Bulletin of the American Physical Society
APS March Meeting 2016
Volume 61, Number 2
Monday–Friday, March 14–18, 2016; Baltimore, Maryland
Session A37: Phase Transitions and Self-Assembly in Biological Systems IFocus
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Sponsoring Units: GSOFT DBIO Chair: Jens Glaser, University of Michigan Room: 340 |
Monday, March 14, 2016 8:00AM - 8:12AM |
A37.00001: Study of the Effect of Ellipsoidal Shape on the Kern and Frenkel Patch Model Thienbao Nguyen, James Gunton, Jeffrey Rickman In their work on the self-assembly of complex structures, Glotzer and Solomon (Nature Materials 6, 557 - 562 (2007)) identified both interaction and shape anisotropy as two of several means to build complex structures. Advances in fabricating materials and new insights into protein biology have revealed the importance of these types of interactions. The Kern and Frenkel (J. Chem. Phys. 118, 9882 (2003)) model of hard spheres carrying interaction patches of various sizes has been used extensively to describe interaction anisotropies important in protein phase transitions. However their model did not also account for shape anisotropy. We studied the role of both shape and interaction anisotropy by applying N=2 and N=4 attractive Kern and Frenkel patches with an interaction range to hard ellipsoids with various aspect ratios and patch coverages. Following Kern and Frenkel, we studied the liquid-liquid phase separation of our particles using a Monte Carlo simulation. We found the critical temperatures for our model using the approximate law of rectilinear diameter and compared them with the original results of Kern and Frenkel. We found that the critical temperatures increased both with aspect ratio and percent coverage. [Preview Abstract] |
Monday, March 14, 2016 8:12AM - 8:24AM |
A37.00002: Effects of Coulomb Repulsion on the Phase Diagram of the Asakura-Oosawa Model Jason Haaga, Elizabeth Pemberton, James Gunton, Jeffrey Rickman We investigate the effect of adding a screened Coulomb charge to a model colloidal system interacting via the Asakura-Oosawa depletion potential. This model has previously been used to study the early stages of amelogenin self-assembly, a crucial process in the formation of dental enamel, by Li et al (Biophysical Journal 101, 2502 (2011)). By employing Monte Carlo simulations, we explore the role of interaction strengths and ranges on phase behavior. We find that charge strength and range have a strong influence on the stable, in the case of long range depletion potential, or metastable, in the case of short range depletion, fluid-fluid phase separation. Coulomb repulsion narrows and flattens the coexistence curve with increasing charge. This talk will also discuss solid-solid transitions present for certain interaction ranges. [Preview Abstract] |
Monday, March 14, 2016 8:24AM - 8:36AM |
A37.00003: Mapping Liquid-liquid protein phase separation using ultra-fast-scanning fluorescence correlation spectroscopy. Ming-Tzo Wei, Shana Elbaum-Garfinkle, Craig B. Arnold, Rodney D. Priestley, Clifford P. Brangwynne Intrinsically disordered proteins (IDPs) are an understudied class of proteins that play important roles in a wide variety of biological processes in cells. We've previously shown that the C. elegans IDP LAF-1 phase separates into P granule-like droplets in vitro. However, the physics of the condensed phase remains poorly understood. Here, we use a novel technique, ultra-fast-scanning fluorescence correlation spectroscopy, to study the nano-scale rheological properties of LAF-1 droplets. Ultra-fast-scanning FCS uses a tunable acoustic gradient index of refraction (TAG) lens with an oil immersion objective to control axial movement of the focal point over a length of several micrometers at frequencies of 70kHz. Using ultra-fast-scanning FCS allows for the accurate determination of molecular concentrations and their diffusion coefficient, when the particle is passing through an excitation volume. Our work reveals an asymmetric LAF-1 phase diagram, and demonstrates that LAF-1 droplets are purely viscous phases which are highly tunable by salt concentration. [Preview Abstract] |
Monday, March 14, 2016 8:36AM - 9:12AM |
