Bulletin of the American Physical Society
2005 72nd Annual Meeting of the Southeastern Section of the APS
Thursday–Saturday, November 10–12, 2005; Gainesville, FL
Session HC: Biophysics I |
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Chair: Jack Sabin, University of Florida Room: Hilton Azalea |
Friday, November 11, 2005 2:00PM - 2:36PM |
HC.00001: Protein-Protein Association: A Transition-State View. Huan-Xiang Zhou Protein-protein association is central to most protein functions. When two proteins approach each other to form a specific complex, translational and rotational freedom becomes restricted, yet the stabilizing interactions between the partners are formed only when they are close to the bound configuration. This asynchronous decrease in translational/rotational entropy and free energy of interactions leads to a free-energy barrier, which can be identified as the transition state for association [1]. The entropic barrier corresponds to low rate of association, which can be enhanced by favorable electrostatic interactions between the associating proteins. The rate enhancement can be predicted from the electrostatic free energy of interaction in the transition state [2]. The transition-state view of protein-protein association nicely explains the widely-observed disparate dependence of association and dissociation rates on ionic strength, which modulates electrostatic interactions [1, 3]. Once the transition state is reached, the proteins are found to undergo nanosecond-scale conformational adjustment to form the specific complex [4]. \newline [1] H.-X. Zhou (2001). Disparate ionic-strength dependence of on and off rates in protein- protein association. Biopolymers 59, 427-433.\newline [2] M. Vijayakumar, K.-Y. Wong, G. Schreiber, A. R. Fersht, A. Szabo, and H.-X. Zhou (1998). Electrostatic enhancement of diffusion-controlled protein-protein association: Comparison of theory and experiment on barnase and barstar. J. Mol. Biol. 278, 1015-1024.\newline [3] H.-X. Zhou (2003). Association and dissociation kinetics of colicin E3 and immunity protein 3: convergence of theory and experiment. Protein Sci. 12, 2379-2382.\newline [4] X. Huang, F. Dong, and H.-X. Zhou (2005). Electrostatic recognition and induced fit in the k-PVIIA toxin binding to Shaker potassium channel. J. Am. Chem. Soc 127, 6836-6849. [Preview Abstract] |
Friday, November 11, 2005 2:36PM - 2:48PM |
HC.00002: Effects of IR-FEL Wavelength, Fluence and Spot size on Porcine Corneal Ablation Gilma Adunas, Shane Hutson The tunability of infrared Free Electron Lasers (FELs) has been previously used to measure the wavelength-dependence of ablation -- both in terms of efficiency and collateral damage. However, interpretation of the wavelength-dependence is complicated by variations of both fluence and spot size. Here, we systematically investigate these effects during FEL ablation of porcine corneal tissue. Ablation efficiency and collateral damage are quantified for a set of five wavelengths (2.77, 3.32, 5.97, 6.26 and 6.45 microns) for which porcine cornea has matching absorption coefficients. Fluences varied from 5-200 J/cm$^{2}$; and spot diameters varied from 60-400 $\mu $m. Our results show that decreasing the spot diameter or decreasing the fluence both decrease the ablation efficiency. Histological analysis of ablation craters has further shown that the wavelength-dependence of collateral damage also varies with fluence. At low fluence, the collateral damage around 2.77 or 6.45-$\mu $m craters is quite comparable. However, at high fluence, both the crater shape and the collateral damage deep to the crater differ strongly. We conclude that the interplay of fluence, spot size and wavelength has strong implications for the interpretation of previous conflicting FEL studies. [Preview Abstract] |
Friday, November 11, 2005 2:48PM - 3:00PM |
HC.00003: Ion-Molecule Collisions - Fragmentation Products and Cross Sections John R. Sabin, Remigio Cabrera-Trujillo, Erik Deumens, Yngve \"{O}hrn In this presentation, I will introduce a theoretical scheme for studying the interaction of fast ions, electrons, and photons with molecules. Although the molecules under consideration are not, perhaps, of the size to make a biologist (or even a biochemist!) feel quite at home, they are the beginnings of a theoretical program to study the details of the interactions of particles with molecules of biological significance. The examples, such as the fragmentation cross section for various channels for protons impinging on ethane, will be illustrative of what we hope we will be able to do with real bio-molecules in time. In particular, I will look at collision and fragmentation cross sections, which are necessary for the understanding of the details of ion-molecule processes. The details of the formalism will be minimal. [Preview Abstract] |
Friday, November 11, 2005 3:00PM - 3:12PM |
HC.00004: Diffusion-limited formation of internal loops in polymer chains Dana Doucet, Adrian Roitberg, Stephen Hagen The speed of diffusional motion of a polypeptide places an upper limit on the speed of protein folding: folding often requires two distant portions of the polypeptide chain to diffuse into contact. Although several studies have investigated the speed at which external (i.e. end-to-end) loops form in polypeptide chains, the more realistic case of internal loops (i.e. connecting two interior points) involves additional excluded volume and potentially slower dynamics. We have used a simple statistical approach to estimate this effect. We generate model chains in continuous, three-dimensional space, where the hard-sphere, excluded volume interaction represents the only deviation from ideal chain behavior. This yields the probability distribution for the distance between particular sites in the chain. We then use a first-passage-time approach (Szabo, Schulten, and Schulten 1980) to estimate the rate of contact formation under various combinations of loop lengths, ``tail'' lengths, and excluded volume. We find that the addition of just a few extra links to an end-to-end loop significantly reduces the speed of loop formation. [Preview Abstract] |
