Bulletin of the American Physical Society
2011 Annual Meeting of the Four Corners Section of the APS
Volume 56, Number 11
Friday–Saturday, October 21–22, 2011; Tuscon, Arizona
Session E6: Biological Physics |
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Chair: Koen Visscher, University of Arizona Room: UA Student Union Santa Cruz |
Friday, October 21, 2011 3:25PM - 3:37PM |
E6.00001: Steered molecular dynamics simulations of a bacterial type IV pilus reveal characteristics of an experimentally-observed, force-induced conformational transition Joseph Baker, Nicolas Biais, Florence Tama Type IV pili (T4P) are long, filamentous structures that emanate from the cellular surface of many infectious bacteria. They are built from a 158 amino acid long subunit called pilin. T4P can grow to many micrometers in length, and can withstand large tension forces. During the infection process, pili attach themselves to host cells, and therefore naturally find themselves under tension. We investigated the response of a T4 pilus to a pulling force using the method of steered molecular dynamics (SMD) simulation. Our simulations expose to the external environment an amino acid sequence initially hidden in the native filament, in agreement with experimental data. Therefore, our simulations might be probing the initial stage of the transition to a force-induced conformation of the T4 pilus. Additional exposed amino acid sequences that might be useful targets for drugs designed to mitigate bacterial infection were also predicted. [Preview Abstract] |
Friday, October 21, 2011 3:37PM - 3:49PM |
E6.00002: Introduction to Non-Invasive Glucose Measurement - A Physicist's Perspective Daniel Blakley, Steven Simske, Pankaj Vadgama The Quest, The Elusive Art and Science, Many Efforts and Investments, Physiology of Blood and Epidermal Regions, Some Methods including Eyes, Breath, Skin Coupling using Spectroscopy, Ring-down Spectroscopy, IR Measurement, Florescence - all as General Introductory Material. [Preview Abstract] |
Friday, October 21, 2011 3:49PM - 4:01PM |
E6.00003: Influence of Crystal Packing on Global Protein Conformation Logan Ahlstrom, Osamu Miyashita X-ray crystallography is the most robust method for solving protein structure. However, packing forces in the crystal lattice select just a snapshot of a protein's conformational ensemble, whereas proteins are flexible and can adopt different conformations. Here we compare molecular dynamics (MD) simulations in solution and the crystal lattice to add dynamical insight to the static X-ray images of proteins. As a model system, we consider the $\lambda $ Cro dimer, whose solved X-ray structures range from a ``closed'' to an ``open'' global conformation. Free energy profiles depicting the conformational space sampled by the dimer in solution show some reported structures correspond to stable states. Yet other conformations, while accessible, lie higher in energy, indicating the effect of crystal packing. Subsequent crystal MD simulations estimated the strength of packing interfaces in the lattice, showing the influence of crystal form and mutation in stabilizing different dimer conformations. Our quantitative results will aid analysis of X-ray data in establishing protein structure-function relationships. [Preview Abstract] |
Friday, October 21, 2011 4:01PM - 4:13PM |
E6.00004: Protein-ligand biosensing: dielectric spectroscopy and numerical simulation of molecular interactions Brett Mellor, Nathan Kellis, Steven Brewer, David Busath, Brian Mazzeo In this study we demonstrate the capability of dielectric spectroscopy, an impedance-based measurement technique, to probe molecular binding interactions in liquid. As a test system, the avidin-biotin binding reaction is used because it is well understood and has a high binding constant. Experiments are first performed on avidin and biotin-labeled bovine serum albumin, showing characteristics of aggregation. Next, experiments are performed on avidin and biotin, showing changes in dipole moment and molecule size after the binding occurs. Numerical methods based on Poisson-Boltzmann pKa shifts and molecular dynamics simulations confirm the measured changes. [Preview Abstract] |
Friday, October 21, 2011 4:13PM - 4:25PM |
E6.00005: Biomembrane Structure and Dynamics Controlled by Dehydration and Osmotic Stress Jacob Kinnun, K.J. Mallikarjunaiah, Avigdor Leftin, Horia Petrache, Michael Brown Membrane deformation and dynamics and their effects on membrane protein function remain mysterious. With osmolytes and dehydration we observe deformation of DMPC-$d_{54}$ lipid membranes via solid-state $^{2}$H NMR spectroscopy. A unified theoretical framework predicts that membrane osmotic pressure depends inversely on the number waters per lipid. Through temperature variation we find osmotic pressure is generated by membrane undulations and lipid protrusions. We extend this thermodynamic framework via a mean-torque model to analyze the compressibility of the lipids. Under pressure, the area per lipid decreases and hydrocarbon thickness increases as described by a compressibility modulus. Changes in membrane thickness result in hydrophobic mismatch which affect protein-lipid interactions. Our findings show how altering membrane structure and dynamics affect membrane protein function. [Preview Abstract] |
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