Bulletin of the American Physical Society
APS March Meeting 2019
Volume 64, Number 2
Monday–Friday, March 4–8, 2019; Boston, Massachusetts
Session Y63: Phase Separation in Biological ProcessesFocus
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Sponsoring Units: GSOFT DBIO Chair: Daphne Klotsa, University of North Carolina at Chapel Hill Room: BCEC 259A |
Friday, March 8, 2019 11:15AM - 11:51AM |
Y63.00001: Protein phase separation and emergent material properties Invited Speaker: Shana Elbaum-Garfinkle Phase separation has emerged as a new paradigm currently revolutionizing our understanding of cell biology and intracellular organization. The assembly of biomolecules into condensed liquid phases (i.e condensates) appears to underlie the formation of membraneless organelles and other liquid compartments with roles in cell signaling, transcriptional regulation and cytoskeletal organization. Understanding the role of liquid material properties in condensate function and dysfunction requires new tools and approaches. We employ model in vitro systems and a combination of quantitative imaging and rheological tools to interrogate the nature of liquid material properties and their contribution to molecular processes and functions. We find that protein-protein and protein-RNA interactions can tune the material properties of condensates; Conversely, the viscous network of condensates can in turn modulate the molecular diffusion within droplets in a length scale dependent manner. This work provides important insight into the physicochemical rules that govern the regulation of protein/RNA liquid phases, from the cellular functions of membraneless organelles, to the potential misregulation of liquid phase separation in disease. |
Friday, March 8, 2019 11:51AM - 12:03PM |
Y63.00002: Controlling biological droplets with chemical reactions David Zwicker Phase separation has recently emerged as an important concept to understand the spatial organization of biological matter. In this talk, I will demonstrate that such biological droplets can be controlled by non-equilibrium chemical reactions that affect the droplet material. Such chemical reactions generate compositional fluxes, which control droplet sizes, counteract the effects of surface tension, and can position solid-like particles inside the droplet. I thus show that combining phase separation of proteins with post-translational modifications provides cells with a toolset to build and control compartments without membranes. |
Friday, March 8, 2019 12:03PM - 12:15PM |
Y63.00003: Stiffness gradients control phase separation in gels and cells Kathryn Rosowski, Robert Style, Tianqi Sai, Thomas Böddeker, Eric Dufresne Living cells compartmentalize various processes using phase separation. The physical mechanisms which control this phase separation are not fully understood. However, the interior of the cell can be simply viewed as a closely packed elastic network, with well-regulated regions of lower or higher stiffness. Using droplet formation in a polymer gel as a model system, we found that phase separation can be controlled by the elasticity of the network, and that droplet size and location evolve over time under a stiffness gradient. Our findings further suggest that elasticity differences in cells may similarly regulate phase separation and could be used by cells to control droplet location. |
Friday, March 8, 2019 12:15PM - 12:27PM |
Y63.00004: How yeast harness 2D liquid-liquid phase separation to organize proteins and lipids in vacuole membranes Sarah Keller, Scott P Rayermann, Glennis E Rayermann, Alex J Merz For decades, scientists have argued about how living cell membranes acquire and maintain liquid regions enriched in specific lipid and protein types. Physicists have long observed liquid-liquid demixing in artificial membranes. Clear identification of the same phase transition in a living biological membrane has heretofore been elusive. By directly imaging micron-scale membrane domains of yeast organelles both in vivo and cell-free, we show that the domains reversibly appear and disappear at a distinct miscibility transition temperature and that the domains merge quickly, consistent with fluid phases. Interesting physical phenomena underlie membrane domains. For example, domains are strongly coupled across both membrane faces (with a coupling parameter of ~0.02 kT/nm2). Similarly, liquid-liquid phase separation can occur near a critical point. Membranes behave as 2-dimensional Ising systems with conserved order parameter; and we have measured the membrane’s effective critical dynamic exponent. A third example is that liquid domains coarsen. As expected, domain radius grows as time1/3.These results have appeared in PRL (2012) and BJ (2013, 2015, and 2017) and Physics Today (2018). |
Friday, March 8, 2019 12:27PM - 1:03PM |
Y63.00005: Physics of non-equilibrium phase separation: Implications for stress granule formation in the cell cytoplasm Invited Speaker: Chiu Fan Lee Phase separation is exploited by biological cells to organize their cytoplasm. Although equilibrium phase separation is a well understood phenomenon, the cell cytoplasm is fundamentally different from a thermal system, with driven chemical reactions and directed movement being two hallmarks of its non-equilibrium nature. In this presentation, I will describe some of the universal features in non-equilibrium phase separation relevant to the cell cytoplasm. I will then discuss their implications for stress granules, which form in the cell cytoplasm when the cell is under stress. |
Friday, March 8, 2019 1:03PM - 1:15PM |
Y63.00006: DNA Local Flexibility Dependent Formation of Liquid-like Droplets Anisha Shakya, John King Associative phase separation of biomacromolecules like proteins and nucleic acids into liquid-like droplets, termed liquid-liquid phase separation (LLPS), has been linked to sans lipid-membrane intracellular organization as well as aggregation mediated diseases. In this work, we have studied the role of sequence-dependent DNA flexibility in LLPS of multiple interacting components. We find that DNA local flexibility, encoded by the DNA sequence, not simply the overall charge density, determines the phase behavior in such systems. |
