Bulletin of the American Physical Society
APS March Meeting 2018
Volume 63, Number 1
Monday–Friday, March 5–9, 2018; Los Angeles, California
Session R55: Soft Materials Containing Synthetic Polymers, Peptides, Proteins, Biomachinery and Beyond I: Peptides and AssembliesFocus
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Sponsoring Units: DPOLY DBIO Chair: Ting Xu, Univ of California - Berkeley Room: LACC 515A |
Thursday, March 8, 2018 8:00AM - 8:12AM |
R55.00001: Molecular knots: discovering privileged topologies with self-assembling models Mattia Marenda, Enzo Orlandini, Cristian Micheletti Molecular knots are increasingly studied not only for their ubiquity in biological contexts, but for their distinctive geometrical features and peculiar mechanical behaviour. Reproducing, and harnessing, such properties in controlled contexts is one of the main objectives of synthetic chemistry where increasingly sophisticated techniques are used to guide the self-assembly of molecular building blocks into constructs with complex topologies [Ayme et. al, Chem. Soc. Rev. 2012]. Following our previous predictive investigation [Polles et al., Nat. Comm., 2015], we present here recent theoretical and computational results showing that schematic, coarse-grained models can help identify privileged topologies for self-assembling constructs. These are knot types that, owing to their geometry and symmetries are ideal target for supramolecular chemistry. The limited set of discovered topologies includes all knot types that have been successfully realised experimentally so far, as well as novel targets. |
Thursday, March 8, 2018 8:12AM - 8:24AM |
R55.00002: Biomolecules for Non-biological Things: Materials Construction through Peptide Design and Solution Assembly Darrin Pochan When using peptides in a self-assembly process, one can take advantage of biomolecular attributes; such as intramolecular folding and secondary structure; in addition to more traditional self-assembling molecular attributes; such as amphiphilicty, hydrogen bonding and electrostatic interactions; to define hierarchical material structure. Furthermore, different self-assembly pathways can be utilized to reproducibly form different nanostructures with the same molecule design. While biomimicry is a powerful guide by which to design new molecules, computational design of new peptides for assembly allows the construction of non-natural, potentially arbitrary structures as well as the use of non-natural chemical functionality within the molecule design targets. A new solution assembled system comprised of coiled coil motifs will be introduced. Depending on the chemical functionality displayed on the exterior of the designed coiled coil bundles, the bundles either remain individually suspended in solution, assemble into 1-d chains, or assemble into 2-D nanomaterials with a desired interbundle packing symmetry, respectively. New peptide building blocks with covalent interactions produce one-dimensional chains and liquid crystalline matter and will be discussed. |
Thursday, March 8, 2018 8:24AM - 8:36AM |
R55.00003: Assembly pathway control of programmable peptide nanomaterials and inorganic templating Yu Tian, Frank Polzer, Huixi Zhang, Kristi Kiick, Jeffery Saven, Darrin Pochan Self-assembly programmability requires specific interactions displayed at specified positions on molecules. We use computationally designed peptides with pre-determined coiled-coil conformations to precisely install local interactions through certain amino acids at certain peptide sequence positions. Primary sequences were designed based on a mathematical model of an anti-parallel, α-helical, homotetrameric coiled-coil bundle. Programmability was achieved with modification of the exterior amino acid residues in the context of desired 2D local symmetries, such as P422 or P222. These designed peptides have shown the ability to self-assemble into 2D nanomaterials. Solution temperature and pH, were explored to kinetically control the assembly process for the accelerated formation of high-quality 2D nanoplatelets; or to drive the assembly process along alternative assembly pathways creating nanomterials with different morphologies, such as nanotubes, nanoplatelets or needles. Furthermore, with modification of an extra included cysteine, these self-assembled peptide nanomaterials can be used to template the growth of gold nanoparticles into controllable organization. |
Thursday, March 8, 2018 8:36AM - 8:48AM |
R55.00004: The Role of Hydrophobicity in the Self-assembly of PDI-peptides Ryan Weber, Martin McCullagh Perylene Diimide (PDI) - peptide derivatives are ideal for the design of switchable |
Thursday, March 8, 2018 8:48AM - 9:00AM |
