Biology subjects

Potoyan, D. A.

Publications and source records attributed to Potoyan, D. A..

24 records · Page 2Linked to original sources

bioRxiv2021

BIAPSS - BioInformatic Analysis of liquid-liquid Phase-Separating protein Sequences

Liquid-liquid phase separation (LLPS) has recently emerged as a cornerstone mechanism underlying the biogenesis of membraneless organelles (MLOs). However, a quantitative molecular grammar of protein sequences that controls the LLPS remains poorly understood. The progress in this field is hampered by the insufficiency of comprehensive databases and associated computational infrastructure for targeting biophysical and statistical analysis of phase separating biopolymers. Therefore, we have created a novel open-source web platform named BIAPSS (BioInformatic Analysis of liquid-liquid Phase-Separating protein Sequences) which contains interactive data analytic tools in combination with a comprehensive repository of bioinformatic data for on-the-fly exploration of sequence-dependent properties of proteins with known LLPS behavior. BIAPSS includes a residue-resolution biophysical analyzer for interrogating individual protein sequences (SingleSEQ tab). The latter allows users to correlate regions prone to phase separation with a large array of physicochemical attributes and various short linear motifs. BIAPSS also includes global statistics derived over the universe of most of the known LLPS-driver protein sequences (MultiSEQ tab) for revealing the regularities and sequence-specific signals driving phase separation. Finally, BIAPSS incorporates an extensive cross-reference section that links all entries to primary LLPS databases and other external resources thereby serving as a central navigation hub for the phase separation community. All of the data used by BIAPSS is freely available for download as well-formatted pre-processed data with detailed descriptions, facilitating rapid implementation in user-defined computational protocols. O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=70 SRC="FIGDIR/small/430806v2_ufig1.gif" ALT="Figure 1"> View larger version (24K): org.highwire.dtl.DTLVardef@1d90ddorg.highwire.dtl.DTLVardef@111d084org.highwire.dtl.DTLVardef@90b3b0org.highwire.dtl.DTLVardef@51d71_HPS_FORMAT_FIGEXP M_FIG TOC - graphical abstract C_FIG Author summaryProteins, especially those with low complexity and intrinsically disordered regions, have recently come into the limelight because of mounting evidence showing that these regions can drive the formation of membraneless organelles (MLOs) in cells. The underlying physical mechanism for forming MLOs is liquid-liquid phase separation (LLPS); a thermodynamically driven process whereby a cellular milieu with a relatively well-mixed distribution of biomolecules gets decomposed into liquid droplets where the concentration of selected biomolecules is higher. Deciphering molecular sequence grammar of phase separation has turned out to be challenging because of the complexity of this process in cells and the vastness of sequence space of LLPS-driver proteins. While the field is still in its infancy the growth of experimental data has already spurred the creation of several major databases which collect and annotate bimolecular systems with confirmed LLPS behavior. What is currently missing is a framework that would leverage the existing databases by integrating them with deep biophysical and bioinformatic analysis for identifying statistically significant features of protein sequences implicated in LLPS. In this work, we have addressed this challenge by creating an open-source web platform named BIAPSS (BioInformatic Analysis of liquid-liquid Phase-Separating protein Sequences) which integrates a comprehensive repository of pre-processed bioinformatic data for LLPS-driver protein sequences with interactive analytic applications for on-the-fly analysis of biophysical features relevant for LLPS behavior. BIAPSS empowers users with novel and effective tools for exploring LLPS-related sequence signals for individual proteins (SingleSEQ tab) and globally by integrating common regularities across subgroups or the entire LLPS sequence superset (MultiSEQ). The long-term plan for BIAPSS is to serve as a unifying hub for the experimental and computational community with a comprehensive set of analytic tools, biophysically featured data, and standardized protocols facilitating the identification of sequence hot spots driving the LLPS, which all can support applications for designing new sequences of biomedical interest.

bioinformatics↗

bioRxiv2020

Sequence-encoded and Composition-dependent Protein-RNA Interactions Control Multiphasic Condensate Topologies

Multivalent protein-protein and protein-RNA interactions are the drivers of biological phase separation. Biomolecular condensates typically contain a dense network of multiple proteins and RNAs, and their competing molecular interactions play key roles in regulating the condensate composition and structure. Employing a ternary system comprising of a prion-like polypeptide (PLP), arginine-rich polypeptide (RRP), and RNA, we show that competition between the PLP and RNA for a single shared partner, the RRP, leads to RNA-induced demixing of PLP-RRP condensates into stable coexisting phases-homotypic PLP condensates and heterotypic RRP-RNA condensates. The morphology of these biphasic condensates (non-engulfing/ partial engulfing/ complete engulfing) is determined by the RNA-to-RRP stoichiometry and the hierarchy of intermolecular interactions, providing a glimpse of the broad range of multiphasic patterns that are accessible to these condensates. Our findings provide a minimal set of physical rules that govern the composition and spatial organization of multicomponent and multiphasic biomolecular condensates.

biophysics↗

bioRxiv2020

Liquid-liquid phase separation driven compartmentalization of reactive nucleoplasm.