Friday, March 8, 2019 1:15PM - 1:27PM |
Y63.00007: Azobenzene-doped, lipid-bilayer vesicles with light-responsive permeability: measuring mechanical response to photochemical excitation by micropipette aspiration Arash Manafirad, Lucas Antony, Juan De Pablo, Sankaran Thayumanavan, Anthony Dinsmore Inspired by the ability of cell membranes to control the permeability of selected solutes across the lipid bilayer membrane, we report on a synthetic system that switches permeability in response to light. We use experiments and simulations to study giant unilamellar lipid vesicles that contain a photoisomerizing unit (azobenzene) that channels photochemical excitation into mechanical energy within the membrane. In experiments with micropipette aspiration, we hold the vesicles at a constant tension and expose them to UV light with controlled dosage. The membrane surface area, interior volume, and stretching modulus are all measured in situ. We find a threshold molar fraction of azobenzene, below which there is no UV-stimulated response. Above that threshold, we find an extension of the aspirated projection length within seconds of exposure. Together with a prior study of glassy membranes, our experiments and simulations show the basic principles by which the injection of photochemical energy drives the membrane away from equilibrium switching membrane properties in a reversible manner. These results will allow us to mimic cell function and to design smart, responsive artificial systems. |
Friday, March 8, 2019 1:27PM - 1:39PM |
Y63.00008: Microfluidic Fabrication of Asymmetric Lipid Vesicles Yuting Huang, Laura Arriaga, David A Weitz Lipid vesicles are aqueous volumes surrounded by a bilayer of lipid molecules, which are amphiphilic molecules with their head groups facing water and tail groups facing oil. These vesicles are simple models that mimic cell membranes and can be used for drug delivery. One interesting type of lipid vesicle is the asymmetric vesicle, in which its bilayer is composed of two dissimilar lipid monolayers. Importantly, all eukaryotic cell membranes exhibit this type of asymmetry and asymmetry is also proposed to enhance mechanical properties of the membrane. Here, we use microfluidics to fabricate mono disperse and highly controllable asymmetric lipid vesicles, which unlike the conventional methods that often end up with highly poly disperse samples. To achieve this, asymmetric vesicles are produced using water/oil1/oil2/water emulsions in a glass capillary device, with different lipids immersed in two different volatile oil phases. Using the asymmetric vesicles, we are trying to measure how mechanical properties are affected by this asymmetry and also how to improve the degree of asymmetry in our vesicles even more. In future, we envision asymmetric lipid vesicles could open a new door in the field lipid based drug delivery systems. |
Friday, March 8, 2019 1:39PM - 1:51PM |
Y63.00009: Molecular dynamics of hydrophobic transport using monolayer-protected nanoparticles Mukarram Tahir, Alfredo Alexander-Katz Proteins such as serum albumin contain apolar pockets in their three-dimensional structure that facilitate the transport of hydrophobic small molecules in biological settings. Nanoscale carriers that can similarly solubilize therapeutic compounds without requiring chemical modification have immense value as drug delivery systems. Here, we use molecular dynamics simulations to demonstrate that gold nanoparticles functionalized with alkanethiol ligands can passively encapsulate hydrophobic molecules. We focus on the encapsulation of long-chain fatty acids and study the thermodynamics and kinetics of incorporation into the nanoparticle's surface monolayer as a function of chain length and unsaturation. We also characterize the structure of the nanoparticle and organization of the encapsulated molecules as a function of loading density and demonstrate that loaded nanoparticles release their cargo into lipid membranes upon contact with fluctuations such as lipid tail protrusions. These observations suggest the possibility of designing nanomaterials that can function as synthetic mimics of transport proteins and have applications in solubilizing apolar pharmaceutical compounds in the aqueous environment of biological systems. |
Friday, March 8, 2019 1:51PM - 2:03PM |
Y63.00010: Multivalent gene regulatory elements localize condensation of transcription machinery Krishna Shrinivas, Benjamin Sabari, Phillip Sharp, Richard Young, Arup K Chakraborty Enhancers are regulatory elements that cooperatively assemble the transcriptional machinery upon binding by sequence-specific transcription factors. Recently, we and others have hypothesized and demonstrated that the transcriptional apparatus forms liquid-like condensates, particularly at cell-type specific enhancer elements called super-enhancers. Many transcription factors (TFs) and coactivators phase separate in vitro, but only at supra-physiological concentrations. A unified mechanism to describe how and why these condensates form around specific genomi loci at physiological conditions is unknown. Here, using a combination of simulation, and complementary in vitro experiments, we propose that specific and multivalent enhancers nucleate localized condensation of TFs and coactivators at physiologic-like conditions. Using thermodynamic guiding principles, we predict key interactions that regulate condensate formation, as well as motif features encoded in DNA that drive phase separation and higher-order organization of the 3-D genome. Experiments validate our predictions, and many of these features are encoded and leveraged by mammalian genomes to assemble high amounts of transcription machinery, implicating phase separation in shaping the gene regulatory landscape. |
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