Bulletin of the American Physical Society
APS March Meeting 2019
Volume 64, Number 2
Monday–Friday, March 4–8, 2019; Boston, Massachusetts
Session V65: Membranes and Channels |
Hide Abstracts |
Sponsoring Units: DBIO Chair: Arman Fathizadeh, University of Texas at Austin Room: BCEC 260 |
Thursday, March 7, 2019 2:30PM - 2:42PM |
V65.00001: Amphiphilic nanoparticles can modify lipid membrane permeability Mukarram Tahir, Alfredo Alexander-Katz Lipid bilayers are the structural foundation of biological membranes and contain a characteristic hydrophobic interior that prevents passive permeation of water and other polar molecules. Proteins embedded in these membranes controllably modify these barrier properties by allowing selecting transport in response to environmental stimuli. Previous work from our group has demonstrated that a certain class of nanoparticles can assume a transmembrane configuration similar to these protein channels, and that charged ligands grafted to these nanoparticles can cross the hydrophobic interior of the membrane at an anomalous rate. In this work, we use molecular dynamics simulations to demonstrate that this ligand flipping behavior is associated with transient water transport across the membrane and can be exploited for altering the permeability of lipid membranes to water and charged solutes. Through a combination of free energy analysis and unbiased simulations, we reveal that this gating ability is sensitive to membrane tension, allowing these nanoparticles to function as synthetic mimics of mechanosensitive membrane channels, and have potential applications ranging from single-cell therapeutics to novel methods of water desalination. |
Thursday, March 7, 2019 2:42PM - 2:54PM |
V65.00002: Direct observation of topological turbulence in the oocyte membrane Jinghui Liu, Tzer Han Tan, Pearson Whitehead Miller, Melis Tekant, Joern Dunkel, Nikta Fakhri Living systems self-organize local interactions into global structures and dynamics. Despite prevalence of such features across biological entities, the underlying self-organization principles have not been fully understood. Here we report on direct observation of a class of biochemical patterns formed during early development in starfish oocytes. The observed patterns maintain long-live structures despite short molecular turn-over times, and each pattern has distinguishing wavelength and orientation in spite of sharing the same local interaction rules. Through field analysis, we find that phase singularity dynamics in the chemical field dominates evolution of observed patterns. The pair interactions between the point singularities drive topological turbulence in phase velocity field. Such topological turbulence shares the same characteristic vortex size across observed patterns, reminiscent of quantum turbulence feature. An Onsager vortex model with pairwise interaction potential captures the essential features of the experimentally observed phase singularity dynamics. We propose topological turbulence in phase velocity field underlies dynamics of the observed self-organized biochemical patterns, propagating order from local molecular to global cellular scales. |
Thursday, March 7, 2019 2:54PM - 3:06PM |
V65.00003: Physical Models of Proton-Pumping Complexes of Mitochondria Membranes Lev Mourokh, Michele Vittadello The models are proposed for all three proton-pumping complexes. The model for Complex IV includes the electron source, electron drain, and three electron sites in between, as well as proton source, proton drain and three proton sites in between. Electon transport occurs along the inner mitochondria membrane and the protons are transferred across the membrane. The chemical potential of the electron source is larger than that of the electron drain, while the protons are pumped to the higher potential.. The middle electron and proton sites are in the close proximity, so their electrostatic interaction facilitates the energy transfer. We suggest that in Complex I the energy exchange is mediated by the conformational changes. In both cases, we use the methods of condensed matter and statistical physics to derive quantum equations of motion for the electron and proton operators in the presence of protein environment and to calculate the electron and proton currents. In the model of the Complex III, we couple the equations of motion to phenological Langevin equation describing electron and proton transport by quinons. |
Thursday, March 7, 2019 3:06PM - 3:18PM |
