Protein Condensate Formation via Controlled Multimerization of Intrinsically Disordered Sequences

Tandem-repeat proteins introduce tuneable properties to engineered biomolecular condensates

The cell's ability to rapidly partition biomolecules into biomolecular condensates is linked to a diverse range of cellular functions. Understanding how the structural attributes of biomolecular condensates are linked with their biological roles can be facilitated by the development of synthetic condensate systems that can be manipulated in a controllable and predictable way. Here, we design and characterise a tuneable synthetic biomolecular condensate platform fusing modular consensus-designed tetratricopeptide repeat (CTPR) proteins to intrinsically-disordered domains. Trends between the CTPR structural attributes and condensate propensity were recapitulated across different experimental conditions and by in silico modelling, demonstrating that the CTPR domain can systematically affect the condensates in a predictable manner. Moreover, we show that incorporating short binding motifs into the CTPR domain results in specific target-protein recruitment into the condensates. Our model system can be rationally designed in a versatile manner to both tune condensate propensity and endow the condensates with new functions.

Compartmentation of multiple metabolic enzymes and their preparation in vitro and in cellulo

Compartmentalization of multiple enzymes in cellulo and in vitro is a means of controlling the cascade reaction of metabolic enzymes. The compartmentation of enzymes through liquid-liquid phase separation may facilitate the reversible control of biocatalytic cascade reactions, thereby reducing the transcriptional and translational burden. This has attracted attention as a potential application in bioproduction. Recent research has demonstrated the existence and regulatory mechanisms of various enzyme compartments within cells. Mounting evidence suggests that enzyme compartmentation allows in vitro and in vivo regulation of cellular metabolism. However, the comprehensive regulatory mechanisms of enzyme condensates in cells and ideal organization of cellular systems remain unknown. This review provides an overview of the recent progress in multiple enzyme compartmentation in cells and summarizes strategies to reconstruct multiple enzyme assemblies in vitro and in cellulo. By examining parallel examples, we have evaluated the consensus and future perspectives of enzyme condensation.

Conformation-Driven Phase Separation in the Linker Domain of Focal Adhesion Kinases

Protein tyrosine kinase 2 (Pyk2), also known as focal adhesion kinase 2, and focal adhesion kinase 1 (Fak1) are two related nonreceptor tyrosine kinases (hereafter referred to as FAKs). Here, we focused on characterizing a linker region of the FAK proteins (hereafter referred to as FAK KFL for Kinase FAT Linker), which in the case of Pyk2 has previously been shown to play a functional role in calcium sensing through its interaction with calmodulin. Using structural nuclear magnetic resonance spectroscopy, we provide chemical shift assignments for the FAK KFLs, defining their conformational properties. Analysis of the FAK KFL conformations revealed their predominantly disordered nature, except for well-defined segments with a significant tendency to form α-helices, which were modeled to form homodimeric interfaces. In addition, we showed that the FAK KFL segments form condensates in vitro under high crowding conditions. By directly comparing the conformational properties of the Pyk2 and Fak1 KFL domains and providing structural data, this study provides valuable insights into the structural basis of FAK KFL interactions. Furthermore, the results show that disordered segments in proteins within the focal adhesion complex undergo phase separation, a process of potential biological significance due to protein clustering.

Localising enzymes to biomolecular condensates increase their accumulation and benefits engineered metabolic pathway performance in Nicotiana benthamiana

The establishment of Nicotiana benthamiana as a robust biofactory is complicated by issues such as product toxicity and proteolytic degradation of target proteins/introduced enzymes. Here we investigate whether biomolecular condensates can be used to address these problems. We engineered biomolecular condensates in N. benthamiana leaves using transient expression of synthetic modular scaffolds. The in vivo properties of the condensates that resulted were consistent with them being liquid-like bodies with thermodynamic features typical of multicomponent phase-separating systems. We show that recruitment of enzymes to condensates in vivo led to several-fold yield increases in one- and three-step metabolic pathways (citramalate biosynthesis and poly-3-hydroxybutyrate (PHB) biosynthesis, respectively). This enhanced yield could be for several reasons including improved enzyme kinetics, metabolite channelling or avoidance of cytotoxicity by retention of the pathway product within the condensate, which was demonstrated for PHB. However, we also observed a several-fold increase in the amount of the enzymes that accumulated when they were targeted to the condensates. This suggests that the enzymes were more stable when localised to the condensate than when freely diffusing in the cytosol. We hypothesise that this stability is likely the main driver for increased pathway product production. Our findings provide a foundation for leveraging biomolecular condensates in plant metabolic engineering and advance N. benthamiana as a versatile biofactory for industrial applications.

Structured protein domains enter the spotlight: modulators of biomolecular condensate form and function

Biomolecular condensates are membraneless organelles that concentrate proteins and nucleic acids. One of the primary components of condensates is multidomain proteins, whose domains can be broadly classified as structured and disordered. While structured protein domains are ubiquitous within biomolecular condensates, the physical ramifications of their unique properties have been relatively underexplored. Therefore, this review synthesizes current literature pertaining to structured protein domains within the context of condensates. We examine how the propensity of structured domains for high interaction specificity and low conformational heterogeneity contributes to the formation, material properties, and functions of biomolecular condensates. Finally, we propose unanswered questions on the behavior of structured protein domains within condensates, the answers of which will contribute to a more complete understanding of condensate biophysics.

