Search bioRxiv⌕ Search

Biology subjects

Pappu, R. V.

Publications and source records attributed to Pappu, R. V..

At least 19 recordsLinked to original sources

Building synthetic cell-cell synapses using engineered scaffold protein condensates

Synaptic assemblies that form at cell-cell junctions are often organized by multivalent scaffold proteins with condensate forming properties. An emerging hypothesis is that these scaffolds provide a thresholding mechanism whereby small increases in the density of cell-cell recognition receptors can trigger all-or-none assembly selectively at the correct partner cell interface. We test this hypothesis by engineering synthetic scaffolded synapses. Coarse-grained simulations suggest that properly-tuned scaffold interactions can yield a sharp condensation threshold. Guided by these simulations, we designed modular scaffold proteins consisting of PDZ domains and intrinsically disordered regions (IDRs) of different molecular grammars. Within a specific region of parameter space, controlled by valency, receptor binding affinity and IDR-driven condensation, the synthetic scaffold proteins exhibit switch-like condensation behaviors, where co-condensates of receptor and scaffold selectively form only at interfaces with the proper partner cell. Notably, orthogonal receptor-scaffold pairs enable a single receiver cell to form multiple distinct interfaces, each associated with a different partner cell. We demonstrate that these synthetic synapse assemblies can recruit different client proteins to enhance intercellular signaling, orient cell division, or sculpt complex synaptic morphologies. Our results illustrate how the ultrasensitive condensation properties of modular scaffold proteins can be harnessed to create novel and highly specific cell-cell interfaces.

synthetic biology↗

Reverse engineering Lewy bodies suggests alpha-synuclein pathology as condensatopathy

Understanding how soluble monomeric alpha-synuclein transitions into pathological alpha-synuclein (Lewy bodies) has remained a central challenge in neurodegeneration. Existing models, largely based on treating cells and animals with pre-formed alpha-synuclein fibrils cannot account for the emergence of the first inclusion without pre-existing seeds. Here, we combine in vitro reconstitutions, computational modeling and a minimal cellular system to show that phase separation of alpha-synuclein with an interacting scaffold can recapitulate Lewy body-like structures. An unbiased proteomics screen, live-cell imaging, correlative light-electron microscopy, and soft X-ray tomography show that Lewy body-like structures are associated with redistribution of actin and membrane-bound organelles, with mitochondria accumulating at their periphery in an actin-dependent manner. Structural analyses further indicate that alpha-synuclein condensates provide local environments in which the insoluble beta-sheets can form. Together, these findings support a seed-independent trajectory from soluble alpha-synuclein through condensation and progressive immobilization to Lewy body-like assemblies and, subsequently, insoluble beta-sheet fibrils. This framework offers a new mechanistic route for understanding the disease progression and promises to guide the design of innovative therapeutic interventions.

neuroscience↗

Competing Molecular Interactions Govern the Dynamical Arrest of G3BP1 Condensates

G3BP1 is a central scaffold of stress granules (SGs). Upon cellular stress, G3BP1 forms complex coacervates with translationally repressed mRNAs and recruits multiple RNA-binding proteins to form reversible biomolecular condensates. Persistent SGs are linked to age-dependent dynamical arrest and impaired disassembly. Here, we employ active and passive nanoscale rheology with optical tweezers to show that G3BP1 condensates evolve from being dominantly viscous fluids to dynamically arrested network glasses characterized by nanoscale caging and elastic memory. Integrating atomistic and coarse-grained simulations with experiments, we find that electrostatic interactions between the oppositely charged intrinsically disordered regions drive condensate ageing. RNA modulates these interactions in a length-and structure-dependent manner, delaying dynamic arrest, whereas Caprin-1 binding to the NTF2L domain has little effect. Together, these findings reveal how competing inter-IDR and IDR-RNA interactions govern condensate ageing and material-state transitions. The findings have broader implications for the regulation of SG dynamics in cells.

biophysics↗

Mast cell extracellular granules are bioactive condensates driven by heparin and polyamine