R55.00005: Site-Mutation of Nucleoporin Consensus Repeats for Understanding Selective Transport of Biomolecules Yun Jung Yang, Shuaili Li, Danielle Mai, Bradley Olsen The nuclear membrane acts as a selective filter that regulates protein transport into the nucleus. The dense nucleoporin matrix rejects non-specific large molecules, and specific binding interactions between FG repeats in nucleoporin and nuclear transport factor (NTF2) allow the passage of specific large molecules. Previously, two nucleoporin-like proteins (NLPs) were designed to mimic selective separation property of nucleoporin. These NLP hydrogels specifically accumulate NTF2 in the hydrogel and allow its rapid penetration. Here, we perform systematic mutations to the NLP sequence to explore how the protein sequence affects transport properties. Mutants are specifically prepared to explore the role of highly conserved regions and electrostatic charge within the sequence. Transport of mutated NTF2 (NTF-W7A), which has lower affinity to FG repeats, is compared to NTF2 to understand the role of binding affinity on transport. Depending on the consensus sequences, the selectivity and transporting rates of NTF and NTF-W7A were changed. This finding gives us a way of tuning permeability and selectivity of biomolecules in the artificial protein gels for filtering and separation technologies. |
Thursday, March 8, 2018 9:00AM - 9:12AM |
R55.00006: Mesoscale properties of phase-separated polymers under confinement and their size scaling Marjan Shayegan, Radin Tahvildari, Kimberly Metera, Stephen Michnick, Sabrina Leslie Sensitive visualization and conformational control of biopolymer interactions at super-molecular dimensions is important because it is at these scales that biopolymers undergo liquid-liquid phase separation inside cells. For example, the phase separation of proteins and nucleic acids from other material inside the cell results in the formation of non-membranous organelles (NMOs). These structures have important functions, but it is unclear how the nanoscale confinement inside the cell may regulate their physical properties. We address this question by using confinement microscopy to gently load polymers into a nanofabricated array of pits. We have tested this approach using solutions of two water-soluble polymers, polyethylene glycol and dextran, as a model system, as well as a reconstituted model of NMOs phase separated from a solution mixture of protein and nucleic acid. Droplets of various sizes (from less than 1 to 20 μm in diameters) were formed under confinement. Particle tracking microrheology was performed to study the mesoscale properties of phase separated droplets in order to explore the relationship between droplet sizes and their internal diffusion properties. In both systems, crowding-induced sub-diffusion as well as spatial heterogeneity are observed. |
Thursday, March 8, 2018 9:12AM - 9:48AM |
R55.00007: Wetting on patchy, protein-like surfaces Invited Speaker: Francesco Stellacci In this talk I will review the field recent progresses in trying to understand the work of adhesion for water on surfaces composed of hydrophobic and hydrophilic patches. The key fundamental question that will be addressed will be that on the additivity (or lack thereof) of the work of adhesion. A series of experiments will be presented to try to prove that the work of adhesion is, in fact, non-additive and that there is a significant structural component to it. In particular new resutls comparing patchy particles identical in everything but the morphology of the ligand shell will be presented. Recent literature will be discussed and novel water structure interfacial spectroscopy results will be shown and discussed. |
Thursday, March 8, 2018 9:48AM - 10:00AM |
R55.00008: Changes in Lipid Bilayer Dynamics caused by the HIV-1 Fusion Peptide William Heller, Piotr Zolnierczuk HIV-1 fusion with a cell membrane involves the interaction between a sequence from the gp41 capsid protein, termed the fusion peptide (FP), and the membrane. To better understand how this transition drives fusion, the interaction between a variant of the HIV-1 gp41 FP with vesicles was studied using neutron spin echo spectroscopy, small-angle neutron scattering and circular dichroism spectroscopy. In the model membrane studied here, the FP associates with membranes as an alpha-helix at the relatively low peptide-to-lipid ratio of 1/200, but was observed to possess a beta-sheet structure at a peptide-to-lipid ratio of 1/50. The concentration-dependent helix-to-sheet transition correlates with slower vesicle dynamics that are consistent with a more rigid vesicle structure. The results provide new insight into how the FP conformational transition drives vesicle fusion. |
Thursday, March 8, 2018 10:00AM - 10:12AM |
R55.00009: Surface Immobilization Of Antimicrobial Peptide (AMP) For Use In Antibacterial Coating Sasmita Majhi, Ankita Arora, Abhijit Mishra Bacterial colonization leading to biofilm formation on surfaces is a common threat to patient safety and health care units. One approach to address this prevailing problem is to develop antibacterial coatings on such surfaces. In addition, using antimicrobial peptides (amps) as the antibacterial agent in such coatings is advantageous because of their broad spectrum antimicrobial activity, low propensity towards pathogen resistance and low immune response. Herein we immobilize designed peptide, CKLR, onto amine coated polystyrene plates using different cross linkers suitable for covalent attachment of peptide such as: EDC, NHS-PEG-Mal and Sulfo-SMCC; to investigate its effect on orientation of peptide and then the associated antibacterial activity. Immobilized surfaces are then subjected to biophysical characterizations including surface topography, wettability, elemental composition and peptide segregation. Further antibacterial efficacy of developed surface is determined using colony forming unit assay, membrane integrity assay and anti-biofilm assay. Immobilized CKLR shows significant reduction in bacterial viability post-contact with coated surface for both gram positive and gram negative bacteria. |