V65.00004: Nanovesicles versus Nanoparticle-Supported Lipid Bilayers: Differences in Equilibrium Structures and Properties Unraveled by Molecular Dynamics Simulations Haoyuan Jing, Yanbin Wang, Parth Rakesh Desai, Kumaran Ramamurthi, Siddhartha Das Molecular Dynamics (MD) simulations are conducted to unravel the equilibrium properties of the nanoparticle-supported lipid bilayers (NPSLBLs) in atomistic details and the findings are compared with that of the similar-sized nanovesicles (NVs). Three key differences emerge. First, the NV is found to contain significantly larger number of lipid molecules in the outer layer/leaflet, while the NPSLBL has equal number of lipid molecules in inner and outer layers. Second, for the NV the lipid molecules in the outer and inner layers showed identical diffusivities, while for the NPSLBL the diffusivity of the lipid molecules in the outer layer was more than double than that of in the inner layer. Finally, the nanoconfined water (located in the cavity for the NV, while being present as a few layers between the inner leaflet and the NP core for the NPSLBL) showed much lesser diffusivity for the NPSLBL as compared to that for the NV. The findings will be key to better understand the structure of this important nanomaterial (namely NPSLBL) with applications in a plethora of disciplines ranging from targeted drug and gene delivery to characterization of curvature-sensitive biomolecules. |
Thursday, March 7, 2019 3:18PM - 3:30PM |
V65.00005: Microfluidic Generation of Giant Lipid Vesicles with Membrane Protein Reconstitution Anqi Chen, Yuting Huang, David A Weitz Giant unilamellar lipid vesicles(GUV) are clean experimental models to study the biophysical mechanisms of biomembranes and transmembrane proteins from a quantitative point of view. Traditional generation methods of GUVs like rehydration or electroswelling produce vesicles with a wide size and composition distribution. These drawbacks limit experiment accuracy, and thus hinder the capacity of experiments to validate theoretical models in lipid membrane biophysics. Here we present a microfluidic emulsion template method to generate monodispersed lipid vesicles with transmembrane protein reconstitution. Compared to other emulsion-templated methods, our protocol allows a wider range of lipid choices, eliminates the influence of residual solvents, requires a shorter incubation time for solvent evaporation, and supports fabrication of lipid vesicles with more complicated structures. Our method opens up opportunities for more quantitative lipid membrane-related experiments and are also potential candidates in synthetic biology constructions. |
Thursday, March 7, 2019 3:30PM - 3:42PM |
V65.00006: Thermodynamic equilibrium of lipid mixtures on curved substrates Piermarco Fonda, Luca Giomi, Daniela Jutta Kraft, Melissa Rinaldin It has been known since long that thermodynamic stability of two-dimensional lipid mixtures is influenced by curvature. Inspired by recent experimental results on lipid membranes coated on colloidal scaffolds, we propose a simple and general framework for interpreting the phase diagram of inhomogeneous closed systems. When the critical behaviour of a system is affected by its shape, we further show how new thermodynamic states can arise in the phase diagram, where lipids are in a mixed phase yet exhibit strong lateral segregation. We prove how different types of inhomogeneous couplings must induce qualitatively different phenomena - such as a curvature dependent line tension - and thus provide a way to distinguish different types of curvature interactions. |
Thursday, March 7, 2019 3:42PM - 3:54PM |
V65.00007: Numerical simulations of intracellular membranes of high genus David Yllanes, George Lykotrafitis, Greg Huber Bilayer membranes within eukaryotic cells adopt dynamic geometries of extraordinary complexity and interdependency. Examples include the continuous vesicular traffic of the endocytic and secretory pathways, the layers of the Golgi apparatus, the inner membranes of mitochondria, and the sheets, tubes, and, indeed, the nuclear envelope itself, comprising the endoplasmic reticulum. Some of these have topological genus zero (or near zero) while others have very high genus. |
Thursday, March 7, 2019 3:54PM - 4:06PM |
