Bulletin of the American Physical Society
APS March Meeting 2020
Volume 65, Number 1
Monday–Friday, March 2–6, 2020; Denver, Colorado
Session W23: Macromolecular Phase Separation in Biology IIIFocus
|
Hide Abstracts |
Sponsoring Units: DBIO DPOLY DSOFT GSNP Chair: Patrick McCall, Max Planck Institute for the Physics of Complex Systems Room: 304 |
Friday, March 6, 2020 8:00AM - 8:36AM |
W23.00001: Valence and Patterning of Aromatic Residues Determine the Phase Behavior of Disordered Prion-Like Domains Invited Speaker: Alex S Holehouse Prion-like domains (PLDs) are intrinsically disordered protein regions that can drive functional liquid-liquid phase separation (LLPS) in vitro and in cells. Curiously, in many neurodegenerative diseases these regions contain mutations, leading to the formation of aggregates which are strongly correlated with disease pathology. An open question reflects the underlying molecular details that explain why some sequences form dynamic reversible assemblies, while others form solid-like aggregates. Here, we use multipronged biophysical approaches that integrates across simulation, experiment, and theory to address this question and uncover the physical principles underlying how an archetypal PLD derived from hnRNPA1 avoids aggregation in favor of LLPS. The extent of compaction of individual PLDs in dilute solutions mirrors the driving forces for temperature-dependent LLPS. This compaction is directly determined by the valence of aromatic residues in PLDs. As a result, the sequence-dependent phase behaviour for PLDs can be predicted using a stickers-and-spacers model. We uncover an evolutionary preference for aromatic residues to be uniformly distributed, as opposed to being clustered, along PLD sequences. We demonstrate that this non-random patterning drives reversible LLPS whereas its disruption leads to aggregation. We conclude that the valence and patterning of aromatic residues are key determinants of LLPS in PLDs. More generally, the valence and patterning of stickers in a stickers-and-spacers model offers a quantitative approach to relate sequence features to full binodal curves. |
Friday, March 6, 2020 8:36AM - 8:48AM |
W23.00002: A Random Heteropolymer Model of Protein Aggregation Martin Falk, Catherine Triandafillou, Arvind Murugan There have been dramatic developments in our ability to functionalize submicron scale objects with molecules enabling specific interactions between building blocks. To guide exploration in this design space, it is natural to look towards biology. In this context, the phenomenon of protein aggregation is a particularly appealing subject of study. Proteins navigate a complex and rugged energy landscape, and the design rules underlying their ability to avoid or take advantage of aggregated states in this landscape can be instructive for synthetic systems as well. We study a simple system consisting of a solution of random heteropolymers, and identify parameters that determine the structure of the aggregated phase. |
Friday, March 6, 2020 8:48AM - 9:00AM |
W23.00003: Actin(g) on phase separation Tina Wiegand, Anthony Hyman, Stephan Grill F-actin networks play a crucial role for cellular integrity and induction of shape changes during development and homeostasis. Actin polymerization is highly regulated by multiple pathways involving nucleating and sequestering factors, or mechanisms that regulate local monomer concentration. Recently, actin partitioning into biomolecular condensates has been reported as an additional mechanism to enhance polymerization kinetics. We reconstitute phase separated droplets of the components wsp-1 and the arp2/3 complex in vitro and study their interaction with actin. We find that actin partitions inside phase separated drops, where it polymerizes into fibers which extrude. We use this assay to study the effect of locally enhanced concentration on branched actin polymerization, the dynamics of active condensates and the mechanical interplay between established actin networks and biomolecular condensates. Our aim is to recapitulate the complex spectrum of kinetic behaviors observed for actomyosin in vivo. |
Friday, March 6, 2020 9:00AM - 9:12AM |
W23.00004: Elasticity dominated small molecule migration in polymer mixtures and gels Buddhapriya Chakrabarti, Biswaroop Mukherjee Surface segregation of the low-molecular weight component in a polymeric mixture leads to degradation of industrial formulations. We report a simultaneous phase separation and surface migration phenomena in oligomer-polymer and oligomer-gel systems following a temperature quench. We compute equilibrium and time varying migrant density profiles and wetting layer thickness using coarse grained molecular dynamics and mesoscale hydrodynamics simulations to demonstrate that surface migration in oligomer-gel systems is significantly reduced due to network elasticity. Further, phase separation processes are significantly slowed in gels, modifying the Lifshitz-Slyozov-Wagner (LSW) law. Our work allows for rational design of polymer/gel-oligomer mixtures with predictable surface segregation characteristics. |
Friday, March 6, 2020 9:12AM - 9:24AM |
