Bulletin of the American Physical Society
Joint Fall 2010 Meeting of the Texas Sections of the APS, AAPT, Zone 13 of SPS and the National Society of Hispanic Physicists
Volume 55, Number 11
Thursday–Saturday, October 21–23, 2010; San Antonio, Texas
Session FM3: Biological and Chemical Physics I |
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Chair: Ahmed Touhami, University of Texas at Brownsville Room: University Center I Pecan Room, 2nd floor |
Friday, October 22, 2010 10:00AM - 10:12AM |
FM3.00001: Laser damage thresholds for \textit{in vitro} retinal pigment epithelial cell by micro thermal sensing Tae Choi, Dienye Atemie, Michael Denton, Gary Noojin, Larry Estlack, Benjamin Rockwell, Robert Thomas A cellular-level, high-resolution temperature sensing system was developed using a micropipette thermocouple sensor. The sensing system was properly calibrated and tested for retinal pigment epithelial (RPE) cells. We have integrated this sensing system with an in-house fluorescence microscope to determine laser damage thresholds for RPE cells. At the damage thresholds, we have determined a maximum temperature rise of 40 $^{\circ}$C at the position $\sim $5 $\mu $m away from the center of a cell. We have also acquired fluorescence images of the cell before and after irradiation. Disappearance of fluorescence clearly signifies the cell damage. Theoretical simulations for photothermal damage show similar trends in temperature rise. [Preview Abstract] |
Friday, October 22, 2010 10:12AM - 10:24AM |
FM3.00002: Correlating Computational Docking Predictions with Raman Spectroscopy for Beta-Lactoglobulin-Porphyrin Complexes James Parker, Lorenzo Brancaleon Computational molecular docking simulations (Dock and AutoDock) may provide a wealth of structural information related to the bound configuration of protein-ligand complexes, but they require verification to ensure their predictions reflect reality. Resonance Raman spectroscopy data has been collected to correlate normal mode vibrations observed in the bound structure to computationally generated structures in order to determine the best match between the compuational model and experiment. This methodology was used to determine the bound structures at an atomistic level of $\beta$-lactoglobulin (BLG) and meso-tetrakis (p-sulfonatophenyl) porphyrin (TSPP) in aqueous solutions at pH 7 and 9. Comparisons of Raman spectra of TSPP before and after binding to BLG yield line shifts that are related to the distortions in the free molecule that are presumed to be generated by the non-covalent binding of the ligand to the protein. Our goal is to define quantitative relationships between the observed line shifts and the computed distortions in the molecular structure using normal mode analysis and DFT computational tools. [Preview Abstract] |
Friday, October 22, 2010 10:24AM - 10:36AM |
FM3.00003: Synthesis of Giant Unilamellar Vesicles (GUV) from Liposomes Prepared by the Rapid Solvent Exchange (RSE) Method Eda Baykal-Caglar Lipid bilayers, which is an important constituent of cell membranes, has been extensively studied by biophysicists. Cell membranes perform many vital cell functions such as signal transduction and transportation of materials needed for the functioning of the cell organelles. Understanding the organization and dynamics of lipid bilayers is important for understanding the processes taking place in cell membranes. Giant Unilamellar Vesicles (GUVs) are cell-sized model systems that allow direct visualization of membrane-related phenomena using fluorescence microscopy. In this study, we investigated the synthesis of GUVs from much smaller liposomes (less than 0.5 microns) produced by the Rapid Solvent Exchange (RSE) method in aqueous solutions of high and low ionic strength. The GUVs synthesized using RSE liposomes are more uniform in lipid composition than that synthesized by other methods. We made a number of modifications to the original electroformation method, and we are able to prepare GUVs from RSE liposomes both in high ionic strength and low ionic strength buffers. Using our optimized procedure, we are also able to produce high quality multi-component GUVs to study the dynamics of lipid domains. [Preview Abstract] |
Friday, October 22, 2010 10:36AM - 10:48AM |
FM3.00004: Binding of Perylene derivatives to Human Serum Albumin Mohammed Farooqi, Mathew Mahindaratne, Mark Penick, George Negrete, Lorenzo Brancaleon The binding and effects of polyaromatic hydrocarbons (PAH) on proteins remains a very important aspect in the study of the function of many proteins. We employ asymmetric perylene derivatives designed to optimize electron donating/accepting properties. Unlike the widely used perylene diimides, these novel perylenes are synthesized with an array of possible electron donating and accepting group that would optimize photoinduced electron transfer (PET). Our study focuses on the interaction of four 3,9-substituted perylenes with Human Serum Albumin(HSA) which is the prime protein model for the binding of PAH. We present absorption and fluorescence spectroscopy results that help elucidate the binding of these perylenes to HSA. We determined that not all perylene derivative bind the protein and that their location is likely different. [Preview Abstract] |
Friday, October 22, 2010 10:48AM - 11:00AM |