Biomolecular condensates are membraneless bodies that organize biochemical reactions typically within cells. However, the roles of condensates in extracellular space--where conditions differ substantially from intracellular space--remain poorly understood. Here, we report mast cell extracellular granules (MCEGs), a stable membraneless entity, are condensates assembled via electrostatic interactions between glycosaminoglycans and polyamines. Disrupting polyamine synthesis or trafficking blocks MCEG formation and compromises the storage of proteases and cytokines. Granules reconstituted with heparin and spermine are sufficient to enrich mediators such as CPA3 and TNF, maintaining an elevated pH and higher concentrations of calcium and zinc compared to the extracellular milieu. This unique environment enhances CPA3 enzymatic activity. Furthermore, the granules increase TNF binding and its bioactivity toward endothelial cells. Together, we reveal MCEGs as functionally active biomolecular condensates with distinct biochemical and immunological properties; MCEGs are formed through sugar-metabolite interactions, expanding the mechanisms of condensate assembly beyond classical protein-protein and protein-RNA interactions.

cell biology↗

Distinguishing near- versus off-critical phase behaviors of intrinsically disordered proteins

Intrinsically disordered prion-like low complexity domains (PLCDs) drive phase transitions that underlie the biogenesis of different biomolecular condensates. The mapping of critical points is essential for generating quantitative assessments of driving forces and for distinguishing phase behaviors in the critical versus off-critical regimes. Computations play an important role in connecting the molecular-scale interactions to mesoscale phase behaviors of PLCDs and other intrinsically disordered proteins. We report results from accurate mapping of the critical regime for an archetypal PLCD. This is achieved by combining large-scale simulations with computations of Binder cumulants and the use of rigorous finite-size scaling approaches. The computed binodal, defined by knowledge of the critical point and intersection of the left arm of the binodal by the overlap and percolation lines, can be demarcated into three distinct regimes. Regime I is farthest from the critical point, with the coexisting dilute phase being akin to a gas of dispersed polymers. Regime II lies above the intersection of the overlap line and the dilute arm of the binodal. Here, coexisting dilute phases are characterized by heterogeneous cluster-size distributions with heavy tails. In Regimes I and II, dense phases are confined percolated networks. Regime III is closest to the critical point. Here, the dense phase becomes unconfined and the percolated network swells to become system-spanning. Thus, Regime III comprises two interconnected, system-spanning networks. In addition to accurately mapping the critical point, we also evaluated methods for identifying the theta temperature. We find that conventional scaling approaches lead to erroneously low estimates of the theta temperature. Instead, accurate estimation of the theta temperature requires direct calculation of the temperature dependence of the two-body interaction coefficient. We discuss the broader implications of these findings for inferring solvent quality from scaling analyses.

biophysics↗

Nuclear-import receptors remodel the dilute phase to suppress phase transitions of RNA-binding proteins with prion-like domains.

AbstractRNA-binding proteins (RBPs) with prion-like domains, including FUS, hnRNPA1, and hnRNPA2, assemble into functional, metastable condensates that organize ribostasis, but can also transition into self-templating fibrils implicated in neurodegenerative proteinopathies such as amyotrophic lateral sclerosis (ALS). How nuclear-import receptors (NIRs) antagonize this pathological transition has remained unresolved. Here, we establish that NIRs regulate the phase behavior of prion-like cargos by remodeling the dilute phase. Quantitative analyses across length scales reveal that Karyopherin-{beta}2 (Kap{beta}2) preferentially binds cargo in the dilute phase to lower the effective concentration of free RBPs thereby elevating the saturation concentration for phase separation and suppressing mesoscale clustering. ALS-linked FUSP525L, which binds Kap{beta}2 weakly, evades this regulation to form pathogenic assemblies. Thus, NIRs harness polyphasic linkage, the thermodynamic relationship between ligand binding and phase equilibria, to reshape the landscape of prion-like RBP assembly states, establishing a paradigm for how ATP-independent chaperones regulate phase behavior to prevent disease-linked aggregation. GRAPHICAL ABSTRACT O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=123 SRC="FIGDIR/small/688546v1_ufig1.gif" ALT="Figure 1"> View larger version (31K): org.highwire.dtl.DTLVardef@1dd32cforg.highwire.dtl.DTLVardef@132ba1eorg.highwire.dtl.DTLVardef@1593c80org.highwire.dtl.DTLVardef@19311d6_HPS_FORMAT_FIGEXP M_FIG C_FIG

