Bulletin of the American Physical Society
APS March Meeting 2020
Volume 65, Number 1
Monday–Friday, March 2–6, 2020; Denver, Colorado
Session U23: Macromolecular Phase Separation in Biology IIFocus
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Sponsoring Units: DBIO DSOFT DPOLY GSNP Chair: Patrick McCall, Max Planck Institute for the Physics of Complex Systems Room: 304 |
Thursday, March 5, 2020 2:30PM - 3:06PM |
U23.00001: Pollen cell walls form from modulated phases Invited Speaker: Asja Radja Pollen cell walls exhibit a huge diversity of morphologies including ordered and disordered arrangements of spikes, stripes, and holes. Electron microscopy images of pollen wall development across the spermatophyte tree reveal that a ubiquitous material called primexine, thought to be made of a mixture of polysaccharides, lipoproteins and glycoproteins, templates these morphologies. Recently, our imaging studies identified that a phase separation of primexine coupled to the cell membrane induces a phase transition to modulated phases which pattern the pollen wall. We formulated a Landau-Ginzburg free energy description of this process in which we treat the primexine concentration as a scalar field coupled to the cell membrane and calculated the equilibrium states. We also studied the dynamics of our model and found that together kinetically-arrested and equilibrium states recapitulate most extant cell morphologies. Further imaging studies indicate that nanoscale patterns form within the phase-separated domains, thus we additionally model the lyotropic liquid crystalline-like phases employing self-consistent field theory simulations. Finally, we completed an evolutionary analysis in which character traits are defined by parameters of our model that reveals while equilibrium patterns have appeared multiple times during evolution, selection does not favor these states. |
Thursday, March 5, 2020 3:06PM - 3:18PM |
U23.00002: Designing morphology of separated phases in multicomponent liquid mixtures Milena S Chakraverti-Wuerthwein, Sheng Mao, Hunter Gaudio, Mikko Haataja, Andrej Kosmrlj Morphology of multiphase membraneless organelles formed via intracellular phase separation plays an important role for their functionality. Yet, very little is known how intermolecular interactions can be tuned to achieve target microstructures of separated phases. To address this, we systematically investigate morphologies of coexisting phases obtained via phase separation in Flory-Huggins liquid mixtures with 4 or more components. We demonstrate that the topology of separated phases is completely determined by their surface tensions, while their volume fractions dictate the geometry of microstructure (e.g. droplets, percolated structure). We developed a novel method based on graphs that enabled us to enumerate all topologically distinct morphologies of separated phases. Each graph is associated with a set of inequalities for surface tensions and this enabled us to reverse engineered intermolecular interaction parameters to realize all topologically distinct morphologies for 4 coexisting phases. The developed approach is general and can be applied to design morphologies with an arbitrary number of coexisting phases. |
Thursday, March 5, 2020 3:18PM - 3:30PM |
U23.00003: Microscopic Model of a Biological Condensate Swan Htun, Han-Yi Chou, Kumar Sarthak, Aleksei Aksimentiev Liquid-liquid phase separation governs the intracellular organization of biological molecules into membraneless organelles also known as biological condensates. Fused in Sarcoma (FUS), an RNA-binding protein, is the principle component of a biological condensate involved in DNA repair. The intrinsically disordered nature of FUS eludes structural characterization using conventional methods. Here, we report a fully-atomistic structure of a FUS condensate obtained through a combination of coarse-grained and all-atom simulations. Using existing structural and biochemical information, we constructed a coarse-grained model of the FUS protein. An ensemble of such proteins was found to undergo phase separation into a liquid-like condensate in a temperature and composition-dependent manner. The final configurations obtained through the coarse-grained simulations were used to construct an all-atom model of the condensate, including the surrounding solvent. The microscopic structure was refined using atomistic simulations and used to probe the condensate’s viscoelastic behavior and identify specific interactions that control its viscosity. The resulting structural model sets the stage for subsequent systematic inquiry into the sequence-structure-function relationship of the condensate. |