W23.00005: Looped liquid-liquid coexistence in protein crystallization Jens Glaser, Sharon C Glotzer The potential of proteins to realize enzyme crystals or act as nanomachines in dense assemblies makes them excellent candidates for the de-novo design of biological materials. In view of the notorious complexity of protein-protein interactions, simplified models of proteins treated as patchy particles offer a promising strategy to obtain insight into the mechanism of crystallization. Here we report liquid-liquid phase separation (LLPS) with a highly asymmetric coexistence region in a computational model of rubredoxin with real molecular shape. The coexistence region terminates in both an upper (UCST) and a lower (LCST) critical solution temperature, and the complex molecular shape explains the closed-loop behavior of the LLPS. A popular conceptual framework of protein crystallization predicts that nucleation is a two-step process controlled by a metastable liquid-liquid critical point. Here, LLPS occurs via the formation of ring-like nucleation precursors if and only if the proteins are capable of crystallizing. Our findings dispute the notion that the nucleation rate may be enhanced by indirectly controlling nucleation through an independent, metastable critical point. Conversely, we show that metastable LLPS is an essential feature of crystallization. |
Friday, March 6, 2020 9:24AM - 9:36AM |
W23.00006: Intermolecular association of the variable domain of dynamin related protein 1 in crowding conditions suggests a role in dynamin assembly James Harden, Ammon Posey, Mehran Bagheri, Megan Harwig, Nolan W. Kennedy, Vincent Hilser, R. Blake Hill Dynamins are an essential superfamily of mechanoenzymes that remodel membranes and often contain a “variable domain” (VD) important for regulation. For the mitochondrial fission dynamin, Drp1, a regulatory role for the VD is demonstrated by mutations that can elongate, or fragment, mitochondria. How the VD encodes inhibitory, and stimulatory, activity is an unresolved issue. This talk focuses on the behaviour of isolated VD from Drp1 isoform 1. Using spectroscopy methods (NMR and circular dichroism) and molecular dynamics (MD) simulations, this VD is shown to be intrinsically disordered (ID). Somewhat surprisingly, microscopy and light scattering studies also indicate that this VD in solution undergoes a liquid-liquid phase separation under the influence of an osmolyte that normally induces ID proteins to fold. Interestingly, these crowding conditions also enhance binding to cardiolipin, a mitochondrial lipid. MD simulations suggest this liquid-liquid phase separation arises from weak, multivalent interactions similar to other systems involving intrinsically disordered regions. These new findings support a model where the variable domain mediates phase separation that enables rapid tuning of Drp1 assembly necessary for fission. |
Friday, March 6, 2020 9:36AM - 9:48AM |
W23.00007: Model for intrinsically disordered proteins with a strong dependence of liquid-liquid phase separation on sequence Antonia Statt, Helena Casademunt, Cliff Brangwynne, Athanassios Panagiotopoulos Phase separation of intrinsically disordered proteins is important for the formation of membraneless organelles, or biomolecular condensates, which play key roles in the regulation of biochemical processes within the cells. In this talk, we present the phase separation behavior of different sequences of a coarse-grained model for intrinsically disordered proteins and show that they exhibit a surprisingly rich phase behavior. Both the fraction of total hydrophobic parts and the distribution hydrophobic parts are investigated. We observed not only conventional liquid-liquid phase separation, but also reentrant phase behavior, in which the liquid phase density decreases at lower temperatures. For some sequences, we also observe formation of open phases consisting of aggregates, rather than a normal liquid. These aggregates had overall lower densities than the conventional liquid phases and complex geometries with large interconnected fibril-like or membrane-like clusters. Minor alterations in the ordering of a given set of amino acids may lead to large changes in the overall phase behavior, a fact of significant potential relevance for biology. |
Friday, March 6, 2020 9:48AM - 10:00AM |
W23.00008: Quantitative droplet FRAP based on physical principles Lars Hubatsch, Louise Jawerth, Anthony Hyman, Christoph Weber Fluorescence recovery after photobleaching (FRAP) is used to characterize a range of dynamic processes, for example binding kinetics and mobility of intracellular proteins, and recently liquid-liquid phase separation (LLPS) in vitro and in vivo. |
Friday, March 6, 2020 10:00AM - 10:12AM |