biochemistry↗

ASAP-ID: Proximity labelling with small tags

Biotinylation-based proximity labelling methods are valuable for discovering protein-protein interactions within cellular systems. However, one limitation of these approaches is that most require fusing the target protein with the enzyme that biotinylates nearby proteins (i.e., TurboID or APEX2), which risks sterically disrupting the proteins native function. Here, we present a method designed to reduce the steric impact of these fusions and offer greater flexibility in labelling modalities. The method, Antibody and Small-tag Assembly on Proteins for Interaction Detection (ASAP-ID), involves a bipartite system. Target proteins are fused to a small peptide antigen that recruits TurboID or APEX2 fused to an antibody directed to the antigen. Using two different antigen/antibody systems (SunTag and MoonTag), we show that ASAP-ID can specifically label human Lamin A in cells. The method works when the target protein and nanobody are co-expressed together in cis (ASAP-IDIC). We also demonstrate that the approach works when the antibody fusion is added in trans to fixed cells post-expression (ASAP-IDIT). ASAP-IDIT identified more than 448 known and previously undescribed interactors of lamin. We further used ASAP-IDIT to study how ALS-mutant profilin 1 affected its interactome. The method identified proteins involved in protein quality control that correlated with aggregation propensity. Moreover, the different mutants showed variation in the cellular location where aggregates formed. ASAP-IDIT revealed preferences for mitochondrial proteins for the two profilin mutants that tend to aggregate in the cytoplasm, C71G and M114T, and nuclear proteins for a mutant more prone to nuclear aggregation. These findings position ASAP-ID as a powerful addition to the proximity labelling toolkit, capable of probing subtle differences in interactomes in a less invasive manner.

biochemistry↗

Computational rheometry of viscoelastic networks: From random graphs to biomolecular condensates

Multivalent biomacromolecules including multi-domain and intrinsically disordered proteins form biomolecular condensates via reversible phase transitions. Condensates are viscoelastic materials that display composition-specific rheological properties and responses to mechanical forces. Graph-based descriptions of microstructures can be combined with computational rheometry to model the outcomes of passive and active mechanical measurements. We consider two types of network models for microstructures. In the Jeffreys model, each edge in the network is a Jeffreys element. In the Stokes-Maxwell model, each edge is a Maxwell element that is embedded in an incompressible viscous fluid that can undergo Stokes flow. We describe results from comparative assessments of the two models for individual elements, ordered lattices, random geometric graphs, structured graphs, and graphs for condensates that are extracted from coarse-grained simulations of disordered proteins. Results from deformation and relaxation tests and flow field analysis reveal how distinct length and time scales contribute to the responses of different types of networks. No single test provides definitive assessments of the connections between material properties and microstructures. Instead, a range of active and passive rheometric tests are essential for distinguishing the responses of different types of networks. Our work establishes computational rheometry as a framework for bridging disparate length and timescales to assess how molecular-scale interactions and dynamics give rise to viscoelastic responses on the mesoscale.

biophysics↗

Molecular grammars of intrinsically disordered regions that span the human proteome