Thursday, March 5, 2020 3:30PM - 3:42PM |
U23.00004: Microstructure in biological phase transition Kamal Bhandari, Jeremy Schmit
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Thursday, March 5, 2020 3:42PM - 3:54PM |
U23.00005: Experimental determination of binodal compositions of protein and peptide solutions Emmanouela Filippidi, Frank Julicher, Anthony Hyman Biomacromolecules such as proteins are known to undergo liquid-liquid phase separation to a dense phase and a dilute phase under certain conditions of temperature, pH, salt and protein concentrations. As the study of proteins is complex due to their zwitterionic nature, hydrogen bonding, inclusion of hydrophobic side chains, pi-cation interactions and presence of metal binding and folded domains, we will study in parallel both a protein, FUS, and simplified peptides of known sequences. |
Thursday, March 5, 2020 3:54PM - 4:06PM |
U23.00006: Spinodal Dynamics in Non-Equilibrium Compression of Two Self-Avoiding Polymer Chains Lili Zeng, Rabea Seyboldt, Zezhou Liu, Xavier Capaldi, Ahmed Khorshid, Paul Francois, Nikolas Provatas, Walter W Reisner Two polymers under 1D confinement can phase separate as a consequence of chain interconnectivity and entropy maximization, and this demixing may be one mechanism leading to bulk chromosomal segregation in bacteria. While there has been considerable theoretical effort to explore this problem, few experiments have attempted to directly investigate segregation/mixing behaviour of two self-avoiding chains in model geometries. In this experiment, two differentially labeled nanochannel confined DNA molecules are compressed against a barrier using hydrodynamic flow. The differential labeling enables us to quantify the concentration profile of each chain along the channel independently. The two DNA molecules will mix given that the applied forcing is strong enough, but instead of simple mixing, we observe a complex phenomena whereby the chains interpenetrate but form alternating, fluctuating bands in which one chain has higher concentration relative to the other. We interpret this phenomenon as a spinodal decomposition of the two polymers and rationalize it using a model based on a 1D convective Cahn-Hilliard equation, a classic model describing spinodal decomposition in driven binary systems. Simulations for such a model yield striking similarity to the experimental observations. |
Thursday, March 5, 2020 4:06PM - 4:18PM |
U23.00007: Relating chemical and physical properties controlling oligonucleotide polyelectrolyte complex phase separation Alexander E. Marras, Jeffrey Vieregg, Michael Lueckheide, Matthew Tirrell Nucleic acids are some of the most highly-charged molecules known, and interact strongly with charged molecules in the cell. Condensation of long double-stranded DNA is a classic problem of biophysics, but the polyelectrolyte behavior of short and/or single-stranded nucleic acids is far less studied despite its importance for both biological and engineered systems. Homopolycations and neutral-cationic block copolymers condense nucleic acids driving macro- or nanoscale phase separation, respectively. Here, we present an investigation of the impact of physical and chemical properties of each polyelectrolyte on complex and micelle assembly. We find molecular details including hybridization, charge density, and chemical structure strongly influence complexation behavior and stability. These observations narrow the design space for optimizing therapeutic micelles and provide new insights into the physics of polyelectrolyte self-assembly. |
Thursday, March 5, 2020 4:18PM - 4:30PM |
U23.00008: Entropic localization of plasmids in nanofluidic compartments Zezhou Liu, Xavier Capaldi, Lili Zeng, Rodrigo Reyes Lamothe, Walter W Reisner Bacteria must stably partition their plasmids to their daughter cells upon division. While purely random partitioning can theoretically ensure stable transmission of plasmids to daughter cells, it is not clear that plasmid partitioning is random. Studies tracking plasmids in vivo show that multi-plasmid clusters present at the cell poles, but the roles played by the cell geometry and chromosome-plasmid interactions are still unclear. Here, we present a nanofluidic device with compartments simulating the confinement induced by a cell membrane. The compartments can be opened and closed by pneumatically actuating the thin membrane lid. The cavities are elliptical with a width varying from around 200 nm to 2 um. A differentially stained T4 DNA molecule and one plasmid molecule are introduced inside the compartment and monitored in real time from their fluorescence signals. We find that the plasmid prefers the peripheral of the cavity as has been observed in in vivo measurements in E. Coli, forming a ring shape distribution. In addition, as the cavity aspect ratio increases, the plasmid shows a preference for the cavity poles. Our results suggest that the free energy landscape formed by chain-chain interaction and the confinement geometry helps promote plasmid localization. |
