Bulletin of the American Physical Society
APS March Meeting 2020
Volume 65, Number 1
Monday–Friday, March 2–6, 2020; Denver, Colorado
Session D35: Biopolymers, Polymer Bioconjugates, and Their Self-Assembled PhasesFocus
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Sponsoring Units: DPOLY DSOFT Chair: Thomas Angelini, University of Florida Room: 507 |
Monday, March 2, 2020 2:30PM - 2:42PM |
D35.00001: Asymmetric Lipid/Polymer Vesicles Yuting Huang 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 for cell membranes and can be used for drug delivery. Similarly, block copolymers are amphiphilic molecules that form vesicles by themselves or with lipids. Like lipid vesicles, polymer vesicles can also be used for drug delivery and cell membrane mimicry. One interesting type of lipid/polymer vesicle is the asymmetric vesicle, in which its bilayer is composed of two dissimilar lipid monolayers or a lipid monolayer and a polymer monolayer. 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 vesicles, which unlike the conventional methods that often end up wit |
Monday, March 2, 2020 2:42PM - 2:54PM |
D35.00002: Polyelectrolyte dynamical self-consistent field theory Sylvia Luyben, Robert Wickham Recent experiments that examine the reconstitution of proteins into artificial triblock copolymer membranes have implicated a charge-driven reconstitution mechanism. As a first step to model the dynamics of this mechanism, we incorporate electrostatic interactions into dynamical self-consistent field theory. We begin with microscopic Langevin equations for interacting polyelectrolytes, solvent, and counterions. These equations are recast as a dynamical functional integral over collective field variables. We then make a saddle-point approximation, leading to a coupled set of dynamical mean field equations which includes the Poisson equation governing the electrostatic potential. Our approach reduces the interacting many-chain problem to a single polyelectrolyte chain in a dynamical mean force field. This simplification enables us to probe a broad range of length- and time-scales. We simulate the dynamics of insertion of a charged triblock copolymer (a model protein) into an oppositely-charged, self-assembled, triblock copolymer membrane. |
Monday, March 2, 2020 2:54PM - 3:06PM |
D35.00003: Dynamics of self-interacting bio-inspired polymers in shear flows Helman Amaya-Espinosa, Alfredo Alexander-Katz, Camilo Aponte-Santamaría Biopolymers interact with each other, triggered by external stimuli, to carry out key biological functions. Blood clotting is a perfect example of that. Triggered by the shear of the flowing blood, the giant von Willebrand factor (VWF) adhesive protein establishes specific interactions with several partners, including with itself via specific protein-protein auto-inhibitory interactions. However, the impact of such self-interactions on the flow-induced non-equilibrium conformational dynamics of such polymers remained unclear. We tackled this question by implementing Brownian dynamics simulations at a coarse-grained resolution of VWF-like self-interacting biopolymers. In the absence of specific interactions, we recapitulated previous estimates of the critical shear-rate upon which the polymer underwent a globular-to-stretched conformation. Introduction of specifically interacting points within the polymer, increased the critical shear-rate roughly by an order of magnitude. Accordingly, our data demonstrate that the state of self-interacting biopolymers, under shear flows, can be effectively tuned by increasing either the number or the strength of self-interacting units. This information is highly useful to understand how specific-molecular interactions modulate VWF assembly. |
Monday, March 2, 2020 3:06PM - 3:18PM |
D35.00004: Computational prediction of molecular shape through the assembly of sequence-controlled polymers Davindra Tulsi, David Simmons Nature employs molecular sequence to control macromolecular shape in order to realize exquisite control over biological nanostructures such as protein assemblies, membranes and DNA complexes. Over the last decade, significant strides have been made in synthesizing artificial sequence-controlled polymers, potentially paving the way for synthetic materials mimicking biological nanostructures. Further advances are hindered by the fact that the relationship between sequence and molecular shape remains poorly understood. Here we employ molecular dynamics simulations to probe the relationship between sequence and molecular shape in model synthetic polymers. Results point to a conformation diagram that provides fundamental physical insights towards design of molecular building blocks for hierarchical assembly. |
Monday, March 2, 2020 3:18PM - 3:30PM |