Intrinsically disordered regions (IDRs) of proteins are defined by functionally relevant molecular grammars. This refers to IDR-specific non-random amino acid compositions and non-random patterning of distinct pairs of amino acid types. Here, we introduce GIN (Grammars Inferred using NARDINI+) as a resource, which we have used to extract the molecular grammars of all human IDRs and classified them into thirty distinct clusters. Unbiased analyses of IDRome-spanning grammars reveals that specialized IDR grammar features direct biological processes, cellular localization preferences, and molecular functions. IDRs with exceptional grammars, defined as sequences with high-scoring non-random features, are harbored in proteins and complexes that enable spatial and temporal sorting of biochemical activities. Protein complexes within the nucleus recruit specific factors through top-scoring IDRs. These IDRs are frequently disrupted via cancer-associated mutations and fusion oncoproteins. Overall, GIN enables the decoding of sequence-function relationships of IDRs and can be deployed in IDR-specific and IDRome-wide analyses.

bioinformatics↗

Nuclear speckle proteins form intrinsic and MALAT1-dependent microphases

Nuclear speckles are enriched in serine / arginine rich splicing factors (SRSFs), such as SRSF1. Splicing factors and proteins such as TDP-43 concentrate into distinct speckle territories to enable pre-mRNA processing. We have discovered that SRSFs and TDP-43 are block copolymers and the protein-specific interplay of inter-block repulsions and attractions drives spontaneous microphase separation. This gives rise to size-limited, ordered assemblies, that are 30 - 45 nm in diameter. Depending on the protein, each microphase comprises several tens to hundreds of molecules. The sub-micron scale territories observed in cells are shown to be clusters of microphases. The regulatory lncRNA MALAT1 binds preferentially to SRSF1 microphases to enhance microphase separation and alter microphase structures. Microphase separation enables the concentration of finite numbers of splicing factors into assemblies with distinct nanoscale structures that can be modulated by MALAT1. Our findings provide a structural framework for the functional organization of splicing factors.

biophysics↗

Chromatin-associated lncRNA-splicing factor condensates regulate hypoxia responsive RNA processing of genes pre-positioned near nuclear speckles

Hypoxia-induced alternative splicing (AS) regulates tumor progression and metastasis. Little is known about how such AS is controlled and whether higher-order genome and nuclear domain (ND) organizations dictate these processes. We observe that hypoxia-responsive alternatively spliced genes position near nuclear speckle (NS), the ND that enhances splicing efficiency. NS-resident MALAT1 long noncoding RNA, induced in response to hypoxia, regulates hypoxia-responsive AS. MALAT1 achieves this by organizing the SR-family of splicing factor, SRSF1, near NS and regulating the binding of SRSF1 to pre-mRNAs. Mechanistically, MALAT1 enhances the recruitment of SRSF1 to elongating RNA polymerase II (pol II) by promoting the formation of phase-separated condensates of SRSF1, which are preferentially recognized by pol II. During hypoxia, MALAT1 regulates spatially organized AS by establishing a threshold SRSF1 concentration near NSs, potentially by forming condensates, critical for pol II-mediated recruitment of SRSF1 to pre-mRNAs.

molecular biology↗

Differential interactions determine anisotropies at interfaces of RNA-based biomolecular condensates

Biomolecular condensates form via macromolecular phase separation, giving rise to coexisting phases delineated by interfaces. Here, we characterize the structures of interfaces formed by phase separation driven by heterotypic interactions in ternary mixtures of two types of RNA molecules and polyethylene glycol. We find that purine-rich RNAs are scaffolds that drive phase separation via strong heterotypic interactions. Conversely, pyrimidine-rich RNA molecules are defined by weaker heterotypic interactions. They function as adsorbents that accumulate at and wet the interfaces of coexisting phases formed by phase separation of scaffolds. Our computations predict that scaffolds and adsorbents have different non-random orientational preferences at interfaces. We tested these predictions using single-molecule super resolution imaging that tracks the motions of fluorogenic probes that are bound to RNA molecules. Motions parallel to the interface were found to be faster than motions perpendicular to the interface. These findings support previous predictions regarding anisotropies of motions at interfaces.

biophysics↗

Driving forces for condensation of synapsin are governed by sequence-encoded molecular grammars