Interfacing bacterial microcompartment shell proteins with genetically encoded condensates

Condensates formed by liquid-liquid phase separation are promising candidates for the development of synthetic cells and organelles. Here, we show that bacterial microcompartment shell proteins from Haliangium ochraceum (BMC-H) assemble into coatings on the surfaces of protein condensates formed by tandem RGG-RGG domains, an engineered construct derived from the intrinsically disordered region of the RNA helicase LAF-1. WT BMC-H proteins formed higher-order assemblies within RGG-RGG droplets; however, engineered BMC-H variants fused to RGG truncations formed coatings on droplet surfaces. These intrinsically disordered tags controlled the interaction with the condensed phase based on their length and sequence, and one of the designs, BMC-H-T2, assembled preferentially on the surface of the droplet and prevented droplet coalescence. The formation of the coatings is dependent on the pH and protein concentration; once formed, the coatings are stable and do not exchange with the dilute phase. Coated droplets could sequester and concentrate folded proteins, including TEV protease, with selectivity similar to uncoated droplets. Addition of TEV protease to coated droplets resulted in the digestion of RGG-RGG to RGG and a decrease in droplet diameter, but not in the dissolution of the coatings. BMC shell protein-coated protein condensates are entirely encodable and provide a way to control the properties of liquid-liquid phase-separated compartments in the context of synthetic biology.

Modulation of Protein-Protein Interactions with Molecular Glues in a Synthetic Condensate Platform

Misregulation of protein-protein interactions (PPIs) underlies many diseases; hence, molecules that stabilize PPIs, known as molecular glues, are promising drug candidates. Identification of novel molecular glues is highly challenging among others because classical biochemical assays in dilute aqueous conditions have limitations for evaluating weak PPIs and their stabilization by molecular glues. This hampers the systematic discovery and evaluation of molecular glues. Here, we present a synthetic condensate platform for the study of PPIs and molecular glues in a crowded macromolecular environment that more closely resembles the dense cellular milieu. With this platform, weak PPIs can be enhanced by sequestration. The condensates, based on amylose derivatives, recruit the hub protein 14-3-3 via affinity-based uptake, which results in high local protein concentrations ideal for the efficient screening of molecular glues. Clients of 14-3-3 are sequestered in the condensates based on their enhanced affinity upon treatment with molecular glues. Fine control over the condensate environment is illustrated by modulating the reactivity of dynamic covalent molecular glues by the adjustment of pH and the redox environment. General applicability of the system for screening of molecular glues is highlighted by using the nuclear receptor PPARγ, which recruits coregulators via an allosteric PPI stabilization mechanism. The condensate environment thus provides a unique dense molecular environment to enhance weak PPIs and enable subsequent evaluation of small-molecule stabilization in a molecular setting chemically en route to the cellular interior.

Programmability and biomedical utility of intrinsically-disordered protein polymers

Intrinsically disordered proteins (IDPs) exhibit molecular-level conformational dynamics that are functionally harnessed across a wide range of fascinating biological phenomena. The low sequence complexity of IDPs has led to the design and development of intrinsically-disordered protein polymers (IDPPs), a class of engineered repeat IDPs with stimuli-responsive properties. The perfect repetitive architecture of IDPPs allows for repeat-level encoding of tunable protein functionality. Designer IDPPs can be modeled on endogenous IDPs or engineered de novo as protein polymers with dual biophysical and biological functionality. Their properties can be rationally tailored to access enigmatic IDP biology and to create programmable smart biomaterials. With the goal of inspiring the bioengineering of multifunctional IDP-based materials, here we synthesize recent multidisciplinary progress in programming and exploiting the bio-functionality of IDPPs and IDPP-containing proteins. Collectively, expanding beyond the traditional sequence space of extracellular IDPs, emergent sequence-level control of IDPP functionality is fueling the bioengineering of self-assembling biomaterials, advanced drug delivery systems, tissue scaffolds, and biomolecular condensates -genetically encoded organelle-like structures. Looking forward, we emphasize open challenges and emerging opportunities, arguing that the intracellular behaviors of IDPPs represent a rich space for biomedical discovery and innovation. Combined with the intense focus on IDP biology, the growing landscape of IDPPs and their biomedical applications set the stage for the accelerated engineering of high-value biotechnologies and biomaterials.