D35.00005: Bottom-up Coarse-grained Molecular Simulations of Peptoids with Enhanced Sampling Mingfei Zhao, Janani Sampath, Christopher J Mundy, Jim Pfaendtner, Andrew L Ferguson Peptoids are a class of synthetic polymers that have similar biocompatibility but high stability compared to peptides. Peptoids can both self-assemble into highly ordered nanostructures and direct the organization of inorganic components. Computational modeling is promising in helping discover and design peptoid-based nanomaterials. Atomistic peptoid models have been developed but only consider small systems due to high computational costs. To reach the time and length scale of peptoid assembly, we develop a coarse-grained (CG) model reparametrized from all-atom (AA) simulations by fitting CG bonded interactions through iterative Boltzmann inversion and nonbonded interactions through potential of mean force matching. We use Parallel Bias metadynamics to obtain good sampling in the cis/trans isomerization. The proposed CG model demonstrates excellent agreement with AA distribution functions and opens a new avenue to the computational inverse design of peptoid-based nanomaterials. |
Monday, March 2, 2020 3:30PM - 3:42PM |
D35.00006: Solution Self-Assembly of Block Copolypeptoids with a Crystallizable Core-Forming Block Naisheng Jiang, Tianyi Yu, Shuo Qian, Igor Kevin Mkam Tsengam, Vijay T John, Donghui Zhang In this study, we investigate the solution self-assembly of coil-crystalline diblock copolypeptoids with one polypeptoid block having long n-alkyl side chains. Poly(N-methyl glycine)-b-poly(N-decyl glycine) (i.e. PNMG-b-PNDG) with lower volume fraction of the crystalline PNDG blocks were found to slowly self-assemble into one-dimensional long worm-like nanofibrils in methanol, which is induced by the crystallization of core-forming PNDG. Upon increasing volume fraction of PNDG, the final micellar morphology changed from worm-like nanofibrils to rigid short nanorods and then two-dimensional nanosheets. The molecular arrangement and self-assembly pathways of these anisotropic nanostructures were investigated by a combination of X-ray/neutron scattering and microscopic techniques to understand the underlying assembly mechanism. We believe the relationship between chemical composition, micellar morphology and self-assembly pathway provided here would not only benefit the rational design of polypeptoid-based nanostructures with tunable size, shape and morphology, but also shed lights on the crystallization-driven self-assembly of comb-shaped polymers bearing long aliphatic side chains in general. |
Monday, March 2, 2020 3:42PM - 4:18PM |
D35.00007: Transforming protein-polymer conjugate purification by tuning protein solubility Invited Speaker: Alan Russell Almost all commercial therapeutic and industrial proteins are purified by processes that include salting-out precipitation in ammonium sulfate. Protein-polymer conjugates are generally synthesized from already pure starting materials and the struggle to separate the conjugates from polymer, native protein, and from differently modified variants has vexed scientists for decades. Since ammonium sulfate precipitation is exclusively used as an initial step in crude protein purifications, it has had little relevance in the delicate purification of protein-polymer conjugates. We have discovered, however, that polymers grown from the surface of proteins have a transformational effect on the solubility of proteins in salt solutions. We generated a family of protein-polymer conjugates with a variety of polymers, grafting densities, and polymer lengths using surface-initiated atom transfer radical polymerization. Covalently attached polymers increased solubility of the conjugates in ammonium sulfate and completely prevented precipitation. Molecular dynamic simulations showed the impact was driven by an anti-polyelectrolyte effect. We then efficiently and simply purified mixtures of conjugates and native proteins. |
Monday, March 2, 2020 4:18PM - 4:30PM |
D35.00008: Characterization of Fiber Formation of Sugar-based Poly(D-glucose carbonate) Amphiphilic Block Copolymers in Solution Jee Young Lee, Yue Song, Karen L Wooley, Darrin John Pochan Designing the new sugar-derived poly(D-glucose carbonate)s (PGC) is motivated by a need to develop sustainable materials in response to a long-term environmental impact of traditional petroleum-based polymers. Herein, the fiber assembly behavior of the PGC amphiphilic BCP with targeted block compositions, chain lengths and side chain chemistries are explored with kinetically controlled assembly pathways varying the solvent compositions. The kinetics of the fiber formation is characterized using cryogenic-TEM and SANS where we find the assembled fibers have a flat interface composed of fused disc subunits. The assembly behavior deviates from the traditional coil-based BCPs due to the inherent stiffness of the glucose backbone resulting a unique chain packing in response to a solvent quality change. To observe the relative chain behavior in the same assembly conditions, both hydrophilic and hydrophobic block equivalent homopolymers are studied using various scattering techniques to obtain polymer chain solution properties for a better understanding of the PGC block copolymer chains. These findings allow us to discover a robust fiber nanostructure that can be achieved by non-traditional polymers and their potential to be used in many engineering applications. |