Friday, November 11, 2005 3:12PM - 3:24PM |
HC.00005: Do proteins really unfold in a shear flow? Juan Jaspe, Stephen J. Hagen Many protein structures unfold (denature) when subjected to extremes of heat, cold, pH, solvent composition, or mechanical stress. One might expect that shearing forces induced by a nonuniform fluid flow would also destabilize proteins, as when a protein solution flows rapidly through a narrow channel. However, although we find many references to shear denaturation in the protein literature, we find no quantitative demonstration of the phenomenon. Therefore we have investigated whether a high shear can destabilize a protein to any measureable extent. We study a small globular protein (horse cytochrome $c$, 104 amino acids) whose fluorescence increases sharply upon unfolding. We pump the sample through a silica capillary (180 $\mu $m ID) at speeds $\sim $ 10 m/s to create a simple shear \textit{dv}$_{z}$/\textit{dx} $\sim $ 5 $\times $ 10$^{5}$ s$^{-1}$, under UV laser illumination. We can detect unfolding of as little as 1{\%} of the sample, or (under favorable conditions) a reduction of $\sim $0.05 kJ/mol in the protein's stability. We will discuss preliminary results along with a simple theoretical perspective on shear denaturation. [Preview Abstract] |
Friday, November 11, 2005 3:24PM - 3:36PM |
HC.00006: Single Channel Activity from Ion Channels in Engineered Tethered Bilayer Membrane Arrays Henk Keizer, Brian Dorvel, Joanna Long, Daniel Fine, Ananth Dodabalapur, Ingo K\"{o}per, Wolfgang Knoll, Peter Anderson, Randolph Duran The demand for rapid \textit{in situ} detection of chemical and biological analytes at high sensitivity has increased interest in the development of biosensors like the commercially available compact glucose sensor. Engineered membrane bound ion channels are promising biological receptors since they would allow for the stochastic detection of analytes at high sensitivity, they can be mutated to alter sensitivity, and they produce a well-defined read-out that is inherently suitable for digitization. In order to perform stochastic sensing it is necessary to be able to measure the ion currents associated with single ion channel opening and closing events. Although sensors based on supported bilayers containing various pore forming proteins have been described, none of these systems have recorded single channel activity. Here we describe the measurement of stochastic activity from synthetic single ion channels, based on the nicotinic acetylcholine receptor (nAChR) from \textit{Torpedo californica}, inserted into individual pixels of a microelectrode array device. The limited size of the gold sense pad surface, 100x100 $\mu $m, and the electrical stability of the overlying lipid bilayer membrane make each pixel sensitive enough to measure single ion channel currents in the picoampere range. [Preview Abstract] |
Friday, November 11, 2005 3:36PM - 3:48PM |
HC.00007: Kinetics of the Formation of Tethered Black Lipid Membranes on Ultraflat Gold Supports: A QCM-D and AFM Study Brian Dorvel, Henk Keizer, Randy Duran The cell membrane is recognized as the foundation to which most essential cellular processes originate and occur; thus elucidation of the structure, dynamics, and function of biomembranes is of fundamental importance if we are to mimic nature. Supported, freestanding lipid bilayers known as black lipid membranes (BLM's) are commonly used as stable biomimetic systems and exist as supported BLM's (sBLM's) and tethered BLM's (tBLM's). Although much work has been done on the kinetics of formation in sBLM's on several substrates, very little is known on the kinetics of tBLM's. By using Quartz Crystal Microbalance with Dissipation Factor (QCM-D) we were able to monitor both the kinetics and viscoelastic properties of tether adsorption and liposome fusion. Atomic Force Microscopy pictures taken complement the QCM-D data, showing the major stages of tBLM formation and pathways of liposome fusion. [Preview Abstract] |
Friday, November 11, 2005 3:48PM - 4:00PM |
HC.00008: Indole Localization in an Explicit Bilayer Revealed via Molecular Dynamics Kristen Norman, Hugh Nymeyer It is well known that the amino-acid tryptophan is particularly stable in the interfacial region of biological membranes, and this preference is a property of the tryptophan side-chain. Analogues of this side-chain, such as indole, strongly localize in the interfacial region, especially near the glycerol moiety of the lipids in the bilayer. Using molecular dynamics calculations, we determine the potential of mean force (PMF) for indoles in the bilayer. We compare the calculated PMF for indole with that of benzene to show that exclusion from the center of the lipid bilayer does not occur in all aromatics, but is strong in indoles. We find three minima in the PMF. Indole is most stabilized near the glycerol moiety. A weaker binding location is found near the choline groups of the lipid molecules. An even weaker binding side is found near the center of the lipid hydrocarbon core. Comparisions between uncharged, weakly charged, and highly charged indoles demonstrate that the exclusion is caused by the charge distribution on the indole rather than the ``lipo-phobic'' effect. High temperature simulations are used to determine the relative contribution of enthalpy and entropy to indole localization. The orientation of indole is found to be largely charge independent and is a strong function of depth within the bilayer. We find good agreement between simulated $S_{CD}$ order parameters for indole and experimentally determined order parameters. [Preview Abstract] |
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