Bulletin of the American Physical Society
15th Annual Meeting of the Northwest Section of the APS
Volume 59, Number 6
Thursday–Saturday, May 1–3, 2014; Seattle, Washington
Session G4: Biophysics |
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Chair: Douglas Juers, Whitman College Room: Alder Commons 106 |
Saturday, May 3, 2014 1:30PM - 2:00PM |
G4.00001: Differential Diffusion as a Root Cause of Cracking of Protein Crystals Invited Speaker: Douglas Juers Protein crystals are nanoporous materials important for high resolution structure determination of proteins via X-ray diffraction. Additionally, their nanoporous character has made protein crystals useful for other applications including separations, catalysis and drug delivery. As materials, protein crystals contain both an ordered array of protein molecules and a disordered aqueous phase, which permeates the crystal inside the pores. The combination of order and disorder confers on the crystals interesting structural, thermal and transport properties. Here we focus on the transport of molecules through the pores and how such transport affects the structural integrity of the crystal. During their use, protein crystals are often subjected to solution changes that can cause damage, including cracking. When a crystal is transferred between two solutions of different composition, solutes and water molecules may enter and/or leave the crystal via its pores. The severity of cracking correlates with differences in both concentration and diffusibility of the entering and exiting molecules. The observed behavior motivates a model in which the key aspect of crystal cracking is differential diffusion of solutes, which causes an osmotic pressure induced stress on the crystal beyond its elastic limit. The result points to some simple guidelines for improved crystal handling. \\[4pt] In collaboration with Rose Cotter, Whitman College. [Preview Abstract] |
Saturday, May 3, 2014 2:00PM - 2:12PM |
G4.00002: Spatial organization of proteins due to membrane-induced interactions Kayla Sapp, Lutz Maibaum We investigate the interaction between lipid bilayers and other cellular components using mathematical modeling and numerical simulations. A biologically relevant example is a collection of actin filaments that suppress membrane shape fluctuations locally. We present a model that takes into account the membrane's elastic behavior, a generic non-specific interaction between proteins, and the coupling between these two systems that we assume to be dominated by geometric effects. This model combines a continuum description of the lipid bilayer with a particle representation of membrane-bound proteins, and employs Brownian Dynamics to study both dynamical and fluctuation effects. We find that the presence of the proteins significantly changes the fluctuations of the membrane, while the bilayer induces an effective interaction between proteins that may lead to the formation of protein clusters even in the absence of protein-protein attractive forces. [Preview Abstract] |
Saturday, May 3, 2014 2:12PM - 2:24PM |
G4.00003: Probing interleaflet coupling in phase separated lipid bilayers under high shear Matthew Blosser, Aurelia Honerkamp-Smith, Sarah Keller Lipid membranes composed of at least three lipid types can phase separate into micron-scale, coexisting liquid phases. Domains in each leaflet are never observed to move out of registration, which indicates a strong interleaflet coupling. Our group has found that this strong coupling persists in asymmetric membranes, where lipid ratios are different in each leaflet [1]. For membranes that lack transmembrane proteins or gel phases, the origin of this strong coupling is not intuitive [2]. Previously, we have found that domain registration persists in supported bilayers to shear rates of 6 seconds$^{-1}$. Here, we use microfluidic techniques to apply higher shear to supported bilayers with the goal of overcoming coupling by moving the membrane's upper leaflet with respect to the lower leaflet. We use a flow cell design by J\"{o}nsson which was previously shown to move bilayers across a substrate [3]. In this system, the leaflet proximal to the substrate flows much slower than the leaflet proximal to the solution, leading to a macroscopic spatial shift between initially apposed regions. This technique of subjecting supported bilayers to high shear allows us to probe interactions between leaflets in the monolayer.\\[4pt] [1] Collins MD, Keller SL (2008) \textit{PNAS,} 105(1):124--128\\[0pt] [2] Devaux PF , Morris R (2004) \textit{Traffic,} 5:241--246\\[0pt] [3] J\"{o}nsson P, Beech JP, Tegenfeldt JO, H\"{o}\"{o}k F (2009) \textit{JACS}, 131(14):5294-5297 [Preview Abstract] |
Saturday, May 3, 2014 2:24PM - 2:36PM |
G4.00004: Phase-locked spiking and stochastic resonance of hair cells Roy Shlomovitz, Yuttana Roongthumskul, Seung Ji, Dolores Bozovic, Robijn Bruinsma The inner ear constitutes a remarkably sensitive mechanical detector. This detection occurs in a noisy and highly viscous environment, as the sensory cells - the hair cells - are immersed in a fluid-filled compartment and operate at room temperature or higher. We model the active motility of hair cell bundles of the vestibular system with the Adler equation, which describes the phase degree of freedom of bundle motion. We explore both analytically and numerically the response of the system to external signals, in the presence of white noise. The theoretical model predicts that hair bundles poised in the quiescent regime can exhibit sporadic spikes - sudden excursions in the position of the bundle. In this spiking regime, the system exhibits stochastic resonance, with the spiking rate peaking at an optimal level of noise. Upon the application of a very weak signal, the spikes occur at a preferential phase of the stimulus cycle. We compare the theoretical predictions of our model to experimental measurements obtained { \it in vitro} from individual hair cells. Finally, we show that an array of uncoupled hair cells could provide a sensitive detector that encodes the frequency of the applied signal. [Preview Abstract] |