A37.00004: Using Symmetry to Design Self-Assembling Protein Cages and Nanomaterials on the Mid-Nanometer Scale Invited Speaker: Todd Yeates Self-assembling molecular structures having diverse cellular functions are widespread in nature. Some of the largest and most sophisticated types are built from many copies of the same or similar protein molecules arranged following principles of symmetry. A long-standing engineering goal has been to design novel protein molecules to self-assemble into geometrically specific structures similar to the extraordinary structures that have evolved in Nature. Practical routes to this goal have been developed by using ideas in symmetry to articulate the minimum design requirements for achieving various types of symmetric architectures, including cages, extended two-dimensional layers, and three-dimensional crystalline materials. The key requirement is that two distinct self-associating interfaces, each conferring one element of rotational symmetry, have to be engineered into the protein molecule (or molecules), following particular geometric specifications. The main principle is that combining two separate symmetry elements into a single molecular entity produces a molecule that necessarily assembles into an architecture dictated by a symmetry group that is the product of the two simpler contributing symmetries. Recent experiments have demonstrated success using a variety of symmetry-based strategies. Strategic variations are emerging that differ from each other with respect to biophysical features such as flexibility vs rigidity in the assembled structures, and with respect to design aspects such as whether the protein interfaces are inherited from natural oligomeric proteins or are designed de novo by advanced computational methods. The success of these strategies has been proven by determining crystal structures of several giant, self-assembling protein cages and clusters (10-25 nm in diameter), created by design. The ability to create sophisticated supramolecular structures from designed protein subunits opens the way to broad applications in synthetic biology and nanotechnology. [Preview Abstract] |
Monday, March 14, 2016 9:12AM - 9:24AM |
A37.00005: Hierarchical assembly of protein nanocrystals into macroscopic gels Daniel Greene, Stanley Sandler, Norman Wagner, Abraham Lenhoff From crystallization screens to downstream processing, protein gel phases are common during protein solution processing. While the structure of crystalline protein is well known, very little is known about the structure of these gel phases. We recently measured the microstructure of a salted-out ovalbumin dense phase and found that nanocrystalline protein clusters, which are only a few unit cells in size, percolate 5 micron gel beads. It is unclear if the behavior seen for ovalbumin is representative of a more general phenomenon. Here we present microstructural measurements on a salted-out monoclonal antibody (mAb) and salted-out ribonuclease-a that support this possibility. Using small-angle x-ray and neutron scattering (SAS) and transmission electron microscopy (TEM), we find both salted-out mAb and ribonuclease-a gels exhibit nanocrystalline regions. Within the mAb gel, the mAb aggregates into hollow tubular structures that are hundreds of nanometers long, have an inner diameter of approximately 15-20 nm and an outer diameter of approximately 20-30 nm. The SAS intensity from these structures contains a peak at high-q that is commensurate with scattering from idealized mAb nanocrystals that are 1-2 unit cells wide. Ribonuclease-a does not appear to from tubular structures, but the SAS intensity contains peaks at high-q that are consistent with the scattering from a nanocrystal 2-3 unit cells wide. Power-law scattering at low-q indicates the nanocrystals aggregate into a gel with fractal dimension 2.5. This research provides insight into the nanostructure and formation of protein gel phases. [Preview Abstract] |
Monday, March 14, 2016 9:24AM - 9:36AM |
A37.00006: The mechanical properties of phase separated protein droplets Louise Jawerth, Mahdiye Ijavi, Avinash Patel, Shambaditya Saha, Frank Jülicher, Anthony Hyman In vivo, numerous proteins associate into liquid compartments by de-mixing from the surrounding solution, similar to oil molecules in water. Many of these proteins and their corresponding liquid compartments play a crucial role in important biological processes, for instance germ line specification in C. elegans or in neurodegenerative diseases such as Amyotrophic lateral sclerosis (ALS). However, despite their importance, very little is known about the physical properties of the resulting droplets as well as the physical mechanisms that control their phase separation from solution. To gain a deeper understanding of these aspects, we study a few such proteins in vitro. When these proteins are purified and added to a physiological buffer, they phase separate into droplets ranging in size from a few to tens of microns with liquid-like behavior similar to their physiological counterparts. By attaching small beads to the surface of the droplets, we can deform the droplets by manipulating the beads directly using optical tweezers. By measuring the force required to deform the droplets we determine their surface tension, elasticity and viscosity as well as the frequency response of these properties. We also measure these properties using passive micro-rheology. [Preview Abstract] |
