Bulletin of the American Physical Society
APS March Meeting 2014
Volume 59, Number 1
Monday–Friday, March 3–7, 2014; Denver, Colorado
Session G16: Focus Session: Soft Matter Perspectives on Protein Self-Assembly I |
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Sponsoring Units: GSNP DBIO DPOLY Chair: Patrick Charbonneau, Duke University Room: 401 |
Tuesday, March 4, 2014 11:15AM - 11:27AM |
G16.00001: Self-assembly of Model Microtubules: Shape, Chirality and Twist Mark Stevens, Shengfeng Cheng The efficient and controlled assembly of complex structures from macromolecular building blocks is a critical open question. Microtubules are one example of a biopolymer that possesses characteristics quite distinct from standard synthetic polymers that are derived from its monomer being a protein. In order to understand microtubule assembly and how to design artificial polymers that possess features similar to those of microtubules, we have used molecular dynamics simulations to study the self-assembly of model monomers into a tubule geometry. The self-assembly of free monomers into tubules yields a tubule pitch that often does not match the chirality of the monomer (including achiral monomers). We show that this mismatch occurs because of a twist deformation that brings the lateral interaction sites into alignment when the tubule pitch differs from the monomer chirality. In order to control the tubule pitch by preventing the twist deformation, we employ a lock-and-key interaction and obtain good control of the self-assembled tubule pitch. These results explain some fundamental features of microtubules. We generally find that the control of the assembly is limited, which explains the range of pitch and protofilament number observed in microtubule assembly. [Preview Abstract] |
Tuesday, March 4, 2014 11:27AM - 11:39AM |
G16.00002: Fibril-based, geometrical microtubule - kinetochore attachments Zsolt Bertalan, Caterina La Porta, Helder Maiato, Stefano Zapperi Mechanical factors involved in regulating the stability of microtubule-kinetochore attachments during cell division are poorly understood. Various aspects of these attachments are essential for proper chromosome segregation. We introduce and simulate a mechanical model of microtubule-kinetochore interactions in which the stability of the attachment is due to the geometrical conformations of curling protofilaments entangled in kinethochore fibrils. The main load of the simulations are done in two dimensions due to the geometric shape of the protofilament curl. However, since the microtubule-kinetochore fibril entanglement is inherently a three dimensional problem, we also model and test the attachment in 3D. The model allows us to reproduce with good accuracy in vitro experimental measurements of the detachment times of yeast kinetochores from MTs under external pulling forces. Numerical simulations also suggest a purely geometrical mechanism that does not require changes in chemical affinities to control the switch between stable and unstable attachments. [Preview Abstract] |
Tuesday, March 4, 2014 11:39AM - 11:51AM |
G16.00003: Nano-structured metallic amyloid fibril networks Kiersten Batzli, Brian Love Amyloid proteins form high aspect ratio fibrillar structures with great chemical and physical stability under specific conditions. By examining the produced networks as novel materials we can envision uses for these high aspect ratio fibrillar structures. Produced fibril networks can be used as templates for the creation of high surface area metallic meshes that may be of use as catalysts or in electronic applications. We have formed fibrillar networks from porcine insulin and have characterized them by TEM, showing that by varying environmental conditions, such as strain rate, the resulting network morphologies may be influenced. We have used electroless deposition techniques to coat insulin fibrils with platinum to produce metallized networks thought to have high catalytic activity. We will present our experience using these coated fibrils to facilitate the reduction of nitrophenol to aminophenol using UV-visible spectroscopy as a gauge. [Preview Abstract] |
Tuesday, March 4, 2014 11:51AM - 12:03PM |
G16.00004: Electrostatic effects in collagen fibrillization Svetlana Morozova, Murugappan Muthukumar Using light scattering and AFM techniques, we have measured the kinetics of fibrillization of collagen (pertinent to the vitreous of human eye) as a function of pH and ionic strength. At higher and lower pH, collagen triple-peptides remain stable in solution without fibrillization. At neutral pH, the fibrillization occurs and its growth kinetics is slowed upon either an increase in ionic strength or a decrease in temperature. We present a model, based on polymer crystallization theory, to describe the observed electrostatic nature of collagen assembly. [Preview Abstract] |
Tuesday, March 4, 2014 12:03PM - 12:15PM |
G16.00005: Surfaces Self-Assembly and Rapid Growth of Amyloid Fibrils Yichih Lin, E. James Petersson, Zahra Fakhraai The mechanism of surface-mediated fibrillization has been considered as a key issue in understanding the origins of the neurodegenerative diseases, such as Alzheimer's and Parkinson's diseases. \textit{In vitro}, amyloid proteins fold through nucleation-elongation process. There is a critical concentration for early nucleating stage. However, some studies indicate that surfaces can modulate the fibril's formation under physiological conditions, even when the concentration is much lower than the critical concentration. Here, we use a label-free procedure to monitor the growth of fibrils across many length scales. We show that near a surface, the fibrillization process appears to bypass the nucleation step and fibrils grow through a self-assembly mechanism instead. We control and measure the pre-fibrillar morphology at different stages of this process on various surfaces. The interplay between the surface concentration and diffusion constant can help identify the detailed mechanisms of surface-mediated fibril growth, which remains largely unexplored. Our works provide a new insight in designing new probes and therapies. [Preview Abstract] |