Asymmetric oligomerization state and sequence patterning can tune multiphase condensate miscibility

Endogenous biomolecular condensates, composed of a multitude of proteins and RNAs, can organize into multiphasic structures with compositionally distinct phases. This multiphasic organization is generally understood to be critical for facilitating their proper biological function. However, the biophysical principles driving multiphase formation are not completely understood. Here we use in vivo condensate reconstitution experiments and coarse-grained molecular simulations to investigate how oligomerization and sequence interactions modulate multiphase organization in biomolecular condensates. We demonstrate that increasing the oligomerization state of an intrinsically disordered protein results in enhanced immiscibility and multiphase formation. Interestingly, we find that oligomerization tunes the miscibility of intrinsically disordered proteins in an asymmetric manner, with the effect being more pronounced when the intrinsically disordered protein, exhibiting stronger homotypic interactions, is oligomerized. Our findings suggest that oligomerization is a flexible biophysical mechanism that cells can exploit to tune the internal organization of biomolecular condensates and their associated biological functions.

Competitive protein recruitment in artificial cells

Living cells can modulate their response to environmental cues by changing their sensitivities for molecular signals. Artificial cells are promising model platforms to study intercellular communication, but populations with such differentiated behavior remain underexplored. Here, we show the affinity-regulated exchange of proteins in distinct populations of coacervate-based artificial cells via protein-protein interactions (PPI) of the hub protein 14-3-3. By loading different coacervates with different isoforms of 14-3-3, featuring varying PPI affinities, a client peptide is directed to the more strongly recruiting coacervates. By switching affinity of client proteins through phosphorylation, weaker binding partners can be outcompeted for their 14-3-3 binding, inducing their release from artificial cells. Combined, a communication system between coacervates is constructed, which leads to the transport of client proteins from strongly recruiting coacervates to weakly recruiting ones. The results demonstrate that affinity engineering and competitive binding can provide directed protein uptake and exchange between artificial cells.

Assembling membraneless organelles from de novo designed proteins

Recent advances in de novo protein design have delivered a diversity of discrete de novo protein structures and complexes. A new challenge for the field is to use these designs directly in cells to intervene in biological processes and augment natural systems. The bottom-up design of self-assembled objects such as microcompartments and membraneless organelles is one such challenge. Here we describe the design of genetically encoded polypeptides that form membraneless organelles in Escherichia coli. To do this, we combine de novo α-helical sequences, intrinsically disordered linkers and client proteins in single-polypeptide constructs. We tailor the properties of the helical regions to shift protein assembly from arrested assemblies to dynamic condensates. The designs are characterized in cells and in vitro using biophysical methods and soft-matter physics. Finally, we use the designed polypeptide to co-compartmentalize a functional enzyme pair in E. coli, improving product formation close to the theoretical limit.

Rediscovering the intricacies of secretory granule biogenesis

Regulated secretion, an essential cellular process, relies on secretory granules (SGs) for the controlled release of a diverse range of cargo molecules, including proteins, peptides, hormones, enzymes, and neurotransmitters. SG biogenesis encompasses cargo selection, sorting, packaging, and trafficking, with the trans-Golgi Network (TGN) playing a central role. Research in the last three decades has revealed significant components required for SG biogenesis; however, no cargo receptor transferring granule cargo from the TGN to immature SGs (ISGs) has yet been identified. Consequently, recent research has devoted significant attention to studying receptor-independent cargo sorting mechanisms, shedding new light on the complexities of regulated secretion. Understanding the underlying molecular and biophysical mechanisms behind cargo sorting into ISGs holds great promise for advancing our knowledge of cellular communication and disease mechanisms.

A Minispidroin Guides the Molecular Design for Cellular Condensation Mechanisms in S. cerevisiae

Structural engineering of molecules for condensation is an emerging technique within synthetic biology. Liquid-liquid phase separation of biomolecules leading to condensation is a central step in the assembly of biological materials into their functional forms. Intracellular condensates can also function within cells in a regulatory manner to facilitate reaction pathways and to compartmentalize interactions. We need to develop a strong understanding of how to design molecules for condensates and how their in vivo-in vitro properties are related. The spider silk protein NT2RepCT undergoes condensation during its fiber-forming process. Using parallel in vivo and in vitro characterization, in this study, we mapped the effects of intracellular conditions for NT2RepCT and its several structural variants. We found that intracellular conditions may suppress to some extent condensation whereas molecular crowding affects both condensate properties and their formation. Intracellular characterization of protein condensation allowed experiments on pH effects and solubilization to be performed within yeast cells. The growth of intracellular NT2RepCT condensates was restricted, and Ostwald ripening was not observed in yeast cells, in contrast to earlier observations in E. coli. Our results lead the way to using intracellular condensation to screen for properties of molecular assembly. For characterizing different structural variants, intracellular functional characterization can eliminate the need for time-consuming batch purification and in vitro condensation. Therefore, we suggest that the in vivo-in vitro understanding will become useful in, e.g., high-throughput screening for molecular functions and in strategies for designing tunable intracellular condensates.

Strategies for Conditional Regulation of Proteins

Design of the next-generation of therapeutics, biosensors, and molecular tools for basic research requires that we bring protein activity under control. Each protein has unique properties, and therefore, it is critical to tailor the current techniques to develop new regulatory methods and regulate new proteins of interest (POIs). This perspective gives an overview of the widely used stimuli and synthetic and natural methods for conditional regulation of proteins.