Thursday, March 5, 2020 4:30PM - 4:42PM |
U23.00009: Computational Insights into Phase Separation of Multivalent Polymers Emiko Zumbro, Alfredo Alexander-Katz Liquid-liquid phase separation has emerged as an important biological process. In membraneless organelles, phase separation in solution is often controlled by weak multivalent interactions between polymers using a variety of bond types. How to control phase compositions and specificity in biological contexts is still not well understood. In this work we compare phase separation of multivalent polymers through non-specific Van der Waals interactions to phase separation through specific reactive-binding interactions. We use a coarse-grain, reactive-binding, Brownian dynamics simulation to investigate the transition dynamics, resulting compositions, and specificity of polymer phase separation. Our results provide insights on how multivalently binding polymers control phase separation in synthetic and biological systems. |
Thursday, March 5, 2020 4:42PM - 4:54PM |
U23.00010: Stable drops: the Gibbs-Thomson condition and drop dynamics Andrew Rutenberg, Samuel Cameron In standard phase separated binary liquids, larger droplets grow while small droplets shrink due to the Gibbs-Thomson condition at droplet boundaries. As a result, the liquid reduces its overall interfacial area between the two phases. The dynamics of these systems can be described by Lifshitz-Slyozov-Wagner theory, and ultimately only one large (bulk) drop will survive in equilibrium. However, some binary liquid-like systems have a preferred, stable droplet size, and their final steady states have multiple microphase-separated droplets. This phenomena not well described by the standard Gibbs-Thomson condition or the standard Lifshitz-Slyozov-Wagner dynamics. This talk addresses three questions for systems with small stable droplets: how does the Gibbs-Thomson condition generalize, how does Lifshitz-Slyozov-Wagner dynamics generalize, and how much of this should apply when stable drops arise from non-equilibrium processes? |
Thursday, March 5, 2020 4:54PM - 5:06PM |
U23.00011: Simulation Informed Thermodynamic Model for Polyampholyte Self-Coacervation with Heterogeneous Charge Distribution Jason Madinya, Charles Sing Livng cells rely on phase separation to achieve many of its critical functions such as organelle formation and signaling and regulatory complexation. Intrinsically disordered proteins (IDPs) often play a role in intracellular liquid-liquid phase separation. IDPs are frequently ampholytic and they can be driven to phase separation through electrostatic interactions. The solution behavior and properties are encoded in the peptide sequence of the proteins, particularly the distribution of the charged residues. Previous work from the authors introduced a Transfer Matrix model for charge-driven polyampholyte phase separation, which resolved the impact of charge sequence on phase separation. This model was limited to looking at homogenous sequences made up of repeating blocks of charge patterns. In this work we present a coarse-grained simulation model to resolve phase separation in polyampholytes with any arbitrary charge sequence. Of particular interest is characterizing the inhomogeneity of the sequence and quantifying the impact on solution behavior. |
Thursday, March 5, 2020 5:06PM - 5:18PM |
U23.00012: Nematic transition and liquid-liquid phase separation in semiflexible polymers – nanoparticle mixtures Supriya Roy, Yeng-Long Chen Adding nanoparticles (NPs) to a polymer matrix may significantly modify its glass transition temperature, dielectric constant, istropic-nematic phase transition behavior, etc. In the present study, we used GPU-accelerated Langevin dynamics simulation to explore how polymer-NP interaction affect the isotropic-nematic (I-N) transition and microstructural modifications of a matrix of semi-flexible polymers with persistence length P=20 and contour length L=25. The mixture is confined under slit. Polymers are modeled as semi-flexible chains with beads of diameter σm=1, and NPs are spheres with σp =2.5. |
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