Tuesday, March 4, 2014 12:15PM - 12:27PM |
G16.00006: Surface Mediated Protein Disaggregation Mithun Radhakrishna, Sanat K. Kumar Preventing protein aggregation is of both biological and industrial importance. Biologically these aggregates are known to cause amyloid type diseases like Alzheimer's and Parkinson's disease. Protein aggregation leads to reduced activity of the enzymes in industrial applications. Inter-protein interactions between the hydrophobic residues of the protein are known to be the major driving force for protein aggregation. In the current paper we show how surface chemistry and curvature can be tuned to mitigate these inter-protein interactions. Our results calculated in the framework of the Hydrophobic--Polar (HP) lattice model show that, inter-protein interactions can be drastically reduced by increasing the surface hydrophobicity to a critical value corresponding to the adsorption transition of the protein. At this value of surface hydrophobicity, proteins lose inter-protein contacts to gain surface contacts and thus the surface helps in reducing the inter-protein interactions. Further, we show that the adsorption of the proteins inside hydrophobic pores of optimal sizes are most efficient both in reducing inter-protein contacts and simultaneously retaining most of the native-contacts due to strong protein-surface interactions coupled with stabilization due to the confinement. [Preview Abstract] |
Tuesday, March 4, 2014 12:27PM - 12:39PM |
G16.00007: Dynamic renormalisation group reveals sequential mechanism of the secondary nucleation of proteins Thomas Michaels, Paolo Arosio, Tuomas Knowles Secondary nucleation has emerged as a key process in the self-assembly of amyloid fibrils associated with a number of neurodegenerative disorders. Secondary nucleation conceptually involves both aggregates and monomers, but a variety of ways exist, in which this process may occur. Elucidation of this complex mechanism using experimental data represents a theoretical challenge. A systematic coarse-graining procedure inspired by the renormalisation group is used to bridge the length- and timescale gaps between detailed microscopic descriptions and the processes observed in experiments. Various mechanisms of secondary nucleation are discussed at different levels of coarse graining and compact terms in the master equation are generated, that provide a single-step description of this process. This treatment is general and allows to test assumptions regarding mechanisms at the microscopic level and to filter their effect on the kinetics at the macroscopic scale. By analysing data from the polymerisation of amylin, we conclude that pre-critical nuclei in islet amyloid polypeptides stay attached to the aggregates during the process of secondary nucleation. [Preview Abstract] |
Tuesday, March 4, 2014 12:39PM - 12:51PM |
G16.00008: The breakup mechanism of biomolecular and colloidal aggregates in a shear flow Breannd\'{a}n \'{O} Conch\'{u}ir, Alessio Zaccone The theory of self-assembly of colloidal particles in shear flow is incomplete. Previous analytical approaches have failed to capture the microscopic interplay between diffusion, shear and intermolecular interactions which controls the aggregates fate in shear. In this work we analytically solved the drift-diffusion equation for the breakup rate of a dimer in flow. Then applying rigidity percolation theory, we found that the lifetime of a generic cluster formed under shear is controlled by the typical lifetime of a single bond in its interior, which in turn depends on the efficiency of the stress transmitted from other bonds in the cluster. We showed that aggregate breakup is a thermally-activated process where the activation energy is controlled by the interplay between intermolecular forces and the shear drift, and where structural parameters determine whether cluster fragmentation or surface erosion prevails. In our latest work, we analyzed floppy modes and nonaffine deformations to derive a lower bound on the fractal dimension df below which aggregates are mechanically unstable, ie. for large aggregates df $\simeq$ 2.4. This theoretical framework is in quantitative agreement with experiments and can be used for population balance modeling of colloidal and protein aggregation. [Preview Abstract] |
Tuesday, March 4, 2014 12:51PM - 1:03PM |
G16.00009: Mechanical and Assembly Units of Viral Capsids Identified via Quasi-Rigid Domain Decomposition Guido Polles, Giuliana Indelicato, Raffaello Potestio, Paolo Cermelli, Reidun Twarock, Cristian Micheletti Key steps in a viral life-cycle, such as self-assembly of a protective protein container or in some cases also subsequent maturation events, are governed by the interplay of physico-chemical mechanisms involving various spatial and temporal scales. These salient aspects of a viral life cycle are hence well described and rationalised from a mesoscopic perspective. Accordingly, various experimental and computational efforts have been directed towards identifying the fundamental building blocks that are instrumental for the mechanical response, or constitute the assembly units, of a few specific viral shells. Motivated by these earlier studies we introduce and apply a general and efficient computational scheme for identifying the stable domains of a given viral capsid. The method is based on elastic network models and quasi-rigid domain decomposition. It is first applied to a heterogeneous set of well-characterized viruses (CCMV, MS2, STNV, STMV) for which the known mechanical or assembly domains are correctly identified. The validated method is next applied to other viral particles such as L-A, Pariacoto and polyoma viruses, whose fundamental functional domains are still unknown or debated and for which we formulate verifiable predictions. [Preview Abstract] |