Multiple biomolecular condensates coexist at the pre- and post-synapse to enable vesicle dynamics and controlled neurotransmitter release in the brain. In pre-synapses, intrinsically disordered regions (IDRs) of synaptic proteins are drivers of condensation that enable clustering of synaptic vesicles (SVs). Using computational analysis, we show that the IDRs of SV proteins feature evolutionarily conserved non-random compositional biases and sequence patterns. Synapsin-1 is essential for condensation of SVs, and its C-terminal IDR has been shown to be a key driver of condensation. Focusing on this IDR, we dissected the contributions of two conserved features namely the segregation of polar and proline residues along the linear sequence, and the compositional preference for arginine over lysine. Scrambling the blocks of polar and proline residues weakens the driving forces for forming micron-scale condensates. However, the extent of clustering in subsaturated solutions remains equivalent to that of the wild-type synapsin-1. In contrast, substituting arginine with lysine significantly weakens both the driving forces for condensation and the extent of clustering in subsaturated solutions. Co-expression of the scrambled variant of synapsin-1 with synaptophysin results in a gain-of-function phenotype in cells, whereas arginine to lysine substitutions eliminate condensation. We report an emergent consequence of synapsin-1 condensation, which is the generation of interphase pH gradients realized via differential partitioning of protons between coexisting phases. This pH gradient is likely to be directly relevant for vesicular ATPase functions and the loading of neurotransmitters. Our study highlights how conserved IDR grammars serve as drivers of synapsin-1 condensation. Research HighlightsO_LIDistinct biomolecular condensates formed by pre-synaptic proteins contain a unique bias of sequence grammars within their IDRs. C_LIO_LIThe IDR of synapsin-1, the essential protein for the clustering of synaptic vesicles, has a conserved compositional bias for Arg and blockiness of proline/polar residues. C_LIO_LIUsing sequence designs, we uncovered how conserved sequence features of the driver IDR of synapsin-1 affect condensation in vitro and in cells. C_LIO_LISynapsin-1 condensates are defined by a measurable interphase pH gradient. C_LI

biochemistry↗

Biomolecular condensates can function as inherent catalysts

We report the discovery that chemical reactions can be catalyzed by condensates formed by intrinsically disordered proteins (IDPs). The proteins themselves lack any catalytic activities. Catalytic functions of condensates emerge as a consequence of sequence-dependent mesoscale electrochemical microenvironments created by phase separation. Stimulated Raman spectroscopy suggests that the catalytic behaviors of condensates are attributable to the spatial variations of water activities across condensate interiors and interfaces. We show that condensates are capable of catalyzing diverse cellularly relevant hydrolysis reactions. Through sequence design, the electrochemical properties of condensates can be programmed to exert control over catalytic behaviors. Incorporation of synthetic condensates into live cells alters transcription profiles and enables the activation of gene circuits that depend on products of hydrolysis reactions catalyzed by condensates. Our discovery of suggests that condensates, depending on their composition-dependent electrochemical properties, can be "Condenzymes", which contribute unexpected emergent chemical functions in cells.

biophysics↗

Backbone-mediated weakening of pairwise interactions enables percolation in mimics of protein condensates

Biomolecular condensates formed by intrinsically disordered proteins (IDPs) condensates are semidilute solutions. These can be approximated as solutions of blob-sized segments, which can be as small as peptide-sized motifs. We leveraged the blob picture to quantify differences between inter-residue interactions in model compound and peptide-based mimics of dense versus dilute phases. The all-atom molecular dynamics simulations use the polarizable AMOEBA forcefield. In model compound solutions, the interactions between aromatic residues are stronger than interactions between cationic and aromatic residues. This holds in dilute and dense phases. Cooperativity within dense phases enhances pairwise interactions leading to finite-sized nanoscale clusters. The results for peptide-based condensates paint a different picture. Backbone amides add valence to the associating molecules. While this maintains or enhances pairwise inter-residue interactions in dilute phases, it weakens pair interactions in dense phases. Weakening of pair interactions enables fluidization characterized by short-range order and long-range disorder. The higher valence afforded by the peptide backbone becomes a generator of system-spanning networks. As a result, dense phases of peptides are best described as percolated network fluids. Overall, our results show how peptide backbones enhance pairwise interactions in dilute phases whole weakening these interactions in dense phases to enable percolation within dense phases.