Monday, March 14, 2016 9:36AM - 9:48AM |
A37.00007: Phase separation and the formation of cellular bodies Bin Xu, Chase P. Broedersz, Yigal Meir, Ned S. Wingreen Cellular bodies in eukaryotic cells spontaneously assemble to form cellular compartments. Among other functions, these bodies carry out essential biochemical reactions. Cellular bodies form micron-sized structures, which, unlike canonical cell organelles, are not surrounded by membranes. A recent in vitro experiment[1] has shown that phase separation of polymers in solution can explain the formation of cellular bodies. We constructed a lattice-polymer model to capture the essential mechanism leading to this phase separation. We used both analytical and numerical tools to predict the phase diagram of a system of two interacting polymers, including the concentration of each polymer type in the condensed and dilute phase. \begin{thebibliography}{1} \bibitem{Rosen} Li P, Banjade S, Cheng HC, Kim S, Chen B, Guo L, Llaguno M, Hollingsworth JV, King DS, Banani SF, Russo PS, Jiang QX, Nixon BT, Rosen MK {\em Phase transitions in the assembly of multivalent signalling proteins} Nature. 2012 Mar 7;483(7389):336-40. \end{thebibliography} [Preview Abstract] |
Monday, March 14, 2016 9:48AM - 10:00AM |
A37.00008: Nucleic Acid-Peptide Complex Phase Controlled by DNA Hybridization Jeffrey Vieregg, Michael Lueckheide, Lorraine Leon, Amanda Marciel, Matthew Tirrell When polyanions and polycations are mixed, counterion release drives formation of polymer-rich complexes that can either be solid (precipitates) or liquid (coacervates) depending on the properties of the polyelectrolytes. These complexes are important in many fields, from encapsulation of industrial polymers to membrane-free segregation of biomolecules such as nucleic acids and proteins. Condensation of long double-stranded DNA has been studied for several decades, but comparatively little attention has been paid to the polyelectrolyte behavior of oligonucleotides. We report here studies of DNA oligonucleotides (10 - 88 nt) complexed with polylysine (10 - 100 aa). Unexpectedly, we find that the phase of the resulting complexes is controlled by the hybridization state of the nucleic acid, with double-stranded DNA forming precipitates and single-stranded DNA forming coacervates. Stability increases with polyelectrolyte length and decreases with solution salt concentration, with complexes of the longer double-stranded polymers undergoing precipitate/coacervate/soluble transitions as ionic strength is increased. Mixing coacervates formed by complementary single-stranded oligonucleotides results in precipitate formation, raising the possibility of stimulus-responsive material design. [Preview Abstract] |
Monday, March 14, 2016 10:00AM - 10:12AM |
A37.00009: The Ion-Specific, Non-Equilibrium Structural Behavior of DNA Hydrogels. Dan Nguyen, Omar Saleh The highly tunable, sequence-dependent hybridization of DNA has enabled construction of DNA hydrogels with applications ranging from drug delivery to responsive materials. Though many have examined the structural characteristics of DNA hydrogels at equilibrium, relatively little is known about their non-equilibrium behavior, apart from their degradation rates when delivering molecular payloads. Here, we examine the effect of changing salt concentration on the dynamic formation, ageing, and degradation of DNA hydrogels comprised of branched DNA nanostars with palindromic overhangs. First, we observe that hydrogel phase is sensitive to the presence of a single unpaired base on the overhang, resulting in either a percolated network or a liquid-liquid phase separated state at high salt concentrations. Particular to the percolated network, we can induce the system to either contract or relax by changing the salt concentration. Decreasing monovalent NaCl induces the network to irreversibly contract whereas decreasing divalent MgCl$_{\mathrm{2}}$ induces the network to reversibly expand; this behavior runs counter to what is expected solely from electrostatic screening. We qualitatively understand these results by assuming that the monovalent salt modulates the dynamic hybridization between nanostar binding partners, whereas the divalent salt drives the dramatic/reversible induction of the `stacked-X' conformation in the DNA nanostars. [Preview Abstract] |
Monday, March 14, 2016 10:12AM - 10:24AM |