Tuesday, March 4, 2014 1:03PM - 1:39PM |
G16.00010: Viral genome structures, charge, and sequences are optimal for capsid assembly Invited Speaker: Michael Hagan For many viruses, the spontaneous assembly of a capsid shell around the nu-cleic acid (NA) genome is an essential step in the viral life cycle. Capsid formation is a multicomponent, out-of-equilibrium assembly process for which kinetic effects and thermodynamic constraints compete to determine the outcome. Understand-ing how viral components drive highly efficient assembly under these constraints could promote biomedical efforts to block viral propagation, and would elucidate the factors controlling assembly in a wide range of systems containing proteins and polyelectrolytes. This talk will describe coarse-grained models of capsid proteins and NAs with which we investigate the dynamics and thermodynamics of virus assembly. In con-trast to recent theoretical models, we find that capsids spontaneously `overcharge'; that is, the NA length which is kinetically and thermodynamically optimal possess-es a negative charge greater than the positive charge of the capsid. When applied to specific virus capsids, the calculated optimal NA lengths closely correspond to the natural viral genome lengths. These results suggest that the features included in this model (i.e. electrostatics, excluded volume, and NA tertiary structure) play key roles in determining assembly thermodynamics and consequently exert selec-tive pressure on viral evolution. I will then discuss mechanisms by which se-quence-specific interactions between NAs and capsid proteins promote selective encapsidation of the viral genome. [Preview Abstract] |
Tuesday, March 4, 2014 1:39PM - 1:51PM |
G16.00011: Hierarchical, Self-Similar Structure in Native Squid Pen Fei-Chi Yang, Robert Peters, Hannah Dies, Maikel Rheinstadter Proteins, chitin and keratin form the elementary building blocks of many biomaterials. How these molecules assemble into larger, macroscopic structures with very different properties is the fundamental question we are trying to answer [1]. Squid pen is a transparent backbone inside the squid, which supports the mantle of the squid. The pens show a hierarchical, self-similar structure under the microscope and the AFM with fibers from 500$\mu $m to 0.2$\mu $m in diameter. The chitin molecules form nano-crystallites of monoclinic lattice symmetry surrounded by a protein layer, resulting in $\beta $-chitin nano-fibrils. Signals corresponding to the $\alpha $-coil protein phase and $\beta $-chitin were observed in X-ray experiments \textit{in-situ}. The molecular structure is highly anisotropic with 90{\%} of the $\alpha $--coils and $\beta $-chitin crystallites oriented along the fiber-axis indicating a strong correlation between the structures on millimeters down to the molecular scale [2]. \\[4pt] [1] ``Self-assembly enhances the strength of fibres made from vimentin intermediate filament proteins'', N. Pinto, \textbf{FC. Yang}, \textit{et al}., submitted to \textit{Biomacromolecules}.\\[0pt] [2] ``Hierarchical, Self-Similar Structure in Native Squid Pen'', \textbf{FC. Yang}, \textit{et al.}, submitted to \textit{Royal Society Interface}. [Preview Abstract] |
Tuesday, March 4, 2014 1:51PM - 2:03PM |
G16.00012: Theoretical model of a soft particle with charged core Dustin Tracy, Anh Phan The numerical and analytical solutions of the electrostatic potentials of soft particles with an ion-permeable charged outer layer and a non-permeable charged core with constant charge densities are found using the Poisson-Boltzmann equations. The charged core is found to significantly alter the local potential within the soft particle, yet it has little effect on the potential outside its particle's boundaries. Previous experimental research into the electrical properties of the MS2 virus agree with these findings. Our results also suggest that there is only a slight change in the potential as the temperature is increased from 290 K to 310 K. The potential profile is found to be significantly affected by the ionic strength in the 1-600 mM range. [Preview Abstract] |
Tuesday, March 4, 2014 2:03PM - 2:15PM |
G16.00013: Stochastic Interactions of Two Brownian Spheres in the Presence of Depletants Mehdi Karzar-Jeddi, Remco Tuinier, Takashi Taniguchi, Tai-Hsi Fan The pair interactions between hard spheres play an essential role in many processes such as macromolecular crowding, binding, self-assembly of particles, and many chemical and food processes. Here we focus on theoretical analysis of the long-time correlated stochastic motion of two hard spheres in a non-adsorbing polymer solution. The hard spheres are held by hypothetical optical traps. The pair mobility tenser is found using a two-layer approximation with pure solvent in the depletion zone surrounding the particle and uniform polymer solution elsewhere. The resulting mobility computed by the boundary integral analysis is used to define the level of thermal fluctuation. Results show how the mobility and the decay of displacement correlation functions modified by the polymer depletion effect. The attractive osmotic potential increases the auto-correlation of the pair particle motion, while reduces the cross-correlation of the particles. This work gives better understanding of the pair interactions in a suspension of non-adsorbing polymers as an essential step toward many-particle interactions. [Preview Abstract] |
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