The nucleus of eukaryotic cells harbors active and out of equilibrium environments conducive to diverse gene regulatory processes. On a molecular scale, gene regulatory processes take place within hierarchically compartmentalized sub-nuclear bodies. While the impact of nuclear structure on gene regulation is widely appreciated, it has remained much less clear whether and how gene regulation is impacting nuclear order itself. Recently, the liquid-liquid phase separation emerged as a fundamental mechanism driving the formation of biomolecular condensates, including membrane-less organelles, chromatin territories, and transcriptional domains. The transience and environmental sensitivity of biomolecular condensation are strongly suggestive of kinetic gene-regulatory control of phase separation. To better understand kinetic aspects controlling biomolecular phase-separation, we have constructed a minimalist model of the reactive nucleoplasm. The model is based on the Cahn-Hilliard formulation of ternary protein-RNA-nucleoplasm components coupled to non-equilibrium and spatially dependent gene expression. We find a broad range of kinetic regimes through an extensive set of simulations where the interplay of phase separation and reactive timescales can generate heterogeneous multi-modal gene expression patterns. Furthermore, the significance of this finding is that heterogeneity of gene expression is linked directly with the heterogeneity of length-scales in phase-separated condensates.

biophysics↗

bioRxiv2020

Phase Transition of RNA-protein Complexes into Ordered Hollow Condensates

Liquid-liquid phase separation of multivalent intrinsically disordered protein-RNA complexes is ubiquitous in both natural and biomimetic systems. So far, isotropic liquid droplets are the most commonly observed topology of RNA-protein condensates in experiments and simulations. Here, by systematically studying the phase behavior of RNA-protein complexes across varied mixture compositions, we report a hollow vesicle-like condensate phase of nucleoprotein assemblies that is distinct from RNA-protein droplets. We show that these vesicular condensates are stable at specific mixture compositions and concentration regimes within the phase diagram and are formed through the phase separation of anisotropic protein-RNA complexes. Similar to membranes composed of amphiphilic lipids, these nucleoprotein-RNA vesicular membranes exhibit local ordering, size-dependent permeability, and selective encapsulation capacity without sacrificing their dynamic formation and dissolution in response to physicochemical stimuli. Our findings suggest that protein-RNA complexes can robustly create lipid-free vesicle-like enclosures by phase separation. Significance statementVesicular assemblies play crucial roles in subcellular organization as well as in biotechnological applications. Classically, the ability to form such assemblies were primarily assigned to lipids and lipid-like amphiphilic molecules. Here, we show that disordered RNA-protein complexes can form vesicle-like ordered assemblies at disproportionate mixture compositions. We also show that the ability to form vesicular assemblies is generic to multi-component systems where phase separation is driven by heterotypic interactions. We speculate that such vesicular assemblies play crucial roles in the formation of dynamic multi-layered subcellular membrane-less organelles and can be utilized to fabricate novel stimuli-responsive microscale systems.

biophysics↗

bioRxiv2019

Disorder mediated oligomerization of DISC1 proteins revealed by coarse-grained computer simulations.

Disrupted-in-Schizophrenia-1 (DISC1) is a scaffold protein of significant importance for neurodevelopment and a prominent candidate protein in the etiology of mental disorders. In this work, we investigate the role of conformational heterogeneity and local structural disorder in the oligomerization pathway of the full-length DISC1 and of two truncation variants. Through extensive coarse-grained molecular dynamics simulations with a predictive energy landscape based model, we reveal the general mechanistic principles of DISC1 oligomerization. We found that both conformational heterogeneity and structural disorder play an important role in the dimerization pathway of DISC1. This study sheds light on the differences in oligomerization pathways of the full-length protein compared to the truncated variants produced by a chromosomal translocation associated with schizophrenia.

biophysics↗

bioRxiv2019

Mesoscale liquid model of chromatin recapitulates large-scale organization of eukaryotic cell nuclei.

The nuclear envelope segregates the genome of Eukaryota from the cytoplasm. Within the nucleus, chromatin is further compartmentalized into architectures that change throughout the lifetime of the cell. Epigenetic patterns along the chromatin polymer strongly correlate with chromatin compartmentalization and, accordingly, also change during the cell life cycle and at differentiation. Recently, it has been suggested that sub-nuclear chromatin compartmentalization might result from a process of liquid-liquid phase separation orchestrated by the epigenetic marking and operated by proteins that bind to chromatin. Here, we translate these observations into a diffuse interface model of chromatin, which we named MEsoscale Liquid mOdel of Nucleus (MELON). Using this streamlined continuum model of the genome, we study the large-scale rearrangements of chromatin that happen at different stages of the growth and senescence of the cell, and during nuclear inversion events. Particularly, we investigate the role of droplet diffusion, fluctuations, and heterochromatin-lamina interactions during nuclear remodeling. Our results indicate that the physical process of liquid-liquid phase separation, together with surface effects is sufficient to recapitulate much of the large-scale morphology and dynamics of chromatin along the life cycle of cells.\n\nSIGNIFICANCE STATEMENTEukaryotic chromatin occupies a few micrometers of nuclear space while remaining dynamic and accessible for gene regulation. The physical state of nuclear chromatin is shaped by the juxtaposition of complex, out of equilibrium processes on one hand and intrinsic polymeric aspect of the genome on the other. Recent experiments have revealed a remarkable ability of disordered nuclear proteins to drive liquid-liquid phase separation of chromatin domains. We have built a mesoscale liquid model of nuclear chromatin which allows dissecting the contribution of liquid behavior of chromatin to nuclear order of eukaryotes. Our results show that liquid-liquid phase separation, together with surface effects is sufficient for recapitulating large-scale morphology and dynamics of chromatin at many stages of the nuclear cycle.

biophysics↗