider significance, messy domain shuffling events can leave behind scraps of domains that can be salvaged, remodeled, and repurposed.

Biomolecule-Based Coacervates with Modulated Physiological Functions

Liquid-liquid phase separation (LLPS) exists widely in living systems, and understanding the working mechanisms of the formed condensed droplets is of great significance for the prevention and treatment of diseases as well as for the development of biomimetic materials. Herein, in this Perspective we try to focus on the in vitro reconstructions of biomolecule-based coacervates and outline the associations between the functional components and droplets as well as the physiological and pathological functions associated with coacervates. Coacervates are formed by functional components through weak, multivalent interactions. The interaction strengths that determine coacervate properties such as electability and phase state, which in turn influence the functional components to limit their fluidity, stability, or diffusion coefficients, are specially discussed. At the end of this Perspective, the current challenges are summarized; progress will require our great efforts to reveal the mechanisms of action at the molecular level and then develop biomolecule-based coacervate models with complexity, integration of methods, and intellectualization.

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).

Tuning Material States and Functionalities of G-Quadruplex-Modulated RNA-Peptide Condensates

RNA encodes sequence- and structure-dependent interactions to modulate the assembly and properties of biomolecular condensates. RNA G-quadruplexes (rG4s) formed by guanine-rich sequences can trigger the formation of liquid- or solid-like condensates that are involved in many aberrant phase transitions. However, exactly how rG4 motifs modulate different phase transitions and impart distinct material properties to condensates is unclear. Here, using RNA oligonucleotides and cationic peptides as model systems, we show that RNA-peptide condensates exhibit tunability in material properties over a wide spectrum via interactions arising from rG4 folding/unfolding kinetics. rG4-containing oligonucleotides formed strong pairwise attraction with peptides and tended to form solid-like condensates, while their less-structured non-G4 mutants formed liquid-like droplets. We find that the coupling between rG4 dissociation and RNA-peptide complex coacervation triggers solid-to-liquid transition of condensates prior to the complete unfolding of rG4s. This coupling points to a mechanism that material states of rG4-modulated condensates can be finely tuned from solid-like to liquid-like by the addition of less-structured RNA oligonucleotides, which have weak but dominant binding with peptides. We further show that the tunable material states of condensates can enhance RNA aptamer compartmentalization and RNA cleavage reactions. Our results suggest that condensates with complex properties can emerge from subtle changes in RNA oligonucleotides, contributing ways to treat dysfunctional condensates in diseases and insights into prebiotic compartmentalization.

Peptide-based coacervates in therapeutic applications

Coacervates are droplets formed by liquid‒liquid phase separation. An increasing number of studies have reported that coacervates play an important role in living cells, such as in the generation of membraneless organelles, and peptides contribute to condensate droplet formation. Peptides with versatile functional groups and special secondary structures, including α-helices, β-sheets and intrinsically disordered regions, provide novel insights into coacervation, such as biomimetic protocells, neurodegenerative diseases, modulations of signal transmission, and drug delivery systems. In this review, we introduce different types of peptide-based coacervates and the principles of their interactions. Additionally, we summarize the thermodynamic and kinetic mechanisms of peptide-based coacervates and the associated factors, including salt, pH, and temperature, affecting the phase separation process. We illustrate recent studies on modulating the functions of peptide-based coacervates applied in biological diseases. Finally, we propose their promising broad applications and describe the challenges of peptide-based coacervates in the future.

Rheology and Gelation of Hyaluronic Acid/Chitosan Coacervates

Hyaluronic acid (HA) and chitosan (CHI) are biopolyelectrolytes which are interesting for both the medical and polymer physics communities due to their biocompatibility and semi-flexibility, respectively. In this work, we demonstrate by rheology experiments that the linear viscoelasticity of HA/CHI coacervates depends strongly on the molecular weight of the polymers. Moduli for coacervates were found significantly higher than those of individual HA and CHI physical gels. A remarkable 1.5-fold increase in moduli was noted when catechol-conjugated HA and CHI were used instead. This was attributed to the conversion of coacervates to chemical gels by oxidation of 3,4-dihydroxyphenylalanine (DOPA) groups in HA and CHI to di-DOPA crosslinks. These rheological results put HA/CHI coacervates in the category of strong candidates as injectable tissue scaffolds or medical adhesives.

A Short Tale of the Origin of Proteins and Ribosome Evolution

Proteins are the workhorses of the cell and have been key players throughout the evolution of all organisms, from the origin of life to the present era. How might life have originated from the prebiotic chemistry of early Earth? This is one of the most intriguing unsolved questions in biology. Currently, however, it is generally accepted that amino acids, the building blocks of proteins, were abiotically available on primitive Earth, which would have made the formation of early peptides in a similar fashion possible. Peptides are likely to have coevolved with ancestral forms of RNA. The ribosome is the most evident product of this coevolution process, a sophisticated nanomachine that performs the synthesis of proteins codified in genomes. In this general review, we explore the evolution of proteins from their peptide origins to their folding and regulation based on the example of superoxide dismutase (SOD1), a key enzyme in oxygen metabolism on modern Earth.