Monday, March 2, 2020 4:30PM - 4:42PM |
D35.00009: Computationally designed bundlemers for hybrid physical-covalent assembly of rigid polymers Nairiti Sinha, Grethe Vestergaard Jensen, Darrin John Pochan Peptide coiled coils present a diverse toolbox for constructing new polymers that display target nanostructures and properties. Computational prediction of coiled coil-forming peptides enables chain and material construction in which coiled coils, also known as ‘bundlemers’, are the modular building blocks. We use bundlemers that form robust antiparallel homotetramers to construct hybrid physical-covalent, supramolecular polymers. By end-functionalizing peptides with complimentary ‘click’ reactive groups, bundlemers are covalently linked to form polymers displaying desired length distributions and flexibility: a short organic linker between bundlemers yields absolutely rigid rods while a flexible linker yields semi-flexible fibers. Small-Angle Neutron Scattering (SANS) along with Transmission Electron Microscopy (TEM) have been used extensively to characterize the structure of the resulting polymers. Furthermore, recombinant expression of the peptides in Escherichia Coli was used to obtain deuterated bundlemer-forming peptides. This has facilitated contrast-matching experiments in SANS with which we have characterized the stability of bundlemers in solution and also investigated the alternating bundlemer assembly design of rigid rods. |
Monday, March 2, 2020 4:42PM - 4:54PM |
D35.00010: Random Heteropolymer Self-Assembly into Protein-Like Nanoparticles Shayna Hilburg, Ting Xu, Alfredo Alexander-Katz Single-chain polymer nanoparticles are currently of great interest due to their potential applications, yet their properties have only recently started to be elucidated. Here, we study self-assembled single polymer nanoparticles to gain molecular insights into their structure and dynamics using molecular dynamics simulations. In particular, we study a four-component synthetic heteropolymer that has been experimentally investigated previously. Prior experimental findings showed favorable interactions with native proteins in non-native environments and during protein folding. Simulations of single chains demonstrate a rich energy landscape for these polymers, evident from the structure and dynamics of the molecules in solution. Specifically, spatial arrangement of amphiphilic monomers is characterized and shows many parallels to biological proteins. Multiple time scales are seen in system dynamics, showing a large impact of component chemistry and sterics. By bridging the gap between angstrom-scale NMR and bulk characterization, all-atom simulations provide valuable insight into potential mechanisms for these heteropolymer’s behavior. |
Monday, March 2, 2020 4:54PM - 5:30PM |
D35.00011: Utilizing nonlinearity of biopolymer matrix in both intracellular and extracellular spaces Invited Speaker: Ming Guo Both living cell cytoskeleton and their extracellular matrix are constituted mainly by biopolymer matrices. The physical properties of these matrices are known to significantly impact cell behavior, such as cell morphology, migration, and stem-cell differentiation. However, cells also constantly reorganize these intracellular and extracellular structures during physiological processes; this is thought to also change the mechanics of these biopolymer matrices, which may then have an immediate impact on cell behavior. In this talk, I will present our recent progress on characterizing the drastic local nonlinear matrix stiffening induced by contraction of individual living cells inside a 3D biopolymer matrix, through direct micromechanical measurement. Moreover, I will introduce a method, called Nonlinear Stress Inference Microscopy, with which we can determine the cell-induced local matrix stress from nonlinear microrheology measurements inside various types of extracellular matrix in 3D. In addition, I will also introduce our recent progress on characterizing the significant role of cytoskeletal intermediate filament in determining nonlinear mechanics, strength, toughness, and stretchability of the mammalian cytoskeleton. |
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