Bulletin of the American Physical Society
2015 Annual Spring Meeting of the APS Ohio-Region Section
Volume 60, Number 3
Friday–Saturday, March 27–28, 2015; Kent, Ohio
Session F4: Biophysics/Soft Matter III |
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Chair: Antal Jakli, Kent State University Room: KSU Student Center 316 |
Saturday, March 28, 2015 11:35AM - 11:50AM |
F4.00001: G-Quadruplex unfolding by Bloom helicase has low-processivity in ATP Jagat Budhathoki, Hamza Balci Non-telomeric G-quadruplex (GQ) structures may result in genomic instability unless they are destabilized by proteins. Bulk biochemical studies have shown that Bloom helicase (BLM) unfolds both intermolecular and intramolecular GQ in the presence of ATP. Using single molecule FRET, we show that binding of BLM to ssDNA in the vicinity of an intramolecular GQ leads to unfolding of the GQ in the absence of ATP. Surprisingly this result has similarity with single strand DNA binding protein (SSB) RPA which also unfolds GQ upon binding to a neighboring overhang. These similarities point to common features where helicases and SSB initiate binding and in some instances is adequate for GQ unfolding. Furthermore, we studied GQ unfolding by BLM in the presence of ATP, the efficiency of which was found to be significantly higher compared to that in the absence of ATP. However, BLM unfolded GQ only a few times before dissociating from the DNA, which points to a GQ unfolding mechanism with low processivity. [Preview Abstract] |
Saturday, March 28, 2015 11:50AM - 12:05PM |
F4.00002: Domain Movement and Dynamics of Norwalk Virus Capsid by Molecular Dynamics (All-Atom and Coarse Grained) Simulations and Normal Mode Analysis Mahendra Thapa, Jarek Meller, Mark Rance Norwalk virus is the major cause of epidemic gastroenteritis in humans. The capsid of the virus consists of 180 copies of a single protein which has a protruding (P) domain and a shell (S) domain mechanism of domain movements of the protein is investigated by Gaussian network model(GNM) Dynamics Simulations (MD): Coarse-grained and all-atom (both conventional MD and accelerated MD). Preliminary results are as follows: (i) slow coordinated motions are identified in the hinge regions, (ii) the C-terminus residue interacts with specific residues and (iii) normal mode analysis, coarse grained MD and all-atom simulation generate largely consistent results. [Preview Abstract] |
Saturday, March 28, 2015 12:05PM - 12:20PM |
F4.00003: Biophysical investigation of lipid droplet fusion Mona Mirheydari, Chiran Ghimire, Hunbin Mao, Elizabeth K. Mann, Edgar E. Kooijman Lipid droplets are important intracellular organelles. Aside from maintaining internal energy stability these intracellular organelles function in processes as diverse as lipid signaling, synthesis of steroid hormones and viral replication. Lipid droplets mature through cell processes like fusion. Recently, we showed that oil droplet fusion can be followed via a specially designed optical trap method whereby two oil droplets are captured in two traps, then brought together. The top trap is turned off so that oil droplets join in the bottom trap. The process of merging within the trap can be separated into two stages: (a) A docking stage which depends strongly on the concentration of ions in the solution and type of anion in solution according to the Hoffmeister series; (b) The physical fusion of the two droplets. To further investigate mechanism of the observed behavior, especially effect of ions, we used a home-built liquid droplet tensiometer to determine the interfacial tension of an oil droplet in solution and its dependence on the type of anion and its concentration. Results show that interfacial tension alone cannot explain the fusion of lipid droplet. The interfacial tension does not significantly change from 10 to 50 mM ion concentration, while the docking rate of oil droplet fusion increases 10 fold. The interfacial tension also shows no trend with the Hoffmeister anion series. [Preview Abstract] |
Saturday, March 28, 2015 12:20PM - 12:35PM |
F4.00004: Dynamics of Stable and Metastable Structures of Liquid Crystal and Lipid Systems at Interfaces Lawrence Honaker, Piotr Popov, Elizabeth Mann, Edgar Kooijman, Antal Jakli Due to the amphiphilic structure and character of liquid crystal molecules, they tend to align in a planar fashion at a boundary with water and homeotropically at a boundary with air. However, the introduction of heteromolecules with long aliphatic tails, such as phospholipids, into the system promotes homeotropic alignment, a conformational change which is easily visually observable. It can be expected that the presence of these lipids induces a uniformly homeotropic texture in the liquid crystalline system, but experimental observations show otherwise. Studies of the textures and features that arise in such systems are presented here with an emphasis on the study of the metastable hybrid textures that develop, their stability, the characteristics of their alignment, and factors that influence their presence. [Preview Abstract] |
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