Bulletin of the American Physical Society
APS March Meeting 2019
Volume 64, Number 2
Monday–Friday, March 4–8, 2019; Boston, Massachusetts
Session K65: Phase Separation in Biological SystemsFocus
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Sponsoring Units: DBIO DPOLY GSNP GSOFT Chair: Jean-Charles Walter, Université de Montpellier Room: BCEC 260 |
Wednesday, March 6, 2019 8:00AM - 8:12AM |
K65.00001: Permeation of small molecules in phase separated lipid bilayer domains Martin Girard, Tristan Bereau Membranes of cells are constituted of lipid bilayers, which can phase separate into ordered domains called rafts. Recent atomic simulations have shown that ionic permeation is enhanced at the gel-liquid interface of rafts near the melting temperature. Herein, we revisit permeation of small molecules at raft interfaces using the coarse-grained MARTINI model. Namely, we study how the free energy of insertion changes with the small molecule, lipid composition and temperature. |
Wednesday, March 6, 2019 8:12AM - 8:24AM |
K65.00002: Aggregation of cells dispersed in packed microgels Cameron Morley, Katherine Kiwimagi, Jesse Tordoff, Ron Weiss, Thomas Angelini Mixtures of different types of living cells within cultured spheroids segregate in space, sometimes forming core-shell distributions. One long-standing potential mechanism behind this process is described by the differential adhesion hypotheses, which states that cells having differing levels of adhesivity will separate into groups. While this hypothesis has been tested in many ways, alternative driving forces have been proposed. To investigate an extreme limit of cell clustering and segregation, we perform studies using only one cell-type at a time, replacing all other cells with passive, non-adhesive microgel particles. Multiple cell types with tunable cadherin densities are dispersed in polyacrylamide microgels at different volume fractions and monitored over time. In this talk, we will present data on the kinetics of aggregation, the physical characteristics of clusters including fractal dimension, and the role of adhesion energy density on aggregates. By treating microgels as passive, non-adhesive “surrogate” cells, we envision testing theoretical models of active matter designed to study cell-cell phase separation, but in this case setting the appropriate parameters to zero. |
Wednesday, March 6, 2019 8:24AM - 8:36AM |
K65.00003: Evolutionary analysis of pollen patterns as a curious consequence of modulated phases Asja Radja, Maxim O Lavrentovich, Alison Sweeney Pollen grain surface morphologies are famously diverse; each species displays a unique, replicable pattern. The function of these microstructures is poorly understood, largely because it is difficult to describe these patterns in a well-defined, mathematical way. It has been shown that the templating of these patterns is created by a phase separation of a polysaccharide mixture on the cell surface. Here we present a characterization of the surface morphologies using a Landau theory of phase transitions to ordered states. We show that 10% of all morphologies can be characterized as equilibrium states with a well-defined wavelength of the pattern. The rest of the patterns have a range of wavelengths on the surface that can be recapitulated by exploring the evolution of a conserved dynamics model. We then perform an evolutionary trait reconstruction where we categorize all extant patterns into one of these two states, further binned by wavelength ranges. Surprisingly, we find that although the equilibrium states have evolved multiple times, evolution has not favored these ordered-polyhedral like shapes and perhaps their patterning is simply a natural consequence of a phase separation process without cross-linkers. |
Wednesday, March 6, 2019 8:36AM - 8:48AM |
K65.00004: Spatial control of irreversible protein aggregation Christoph Weber, Thomas Michaels, L Mahadevan Liquid cellular compartments form in the cytoplasm and can regulate aberrant protein aggregation. Yet the mechanisms by which these compartments affect protein aggregation remain unknown. Here, we combine kinetic theory of protein aggregation and liquid-liquid phase separation to study the spatial control of irreversible protein aggregation in the presence of liquid compartments. We find that even for weak interactions aggregates strongly enrich inside the liquid compartment relative to the surrounding cytoplasm. This enrichment is caused by a positive feedback mechanism of aggregate nucleation and growth driven by a flux maintaining the phase equilibrium between the compartment and the cytoplasm. Our model establishes a link between specific aggregating systems and the physical conditions maximizing aggregate enrichment in the compartment. The underlying mechanism of aggregate enrichment could be used to confine cytotoxic protein aggregates inside droplet-like compartments but may also represent a common mechanism to spatially control irreversible chemical reactions in general. |
Wednesday, March 6, 2019 8:48AM - 9:00AM |