V65.00008: Simulation of the passive permeation of potassium ion through phospholipid membranes: Thermodynamics and kinetics Arman Fathizadeh, Ron Elber Here we revisit the problem of passive ion permeation through a phospholipid membrane and find new rich mechanisms that were not captured in earlier investigations by introducing new coarse variables. Numerous experimental and simulation studies have been performed on passive permeation through membranes. Most of simulation studies only consider one reaction coordinate that is the vertical position of the center of mass of the permeant with respect to the center of mass of the membrane. However, when the permeant is positively charged, it interacts stronlgy with the phosphate groups and permeation is accompanied by significant distortions of the membrane. To model ther distortion of the membrane, we introduce two new coarse variables: the minimal distances of the positively charged group from the phosphate groups of each leaflet. We illustrate the efficiency of this new set of coarse variables on permeation of a single potassium ion. Using Milestoning, we were able to calculate free energy landscape, mean first passage time, and the permeability of the ion in the space of the two new coarse variables. The results compared favorably to the available experimental data. |
Thursday, March 7, 2019 4:06PM - 4:18PM |
V65.00009: Assembly of mechanosensitive channels can regulate whole cell volume Smitha Hegde, Alexandru Paraschiv, Andela Saric, Teuta Pilizota E.coli’s membrane embedded mechanosensitive channels (MSC) protect them from bursting when the intracellular osmotic pressure increases due to hyposmotic shock. MSC sense an increased membrane tension and respond by opening a large pore to passively let out cytoplasmic solutes. Using epifluorescence microscopy to look at single E.coli cells, we previously demonstrated that upon a hyposmotic shock cells rapidly swell due to water diffusion into the cytoplasm. Subsequently, MSC open to recover cell volume and osmotic pressure by solute efflux which lasted upto few minutes. Our phenomenological model explained the observed dynamics, however, could not capture large cell-to-cell variability. So, we propose a coarse-grained model which considers MSC dynamic aggregation and incorporate into the phenomenological model. Results suggests that MSC cluster at lower membrane tensions and disaggregate at higher membrane tensions, altering MSC’s opening probability, which also depended on tension. Additionally, we constructed a hepta-mutant (all 7 MSC genes deleted) and show that upon hyposmotic shock, the mutant swells but fails to recover cell volume; we illustrate the cells’ survivability and dynamics of death when they fail to restore internal pressure. |
Thursday, March 7, 2019 4:18PM - 4:30PM |
V65.00010: Membranes and Machine Learning: Designing a Model of Antibiotic Activity to Bypass Gram Negative Membranes and Efflux Pumps Rachael Mansbach, Cesar López, Nicolas Hengartner, Helen Zgurskaya, S Gnanakaran Due to the growing prevalence of antibiotic-resistant bacteria, there is a pressing need for rapid design of new antibiotics with unique modes of action. Gram negative bacteria in particular pose a thorny problem for antibiotic design due to the combined effects of their impermeable outer membranes and their antibiotic-removing efflux pumps. We employ a combined theoretical and experimental approach to understand the limiting factors on antibiotic efficacy in p. aeruginosa and rationally design experiments to rapidly zero in on promising antibiotic candidates. By using machine learning to identify a relevant subset of descriptors produced by simulation and experiment for predicting experimentally-measured minimum inhibitory concentrations of different antibiotic candidates, we are able to learn a self-consistent model of antibiotic retention based on a simple kinetic approximation. We separately employ a Gaussian process regressor to direct a search for antibiotic candidates with optimal experimental and simulated properties. This work leads to heightened understanding of the qualities important to antibiotic retention in Gram negative bacteria and offers a simple way to narrow the experimental design space of antibiotic candidates, allowing for rapid, high-throughput screening. |
Thursday, March 7, 2019 4:30PM - 4:42PM |
V65.00011: Diffusion Rate of Cholesterol through a Single Lipid Bilayer Yangmingyue Liu, Michael Stanfield, Neti Bhatt, Arthur Ralko, Wonwha Cho, Justin Lorieau, Ursula Perez-Salas Our lab has measured the rate and energetics of the intramembrane diffusion (flip-flop) of the steroid-lipid cholesterol using small angle neutron scattering (SANS) and found that the diffusion rate was much slower (hundreds of minutes) than the accepted value (under a second). Our work showed that the discrepancy was due to artifacts produced by differences between cholesterol and its analogues or by the use of compounds, like cyclodextrin, that, our group argued, disrupts the membrane. Our results were based on measurements in which cholesterol flip-flop within the membrane occurred while cholesterol was also diffusing between different membranes (exchange). So, our team has been taking steps to eliminate exchange from the measurement, thus measuring the flip-flop diffusion rate directly. We used a new method to craft an asymmetric distribution of cholesterol in the lipid bilayers of unilamellar vesicles to measure the rate at which cholesterol diffuses through the bilayer. We used orthogonal cholesterol sensors, nuclear magnetic resonance spectroscopy (NMR), and SANS in order to follow the change of cholesterol’s distribution within the bilayers as a function of time and temperature. |