Saturday, May 3, 2014 2:36PM - 2:48PM |
G4.00005: Microrheology of Type I Collagen with Holographic Optical Tweezers Matthew Cibula, Christopher Jones, Bo Sun Collagen proteins are the main component of the extracellular matrix which is abundant throughout the human body and integral in wound healing. These proteins form an inhomogeneous elastic material with polarized domains which respond to cellular activity. Most previous studies have considered collagen as a homogeneous elastic material and used bulk rheology to characterize its mechanical properties. However, examination with confocal microscopy reveals that the collagen fibers form an anisotropic porous material. In order to examine the structure-property consequences, we use holographic optical tweezers (HOT) to measure the local rigidity tensor with piconewton forces -- the same range of forces exerted by single molecular motors. HOT enables us to position the trap in three dimensions around micron-sized beads embedded in the gel. We place a trap adjacent to a bead's equilibrium position and measure the relative displacement, using radial position tracking to record the bead's position in 2D. Rayleigh-Somerfield back propagation is implemented to measure vertical bead displacements in the gel. We use these techniques to calculate the rigidity tensor for many particles to measure the size and polarization of collagen domains. [Preview Abstract] |
Saturday, May 3, 2014 2:48PM - 3:00PM |
G4.00006: Structural Properties of DNA Base Pair Mismatches with Molecular Dynamics Adelaide Kingsland, Lutz Maibaum Mismatches in DNA can have disastrous consequences, yet little theoretical study has been done to elucidate the mechanics of DNA mismatches. Further, the exact mechanism by which mismatches are repaired is unknown. Both matched and mismatched DNA sequences were studied using molecular dynamics in biased and unbiased simulation. Significant differences were found between matched and mismatched pairs in structure, hydrogen bonding, and base flip. Mismatched pairs show greater movement in the x-y plane and a lower free energy barrier for base flip than do matched pairs. This supports experimental findings that the primary mechanism utilized by mismatch repair enzymes is to fully flip the base into the active site. Because the free energy of base flip is lower for mismatched systems, mismatch repair enzymes should show an enhanced preference for mismatched pairs. [Preview Abstract] |
Saturday, May 3, 2014 3:00PM - 3:12PM |
G4.00007: A View to a Kill: T6SS-Mediated Cell Killing Visualized by Fluorescence Microscopy Jacqueline Corbitt, Michele LeRoux, Joseph Mougous, Paul Wiggins The Type Six Secretion System (T6SS) is a bacterial toxin-delivery system targeting bacterial cells which neighbor the donor, promoting recipient cell death. The T6SS is widely conserved among Gram-negative bacteria and may be a central determinant in bacterial fitness in polymicrobial communities of particular relevance to chronic infection. Sequence homology of secretion system components to the T4 bacteriophage tail spike, cryoEM reconstructions of the secretion system and fluorescence imaging are all consistent with a dynamic mechanism of secretion. The complex system, which is composed of at least 15 proteins, forms a puncturing apparatus/delivery system which uses a donor protein filament to puncture the recipient cell wall to deliver protein toxins. Using quantitative imaging analysis of multiple fluorescent fusions, we present a detailed characterization of T6SS system dynamics visualized in single cells in multiple bacterial species, developing a model of T6SS function. We present quantitative measurements of the dynamics of the secretion system - from the assembly to contraction to disassembly - in conjunction with quantitative measures of system function, including recipient cell lysis. [Preview Abstract] |
Saturday, May 3, 2014 3:12PM - 3:24PM |
G4.00008: Robustness of MinD oscillation in E. coli with diverse cell shapes Jeff Schulte, Rene Zeto, David Roundy The dynamics of the Min-protein system help \emph{Escherichia coli} regulate the process of cell division by identifying the center of the cell. We model the Min-protein reaction cycle, using a set of reaction-diffusion differential equations, in bacteria that have been forced into unusual flattened shapes as have recently been experimentally observed. We find that a regular two pole oscillation pattern is robust and exhibited in a large variety of cell shapes and sizes. Stability analysis of an infinite slab with our cell thickness yields a characteristic distance at which solutions become unstable, and this distance can be seen to correspond to a cell length below which protein movement dampens out within the cell. We also see evidence of the emergence of more complicated oscillation patterns when the lengthwise direction is well above this characteristic distance and the width is just above. [Preview Abstract] |
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