K65.00005: Density and viscosity measurements on the liquid condensates of FUS protein low-complexity domain Chao Ji, Eric Girardi, Nicholas Fawzi, Jay Tang Recent discoveries have revealed in living cells the formation of liquid droplets consisting of proteins, RNA & DNA. Changes in interactions among these biomolecules may result in devastating diseases, such as amyotrophic lateral sclerosis (ALS). Thus, investigating the physical properties of these liquid droplets in connection with liquid-liquid phase transition is relevant to biomolecular functions and potential therapeutic interventions. We report experiments on the dense liquid droplets formed by FUS (Fused in Sarcoma) low-complexity domain, a section of a protein involved in the development of ALS. By applying a ball drop method under a microscope, we found the density of the protein droplets greater than that of water by 10-15%, indicative of the protein concentration ~200mg/ml. The viscosity of the dilute phase containing FUS droplets is similar to that of water, but viscosity within FUS droplets is very high, ~4000 that of water. Additionally, we found FUS droplets wet solid surface poorly based on the contact angle measurement. These results confirm extremely high protein concentration and strong intermolecular cohesiveness within the condensate state. |
Wednesday, March 6, 2019 9:00AM - 9:12AM |
K65.00006: Multicomponent Equilibrium Model for the Effects of Charge Regulation on Liquid-liquid Phase Separation of a Globular Eye Lens Protein George M Thurston, John F Hamilton, David Ross, Aaron Fadden, Christopher W Wahle, Lea Vacca Michel, Julia Faraone, Symeon Bushunow We study how charge regulation affects liquid-liquid phase separation of bovine gammaB-crystallin. Our grand-canonical distribution model indicates that hundreds of charging patterns have enough probability to affect protein interactions. We measured times for rotational diffusion via nuclear magnetic resonance, and for translational diffusion to neighbors with quasielastic light scattering. Both times are orders of magnitude faster than time scales for some protonation state changes of titrating residues. Here, we apply chemical equilibrium conditions to a first-order perturbation model for the multicomponent, pattern-dependent free energy. Standard chemical potentials result from our existing dilute solution model. We estimate screened electrostatic, pattern-pair dependent interactions using a linearized Poisson-Boltzmann code that accounts for dielectric heterogeneity and includes all titratable groups. We estimate van der Waals interactions using a simplified protein geometry, and adopt an effective Hamaker coefficient by comparison with the experimental second virial coefficient. This model provides a framework for evaluating how charging pattern probabilities change with increasing concentration, and how they affect liquid-liquid coexistence. |
Wednesday, March 6, 2019 9:12AM - 9:24AM |
K65.00007: Mediator and RNA polymerase II forms phase-separated bodies and colocalizes with centrosomes during mitosis. Choongman Lee, Won-Ki Cho, Jan-Hendrik Spille, Ibrahim Cisse In interphase, transcriptional proteins such as RNA polymerase II and Mediator are known to form phase-separated bodies to regulate an expression level of SE-controlled genes. However, a behavior of such proteins during mitosis, a cell cycle stage in which most transcriptional activities are silent, is still poorly understood. Here, we show that RNA polymerase II and Mediator form phase-separated bodies during mitosis. Unlike condensates in interphase which are formed based on clustered enhancer elements, condensates in mitosis are formed based on pericentriolar materials, which are phase-separated bodies in mitosis. We suggest that centrosomes play a role of not only microtubule-organizing centers but also protein storages for immediate transcriptional activities after mitosis. |
Wednesday, March 6, 2019 9:24AM - 9:36AM |
K65.00008: Liquid-like protein condensates are glassy Louise Jawerth, Elisabeth Fischer-Friedrich, Anthony Hyman, Frank Julicher Liquid-like protein condensates (LLPCs) are intracellular compartments that segregate material without the use of a membrane. The liquid-like behavior of the condensates is a defining characteristic and the viscosity, surface tension and other material properties determine how segregated species diffuse into and within condensates; they, thus, critically impact the biological function of the condensates. It has become increasingly clear that some LLPCs do not have time-independent material properties, but can, instead, transition to more solid, gel-like materials. Here, we present our efforts to quantify these new materials as they age in vitro. We measure the visco-elastic material properties of two proteins, PGL-3 and FUS, by means of a combination of active and passive microrheology. At early times, we find that the droplets behave much like simple liquids but gradually become more elastic. Surprisingly, the changing mechanical properties can all be scaled onto a single master curve using one characteristic time scale which grows as the sample ages. This and other features we observe bear a striking resemblance to the behaviors observed in materials with glass-like aging suggesting that LLPCs are in fact not simple liquids but, rather, a type of soft glass. |
Wednesday, March 6, 2019 9:36AM - 9:48AM |
K65.00009: Effective long range interactions generated by polymer fluctuations induce bound particle phase separation Gabriel David, Jean-Charles Wallter, Chase Broedersz, Jérôme Dorignac, Frédéric Geniet, Andrea Parmeggiani, Nils-Ole Walliser, John Palmeri The confinement of chemical species within the cytoplasm is mandatory for the spatio-temporal organization of chemical activities in the cell. Cells indeed compartmentalize the intracellular space using either membrane-bound vesicles or membrane-less organelles. For the latter, cells may employ phase separation of chemical species in order to create localized high density regions in which specific reactions may occur. Such biological phase separation mechanisms often need polymeric scaffolds such as RNA or DNA to bind the chemical species. We propose a general theoretical 3D framework for such polymer-bound particles from which we derive an effective 1D lattice gas model with both nearest neighbor and long range interactions, the latter arising from polymer fluctuations. We argue that 1D phase transitions exist in such system for both Gaussian and self-avoiding polymers and, using a variational method that goes beyond mean field theory, we obtain the mean occupation/temperature phase diagram. To illustrate this model, we apply it to the biologically relevant case of the ParABS system, a prevalent bacterial DNA segregation system, to study the formation of ParBS complexes on DNA. |