A37.00010: Counterion Distribution Around Protein-SNAs probed by Small-angle X-ray scattering Kurinji Krishnamoorthy, Michael Bedzyk, Sumit Kewalramani, Liane Moreau, Chad Mirkin Protein-DNA conjugates couple the advanced cell transfection capabilities of spherical DNA architecture and the biocompatible enzymatic activity of a protein core to potentially create therapeutic agents with dual functionality. An understanding of their stabilizing ionic environment is crucial to better understand and predict their properties. Here, we use Small-angle X-ray scattering techniques to decipher the structure of the counterion cloud surrounding these DNA coated nanoparticles. Through the use of anomalous scattering techniques we have mapped the local concentrations of Rb$^{+}$ ions in the region around the Protein-DNA constructs. These results are further corroborated with simulations using a geometric model for the excess charge density as function of radial distance from the protein core. Further, we investigate the influence of solution ionic strength on the structure of the DNA corona and demonstrate a reduction in the extension of the DNA corona with increasing concentration of NaCl in solution for the case of both single and double stranded DNA shells. Our work reveals the distribution of counterions in the vicinity of Protein-DNA conjugates and decouples the effect of solution ionic strength on the thickness of the DNA layer. [Preview Abstract] |
Monday, March 14, 2016 10:24AM - 10:36AM |
A37.00011: Electrolyte-Mediated Assembly of Charged Nanoparticles Sumit Kewalramani, Michael Bedzyk, Guillermo Guerrero-García, Liane Moreau, Jos Zwanikken, Chad Mirkin, Monica Olvera de la Cruz Solutions at high salt concentrations are used to crystallize or segregate colloids, proteins and polyelectrolytes via an unknown mechanism referred to as ``salting-out''. Here, we show salting-out is a long-range interaction controlled by electrolyte concentration and nanoparticle charge density. Small-angle X-ray scattering (SAXS) shows that DNA-coated Au nanoparticles designed to prevent inter-particle assembly via Watson-Crick hybridization undergo ``gas'' to FCC to ``glass-like'' transitions with increasing NaCl or CaCl$_{\mathrm{2\thinspace }}$concentration. Simulations reveal that the crystallization is concomitant with inter-particle interactions changing from purely repulsive to a long-range potential well condition. Liquid-state theory explains this attraction as a sum of cohesive and depletion forces. Our work reveals the mechanism behind salting-out and suggests new routes for the successful crystallization of colloids and proteins using concentrated salts. [Preview Abstract] |
Monday, March 14, 2016 10:36AM - 10:48AM |
A37.00012: Modeling of DNA-Mediated Self-Assembly from Anisotropic Nanoparticles: A Molecular Dynamics Study Jaime Millan, Martin Girard, Jeffrey Brodin, Matt O'brien, Chad Mirkin, Monica Olvera de la Cruz The programmable selectivity of DNA recognition constitutes an elegant scheme to self-assemble a rich variety of superlattices from versatile nanoscale building blocks, where the natural interactions between building blocks are traded by complementary DNA hybridization interactions. Recently, we introduced and validated a scale-accurate coarse-grained model for a molecular dynamics approach that captures the dynamic nature of DNA hybridization events and reproduces the experimentally-observed crystallization behavior of various mixtures of spherical DNA-modified nanoparticles. Here, we have extended this model to robustly reproduce the assembly of nanoparticles with the anisotropic shapes observed experimentally. In particular, we are interested in two different particle types: (i) regular shapes, namely the cubic and octahedral polyhedra shapes commonly observed in gold nanoparticles, and (ii) irregular shapes akin to those exhibited by enzymes. Anisotropy in shape can provide an analog to the atomic orbitals exhibited by conventional atomic crystals. We present results for the assembly of enzymes or anisotropic nanoparticles and the co-assembly of enzymes and nanoparticles. [Preview Abstract] |
Monday, March 14, 2016 10:48AM - 11:00AM |
A37.00013: Two-stages of chiral selectivity in the molecular self-assembly of tryptophan Nathan Guisinger Both chirality and molecular assembly are essential and key components to life. In this study we explore the molecular assembly of the amino acid tryptophan (both L- and D- chiralities) on Cu(111). Our investigation utilizes low temperature scanning tunneling microscopy to observe resulting assemblies at the molecular scale. We find that depositing a racemic mixture of both L- and D- tryptophan results in the assembly of basic 6 molecule ``Lego'' structures that are enantiopure. These enantiopure ``Legos'' further assemble into 1-dimensional chains one block at a time. These resulting chains are also enantiopure with chiral selectivity occurring at two stages of assembly. Utilizing scanning tunneling spectroscopy we are able to probe the electronic structure of the chiral Legos that give insight into the root of the observed selectivity. [Preview Abstract] |
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