Thursday, March 8, 2018 10:12AM - 10:24AM |
R55.00010: Catalysis in Stimuli-Responsive Nanoreactors: Towards Colloidal Enzymes and Feedback Control Rafael Roa, Won Kyu Kim, Matej Kanduč, Joachim Dzubiella Responsive nanoreactors are composed of catalytically active nanoparticles coated by a stimuli-responsive polymer shell, whose permeability controls the activity of the process. The shell permeability, and with that the catalytic reaction, can adjust with the properties of the environment and thus can be flexibly tuned and switched, e.g., by the temperature [1], salt concentration, or solvent composition. We provide a general theory for diffusion-influenced reactions for a wide class of emerging nanoreactors, explicitly including shell permeability effects [2,3,4]. Our theory enables to rationally design nanoreactor activity and selectivity. Furthermore, the chemo-mechanical coupling in these nanoreactors is highly nonlinear and can lead to fascinating feedback-controlled phenomena like self-regulatory or oscillating catalysis, serving as a starting point for adaptive and programmable nanocatalysis and the development of colloidal-scale enzymes. |
Thursday, March 8, 2018 10:24AM - 10:36AM |
R55.00011: Development of Catalytic Materials Based on the Stabilization of Organophosphorus Hydrolase in Organic Solvents Christopher DelRe, Brian Panganiban, Baofu Qiao, Charley Huang, Tim Li, Patrick Dennis, Monica Olvera De La Cruz, Ting Xu Organophosphates (OPs) are a class of acutely toxic nerve agents that have frequently been employed in chemical warfare and as pesticides. Recent events around the globe involving these chemicals – including the reported use of VX and sarin gas on civilians – combined with the 3 million annual cases of pesticide poisoning demonstrate the need to develop methods for effective degradation of and protection against exposure to OPs. Organophosphorus hydrolase (OPH) is an enzyme that has been shown to efficaciously degrade OPs, making OPH a promising building block for a functional catalytic material. However, many materials processing techniques require the use of organic solvents, in which OPH denatures and precipitates. |
Thursday, March 8, 2018 10:36AM - 10:48AM |
R55.00012: Local Heterogeneous Domains Drive Stability of Proteins in Non-Aqueous Solution Baofu Qiao, Brian Panganiban, Ting Xu, Monica Olvera De La Cruz Local heterogeneous environment provide much richer phenomena than homogeneous solutions. For instance, our recent work reveals the presence of finger-shaped water channels at water-oil interface, which facilitate ion transport.1 Another example is the hydrophilic and hydrophobic patches covering the surface of globular proteins. In the present work, the influences of these surface heterogeneous domains are quantified in stabilizing the structures and activities of proteins in organic solvent with the assistance of amphiphilic random heteropolymers. By means of all-atom, explicit solvent molecular dynamics simulations we quantify the adsorption of the random copolymer surfactant onto the hydrophilic patches of the protein surface. The protein-polymer complex forms a giant core-shell structure dissolved in organic solution. This work thus shed significant insights for the remarkable impacts of small-size heterogeneous domains. |
Thursday, March 8, 2018 10:48AM - 11:00AM |
R55.00013: Nature-Inspired Polymer Design with Protein-Like Functionality Tao Jiang, Baofu Qiao, Monica Olvera De La Cruz, Ting Xu Nature has shown the power of directing functional protein folding according to protein principles. It is intriguing to test our understanding of those rules by designing synthetic protein analogues. This endeavor holds potentials for creating biomaterials beyond nature’s capability. The major challenge lies in the lack of effective strategies to transfer protein information encoded in protein sequences to synthetic scaffolds. It is challenging to synthesize high molecular weight linear molecules with precise sequence control as demonstrated in protein primary structures. Here we design protein-like polymer folding in biological membrane, leading to channel protein’s bioactivity. We use copolymers comprising different monomers to tailor polymer-polymer, and polymer-membrane interactions through adjusting polymer amphiphilicity and Coulombic charges, following folding rules of transmembrane proteins. Experimental results suggest that several polymers adopt a transmembrane protein-like shape in membrane environment, and function as efficient ion transporters. The unnatural polymers represented here provide robust starting scaffolds for generating biomimetic soft materials with great chemical diversity and processibility. |
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