Wednesday, March 6, 2019 9:48AM - 10:00AM |
K65.00010: Motif Sequences and the Statistical Physics of Intracellular Phase Separation Benjamin Weiner, Yigal Meir, Ned Wingreen Intrinsically Disordered Proteins (IDPs) lack a unique folded structure, and yet perform diverse and important functions inside cells. Recent work suggests that some IDPs promote the formation of membrane-less organelles via phase separation, helping cells spatially organize their biomolecules. Classical theories of phase separation focus on homogeneous polymers, but IDPs have evolved particular sequences of interacting motifs. How does an IDP’s motif sequence determine its physical properties? We propose a statistical physics model of IDPs to elucidate the relationship between motif sequence, conformational disorder, and biological function. |
Wednesday, March 6, 2019 10:00AM - 10:12AM |
K65.00011: Phase separation and migration in 2D cell co-cultures Manuel Gomez-Bera, Supravat Dey, Moumita Das During morphogenesis, whether in the context of the formation of embryos or of tumors, different types of cells live in close proximity. These cells often have different physical properties. Breast epithelial cells, for example, are generally more adhesive than their cancerous counterparts. This is due to the downregulation of the protein E-cadherin, which facilitates cell-cell adhesion, in cancer cells. Cancer cells are also often more deformable than non-cancerous cells of the same tissue type. We investigate how these differences impact the organization and migration within a binary cell population. To address this, we model and simulate this system as a two-dimensional binary mixture of soft, active particles with different mechanical and adhesive properties. We characterize the phase separation in the system by monitoring the organization and growth of cell clusters with time, and the dynamics in terms of tagged cell trajectories and speeds, mean squared displacements, and non-affine motion. Our results may provide interesting insights into tumor organization, and metastasis. |
Wednesday, March 6, 2019 10:12AM - 10:24AM |
K65.00012: In vivo dynamics and phase state of natural lipid droplets Margarita Fomina, Eugene Mamontov, Hugh O'Neill All organisms store lipids as energy resource for metabolism. Such lipids are accumulated in the form of intracellular droplets. The lipid droplets (LDs) contain un- and saturated triglycerides. Uncovering biophysics of LDs is crucial for metabolism manipulation or reducing lipid storage. The type and organization of lipids affect their phase state and dynamics in the droplet. We studied LDs in fresh human and porcine subcutaneous fat tissues, as well as yeast cells using quasi-elastic neutron scattering, probing molecular motions in a time scale of 6-400 ps and a length scale of 3-20 A. The detected two-component dynamics in the droplet is associated with lipid unrestricted diffusion (D~0.006 A2/ps) and motions of its hydrocarbon chains (D~0.2 A2/ps) in a restricted volume (5-12 A). The dynamics of lipids is reduced below 305 K and 266 K in porcine and human tissues, respectively, due to a fluid-gel phase transition of lipids. However, LDs in the yeast cells remain in a fluid-like state within range of 280-310 K. We believe, phase behavior of LDs is different in the tissues and microorganism due to lipid composition. Lipid packing in the droplet is tight in the tissues, having saturated lipids, and loose in the yeast droplet, having equal proportions of un- and saturated lipids. |
Wednesday, March 6, 2019 10:24AM - 10:36AM |
K65.00013: The role of motility in Myxococcus xanthus droplet formation and droplet geometries Cassidy Yang, Katherine Copenhagen, Joshua Shaevitz Myxococcus xanthus, a rod-shaped soil bacterium lacking long-range interactions, collectively bead from |
Wednesday, March 6, 2019 10:36AM - 10:48AM |
K65.00014: Mechanical Interplay of Chromatin and Liquid-Liquid Phase Separated Condensates Daniel Lee, Yi-Che Chang, Yongdae Shin, David Sanders, Dan Bracha, Pierre Ronceray, Ned Wingreen, Cliff Brangwynne DNA is organized into chromatin, a complex material which stores information and controls gene expression. One mechanism for biological organization, particularly in the crowded nucleus, is liquid-liquid phase separation (LLPS). Here, we use two optogenetic technologies to show that liquid condensates displace chromatin as they grow. We also demonstrate that these synthetic condensates localize to regions of low-density chromatin. We develop a minimal physical model to explain this stiffness selectivity, wherein droplets prefer low-density chromatin regions due to a lower mechanical energy of deformation. By utilizing these spatiotemporally-controllable optogenetic systems, we construct a phase diagram of an intrinsically disordered transcriptional regulator and estimate the stiffness of the chromatin network. Our work thus not only sheds light on the role of LLPS in chromatin organization but also uses the physical principles of phase separation to elucidate mesoscale features of the nucleus. |
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