biophysics↗

Biomolecular condensates are characterized by interphase electric potentials

Biomolecular condensates form via processes that combine phase separation and reversible associations of multivalent macromolecules. Condensates can be two- or multi-phase systems defined by coexisting dense and dilute phases. Here, we show that solution ions can partition asymmetrically across coexisting phases defined by condensates formed by intrinsically disordered proteins or homopolymeric RNA molecules. Our findings were enabled by direct measurements of the activities of cations and anions within coexisting phases of protein and RNA condensates. Asymmetries in ion partitioning between coexisting phases vary with protein sequence, condensate type, salt concentration, and ion type. The Donnan equilibrium set up by asymmetrical partitioning of solution ions generates interphase electric potentials known as Donnan and Nernst potentials. Our measurements show that the interphase potentials of condensates are of the same order of magnitude as membrane potentials of membrane-bound organelles. Interphase potentials quantify the degree to which microenvironments of coexisting phases are different from one another. Importantly, and based on condensate-specific interphase electric potentials, which are membrane-like potentials of membraneless bodies, we reason that condensates are mesoscale capacitors that store charge. Interphase potentials lead to electric double layers at condensate interfaces. This helps explain recent observations of condensate interfaces being electrochemically active.

biophysics↗

Direct computations of viscoelastic moduli of biomolecular condensates

In vitro facsimiles of biomolecular condensates are formed by different types of intrinsically disordered proteins including prion-like low complexity domains (PLCDs). PLCD condensates are viscoelastic materials defined by time-dependent, sequence-specific complex shear moduli. Here, we show that viscoelastic moduli can be computed directly using a generalization of the Rouse model and information regarding intra- and inter-chain contacts that is extracted from equilibrium configurations of lattice-based Metropolis Monte Carlo (MMC) simulations. The key ingredient of the generalized Rouse model is the Zimm matrix that we compute from equilibrium MMC simulations. We compute two flavors of Zimm matrices, one referred to as the single-chain model that accounts only for intra-chain contacts, and the other referred to as a collective model, that accounts for inter-chain interactions. The single-chain model systematically overestimates the storage and loss moduli, whereas the collective model reproduces the measured moduli with greater fidelity. However, in the long time, low-frequency domain, a mixture of the two models proves to be most accurate. In line with the theory of Rouse, we find that a continuous distribution of relaxation times exists in condensates. The single crossover frequency between dominantly elastic versus dominantly viscous behaviors is influenced by the totality of the relaxation modes. Hence, our analysis suggests that viscoelastic fluid-like condensates are best described as generalized Maxwell fluids. Finally, we show that the complex shear moduli can be used to solve an inverse problem to obtain distributions of relaxation times that underlie the dynamics within condensates.

biophysics↗

Metastable condensates suppress conversion to amyloid fibrils

Stress granules form via co-condensation of RNA-binding proteins containing prion-like low complexity domains (PLCDs) with RNA molecules. Homotypic interactions among PLCDs can drive amyloid fibril formation that is enhanced by ALS-associated mutations. We report that condensation-versus fibril-driving homotypic interactions are separable for A1-LCD, the PLCD of hnRNPA1. Separable interactions lead to thermodynamically metastable condensates and globally stable fibrils. Interiors of condensates suppress fibril formation whereas interfaces have the opposite effect. ALS-associated mutations enhance the stability of fibrils and weaken condensate metastability, thus enhancing the rate of fibril formation. We designed mutations to enhance A1-LCD condensate metastability and discovered that stress granule disassembly in cells can be restored even when the designed variants carry ALS-causing mutations. Therefore, fibril formation can be suppressed by condensate interiors that function as sinks. Condensate sink potentials are influenced by their metastability, which is tunable through separable interactions even among minority components of stress granules.

biophysics↗