FM3.00005: Control of Stochastic Master Equation Models of Genetic Regulatory Networks by Approximating Their Average Behavior Mehmet Umut Caglar, Ranadip Pal The central dogma of molecular biology states that ``information cannot be transferred back from protein to either protein or nucleic acid.'' However, this assumption is not exactly correct in most of the cases. There are a lot of feedback loops and interactions between different levels of systems. These types of interactions are hard to analyze due to the lack of data in the cellular level and probabilistic nature of interactions. Probabilistic models like Stochastic Master Equation (SME) or deterministic models like differential equations (DE) can be used to analyze these types of interactions. SME models based on chemical master equation (CME) can provide detailed representation of genetic regulatory system, but their use is restricted by the large data requirements and computational costs of calculations. The differential equations models on the other hand, have low calculation costs and much more adequate to generate control procedures on the system; but they are not adequate to investigate the probabilistic nature of interactions. In this work the success of the mapping between SME and DE is analyzed, and the success of a control policy generated by DE model with respect to SME model is examined. Index Terms--- Stochastic Master Equation models, Differential Equation Models, Control Policy Design, Systems biology [Preview Abstract] |
Friday, October 22, 2010 11:00AM - 11:12AM |
FM3.00006: Probing Protein Conformation Changes in Food Nanostructure Ahmed Touhami, Marcela Alexander , Milena Corredig Here we use AFM-single molecule force spectroscopy to probe the conformational changes in Beta-lactoglobulin (BLG) protein adsorbed onto the oil-in-water interface due to variations in pH. Single oil droplets are mechanically trapped and the AFM tip is used to grape and unfolds BLG molecules. The changes in the contour length upon each unfolding event were determined by fitting the WLC model of polymer elasticity to each of the BLG peaks of the force-extension profiles. Our results show clearly that BLG on the same oil droplet adopts different conformations at different pH regions. While at pH 2.5, the unfolded BLG has a contour length similar to the total length of single monomer with two large unfolding barriers, the protein exists mainly as a dimer formed of several smaller domains at pH 6.8. Furthermore, at pH 9 the interactions between the AFM tip and the BLG layer on the oil droplet are dominated by an important repulsion due to the highly negatively charged BLG layer. This study demonstrates a novel application of single molecule force spectroscopy to investigate the underlying mechanisms by which proteins can be used to stabilize food products. [Preview Abstract] |
Friday, October 22, 2010 11:12AM - 11:24AM |
FM3.00007: Particle Tracking of Fluorescent Microspheres Zofia Kaminski, Joachim Mueller, Serkan Berk In this research, the diffusion coefficients of the fluorescent microspheres and the relation of those coefficients to particle radius were investigated. An additional focus was to see how well the measured radius of the microspheres compared to the radius as reported by the manufacturer and to measure the distribution of radii in a sample. This study further developed the critical process of ensuring particle movement within the sample volume and made preliminary sample measurements.The methods developed for tracking microspheres will later be used to determine the radii of virus like particles (VLPs), which are a non-infectious model system of the HIV virus. Results from our measurements will be reported. [Preview Abstract] |
Friday, October 22, 2010 11:24AM - 11:36AM |
FM3.00008: pH Dependant Binding and Irradiation of Protoporphyrin IX to Human Serum Albumin Sarah Rozinek, Lorenzo Brancaleon Irradiation of the non-covalent complex, protoporphyrin IX (PPIX) bound to $\beta $-lactoglobulin ($\beta $-lg), causes a modest unfolding of the protein localized to Trp19. PPIX binds to $\beta $-lg at a site affected by the pH of the solution. At physiological pH, PPIX is known to bind HSA in hydrophobic binding sites located in subdomain IIA and IIIA. However, no evidence is presented for the binding behavior of PPIX to HSA in non-physological pH confirmations, nor on the effects of irradiation on the bound system at any pH. The combination of spectroscopic data and molecular simulations suggests that distinct PPIX-compatible binding sites become available at each confirmation of HSA at pH 3, 7.4, and 9. [Preview Abstract] |
Friday, October 22, 2010 11:36AM - 11:48AM |
FM3.00009: Expression of Trans-Membrane Proteins \textit{in vitro} Using a Cell Free System Natalie Weisse, Vincent Noireaux, Jerome Chalmeau Trans-membrane proteins represent a significant portion of the proteins expressed by cells. The expression of proteins \textit{in vitro}, however, remains a challenge. Numerous expression approaches have been developed with cell free expression (CFE) being one of the most promising. CFE is based on a transcription-translation system that has been extracted from \textit{E. coli} bacteria. Adding the desired DNA allows expression of a selected protein, and in the presence of phospholipids the expression of trans-membrane proteins becomes possible. In order to express trans-membrane proteins in a closed native environment, the cell free system (CFS) is encapsulated with a phospholipid bilayer, creating an artificial cell. To verify protein expression, AquaporinZ (AqpZ), a well-known trans-membrane protein tagged with a green fluorescent protein (eGFP), was used so the expressed proteins could be seen under a fluorescent microscope. These artificial cells will serve as an experimental platform for testing the viability of the expressed trans-membrane proteins. Results from the manipulation of these artificial cells by attaching them to the slide surface through streptavidin-biotin bonding will be presented. [Preview Abstract] |
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