W23.00009: Probing ATPase Dependent Physical Properties of Biological Condensates Sebastian Coupe, Yoon Jung, Nikta Fakhri Biological condensates are membraneless organelles, formed through nonspecific or multivalent ribonucleoprotein interactions, which are thought to be involved in the biochemical organization of the cell. There is increasing evidence for the regulation of these biological condensates by DEAD-box RNA helicases, which canonically remodel RNA-protein and RNA-RNA interactions in an ATP-dependent manner. The specific relationship between helicase activity and condensate properties such as viscosity, elasticity, and network architecture has not been investigated to date. DEAD-box helicase LAF-1, a critical component of the P granule condensate of C. elegans, phase separates in vitro. The ability for LAF-1 to interact with RNA and the effect of RNA on its droplet fluidity have been previously studied, however the interplay between its enzymatic function and droplet properties has not been established. We analyze the diffusion of single-walled carbon nanotubes, which are infrared-fluorescent, photostable, passive probes, to analyze the physical properties of LAF-1 droplets. In studying how this model condensate system responds to base-pairing RNAs, ATP, and accessory proteins we will shed light on principles underlying energetic regulation of condensate fluidity. |
Friday, March 6, 2020 10:12AM - 10:24AM |
W23.00010: The robust bioinformatic analysis of the protein sequences with phase behavior Aleksandra Elzbieta Badaczewska-Dawid, Davit Potoyan Liquid-liquid phase separation (LLPS) of many proteins is critical in the biological function of membrane-less organelles. Reversible nature of biomolecular PS in cells suggests that phases of proteins and nucleic acids are like to be tightly regulated. Post-translational modifications and single-residue mutations have been shown to lead to the dissolution of biomolecular droplets or phase transition into aggregated forms. Based on the wealth of experimental data, it reasonable to expect that the PS of proteins is highly sequence-specific. |
Friday, March 6, 2020 10:24AM - 10:36AM |
W23.00011: Effects of protein charge and charge patterning on complex coacervation for enzymatic microreactors Nicholas Zervoudis, Allie Obermeyer Complex coacervation is a liquid-liquid phase separation phenomenon that has shown promise encapsulating proteins and improving protein stability to a variety of perturbations. Cells utilize the process of complex coacervation to create microcompartments, termed membraneless organelles, for increased spatiotemporal control in cellular functions. Here, polypeptide-tagged green fluorescent protein (GFP) mutants and poly(4-vinyl N-methylpyridinium) were used to investigate the effects of protein charge patterning on coacervate phase behavior. Tagged mutants achieved coacervate concentrations higher than previously reported while retaining their secondary structure, suggesting that complex coacervation is a potentially attractive avenue for encapsulating enzymes for biocatalytic applications. Preliminary data has indicated the ability to form liquid-liquid phase separated microcompartments containing multiple enzymes. Using a model colorimetric cascade reaction, these multi-enzyme-polyelectrolyte coacervates have been used to evaluate the catalytic efficiency in biomimetic microcompartments and have the potential to inform the design of novel microcompartments for the production of industrially-relevant chemicals. |
Friday, March 6, 2020 10:36AM - 10:48AM |
W23.00012: The role of a hidden ordered domain in controlling the material properties of RNA-protein condensates Ian Seim, Daphne Klotsa, Amy S Gladfelter Biomolecular condensates are a diverse class of membraneless, intracellular bodies that organize biochemistry. The constituent molecules, often RNA and protein, phase separate from a soluble pool into condensates which are crucial for normal physiological function but are also implicated in the development of several neurological diseases. Condensates can range from liquid-like droplets to solid-like aggregates. However, the distribution of condensate material properties along the viscoelastic continuum has not been well characterized, the molecular basis is poorly understood, and the corresponding functional consequences for cells are largely unknown. We have identified a coiled-coil (CC) motif within the disordered polyQ tract of a phase separating protein that strongly influences the material states of resulting RNA-protein condensates. By mutating specific residues in the CC, we demonstrate a range of material states in vitro, characterized by kinetic mean-field modeling of condensate formation. The CC domain structure is predicted by atomistic monte carlo simulations which are complemented by circular dichroism. Finally, integration of CC mutants into cells provides an in vivo system that demonstrates a link between the material state of condensates and cell function. |
Follow Us |
Engage
Become an APS Member |
My APS
Renew Membership |
Information for |
About APSThe American Physical Society (APS) is a non-profit membership organization working to advance the knowledge of physics. |
© 2024 American Physical Society
| All rights reserved | Terms of Use
| Contact Us
Headquarters
1 Physics Ellipse, College Park, MD 20740-3844
(301) 209-3200
Editorial Office
100 Motor Pkwy, Suite 110, Hauppauge, NY 11788
(631) 591-4000
Office of Public Affairs
529 14th St NW, Suite 1050, Washington, D.C. 20045-2001
(202) 662-8700