Thursday, March 7, 2019 4:42PM - 4:54PM |
V65.00012: Real-time measurements of lipid domain rearrangements, membrane thickness, and intermembrane forces during membrane hemifusion Kai Kristiansen, Dong Woog Lee, Stephen Donaldson, Nicholas Cadirov, Xavier Banquy, Jacob Israelachvili We have developed a Fluorescence Surface Forces Apparatus (FL-SFA), which can fluorescently image the surfaces while measuring interaction forces and distance between surfaces in real-time. Using the FL-SFA, hemifusion of two supported model lipid bilayers was monitored. At the membrane-membrane contact, the localization of liquid disordered phases and depletion of liquid ordered domains are observed during lipid membrane hemifusion. Interaction forces and lipid membrane thicknesses are simultaneously measured together with the fluorescence images of model membranes. The results show that the domain rearrangements decrease the energy barrier to fusion illustrating the significance of dynamic domain transformations in membrane fusion processes. Importantly, the FL-SFA can unambiguously correlate interaction forces and in situ imaging in many dynamic interfacial systems. |
Thursday, March 7, 2019 4:54PM - 5:06PM |
V65.00013: Influence of Pressure-Induced Fluid Flow on DNA Translocation Dynamics in Solid-State Nanopores Kun Li, Derek Stein We studied the translocation dynamics of DNA through solid-state nanopores under the influence of an electrokinetic driving force and a pressure-driven fluid flow. Through the use of long, λ-DNA molecules, we sought to probe conformation-dependent translocation modes that were not observable in the pioneering experiments of Lu et al. (Nano Lett. 2013 Jul 10; 13(7): 3048–3052) on short molecules. We fabricated nanopores in 10-nm thick SiN membrane using the controlled dielectric breakdown (CBD) technique, which gave useable nanopores about 90% of the time. Then a pressure difference was applied across the nanopore to provide a drag force to counter the electrokinetic driving force. We monitored the disruptions of the ionic current through the nanopore and studied the influence of the applied pressure on the distribution of translocation times and the integrated charge deficits (ECDs) of λ-DNA translocations. We present the results of measurements with applied pressures ranging from 0 to 300 kPa and a theoretical analysis that models the initial polymer configurations and the fluid and electrokinetic force profiles. |
Thursday, March 7, 2019 5:06PM - 5:18PM |
V65.00014: Improving membrane protein expression by optimizing simulated integration efficiency Michiel Niesen, Thomas Miller Integral membrane proteins (IMPs) are critical for the transport of information and matter across the cell membrane. However, their study is often hindered by difficulties in obtaining sufficient purified IMP using heterologous overexpression. |
Thursday, March 7, 2019 5:18PM - 5:30PM |
V65.00015: A Biophysical Model of Intermediate Phases in Developing Cell Plates. Muhammad Zaki Jawaid, Georgia Drakakaki, Daniel Lee Cox Plant cell cytokinesis is a fascinating process that involves the formation of a cell plate via a homotypic fusion of vesicles. Cell plate formation depends on organized vesicle delivery, accumulation, fusion, and membrane maturation, along with the timely deposition of polysaccharides such as callose, cellulose, and cross-linking glycans. One unanswered question is the role of callose in cell plate formation1. We hypothesize that callose deposition produces an anisotropic driving force that acts along the periphery of the cell plate. A biophysical model based on the Helfrich general shape equation2 is presented to explain flat regions within the developing cell plate. The increase in callose deposits is reflected in the increase of membrane area and the anisotropic driving force. By postulating a force per callose polymer of 0.25-0.3pN, as well as an osmotic pressure difference of 0.01MPa and a finite surface tension of 0.0014N/m, we can achieve stable disks of radius 80-100nm, in agreement with observed sizes corresponding to intermediate stages of plate development. |
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