Bulletin of the American Physical Society
2006 APS March Meeting
Monday–Friday, March 13–17, 2006; Baltimore, MD
Session R29: Biomolecular Structure and Function |
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Sponsoring Units: DBP Chair: Sonya Bahar, University of Missouri, St. Louis Room: Baltimore Convention Center 326 |
Wednesday, March 15, 2006 2:30PM - 2:42PM |
R29.00001: The Impact of Cholesterol on Lateral Organization in a Three-Species Non-Equilibrium Model of a Biomembrane Andrew P. Paradis, Susan R. McKay, Samuel T. Hess Experimentally, cholesterol strongly influences many biological functions in cells. This study examines the mechanisms by which cholesterol affects membrane organization using a simple non-equilibrium model with exo- and endocytosis events. Three species, representing cholesterol, saturated and unsaturated lipids, move and interact on a two dimensional triangular lattice, simulated using a Metropolis algorithm. Interaction energies among the three species are adjustable, as are the rate and size of simulated endo- and exocytosis events. These events keep the system substantially out of equilibrium and yield a striped pattern comparable to those seen experimentally. [1] \newline \newline [1] Baumgart T, Hess ST, and Webb WW. Nature. 2003 Oct 23;425(6960):821-4. [Preview Abstract] |
Wednesday, March 15, 2006 2:42PM - 2:54PM |
R29.00002: Lipid Bilayers and Titanium: Controlling Surface Adsorption Linda S. Hirst, Emily Parker, Noel C. MacDonald, Cyrus R. Safinya Used extensively for implants, titanium is relatively inert in the body, and considered a biocompatible metal. We have investigated the interactions of cationic lipid mixtures with a highly polished bulk TiO$_{2}$ surface and report the observation of an interesting cationic lipid tubule phase stabilized in 2D on the TiO$_{2}$ surface. This phase is distinct from the bulk tubule phase observed in some mixtures as the tubules form a network with small mesh size and appear to be more flexible. Cationic lipid vesicles were formed under various salt conditions and deposited on the TiO$_{2}$ surface via vesicle absorption, then observed with fluorescence microscopy. In certain mixtures, bulk tubule phases were observed. When deposited on glass the bulk tubule phase became unstable and bilayers gradually formed on the glass surface. However, deposition of the same cationic mixtures on TiO$_{2}$ resulted in the formation of a 2D network of lipid tubules on the surface. The network, although pinned to the surface remained fluid in nature, as confirmed by FRAP experiments. The tubules appear to be only weakly attracted to the TiO$_{2}$ and this may explain their stability on the surface. [Preview Abstract] |
Wednesday, March 15, 2006 2:54PM - 3:06PM |
R29.00003: Growth and Morphology of Solid-like Domains in Binary Giant Lipid Vesicles Paul Beales, Vernita Gordon, Zhijun Zhao, Stefan Egelhaaf, Wilson Poon Giant lipid vesicles are important, optically-resolvable, model systems for studying physical phenomena in biomembranes and have important applications as technological containers in the engineering of novel soft materials. Giant vesicles containing two different lipid components are well-mixed in the fluid phase; as the temperature is lowered phase separation occurs between fluid and solid-like phases. We observe this phase separation using confocal fluorescence microscopy. The varied domain morphologies have previously been assumed to result from interplay between line tension and the elastic properties of the bilayer. However, we find that the domain morphology can be understood from the structure of the solid-like phase: the molecular scale lipid organization determines the mesoscopic domain shape analogous to how unit cell symmetries determine the shape of three-dimensional crystals. We also show that the domains grow by a non-equilibrium mechanism that is well-know to occur in alloys. Slow diffusion in the solid-like phase results in a compositional gradient within these domains. [Preview Abstract] |
Wednesday, March 15, 2006 3:06PM - 3:18PM |
R29.00004: Laser Tweezer Deformation of Giant Unilamellar Vesicles Cory Poole, Jozsef Meszaros, Kumar Senthil, Wolfgang Losert In an aqueous solution phospholipid bilayers self-assemble to form a closed surface which is called a vesicle. Vesicles have been studied extensively due to their relevance as a model for biomembranes as well as their practical uses for chemical containment and transport. We use a holographic optical tweezer array to study the mechanical response of giant unilamellar vesicles to applied stresses. By producing vesicles with encapsulated silica microspheres we use the tweezers to indirectly manipulate vesicled. Two or more spheres are used to stretch the vesicle membrane and subsequently the vesicle relaxes back to an equilibrium shape. These deformations are imaged at millisecond temporal resolution with spatial resolution on the order of 20 nm, and characteristic time and length scales of the relaxation are calculated. Further we are able to directly deform the membrane by pulling on the fluid utilizing an index of refraction mismatch between the inside and outside of the vesicle. We image the vesicle and extract the vesicle shape. Fourier analysis is used to track the vesicle as it returns to equilibrium after being stretched. We compare these deformations to preliminary data on deformations due to polymerization induced on both the inside and outside of vesicles. [Preview Abstract] |
Wednesday, March 15, 2006 3:18PM - 3:30PM |
R29.00005: Nanoscale characterization of solid-supported phospholipid multilayer films Wilfred Ngwa, Andrew Gao, Tania Cubano, Kezheng Chen, Alok Sahgal, Weili Luo Using atomic force microscopy (AFM) and the auxiliary molecular force probe (MFP) technique, we have studied the structure and nanomechanical response to nano-indentation of multilayered films of dioleoylphosphatidylcholine (DOPC) films prepared by solution spreading, spin-coating and capillary methods. Estimates for the Young's modulus for the different methods are found to be similar for sufficiently thick films. Our results demonstrate that previously reported estimates for the Young's modulus of adsorbed vesicles and lipid bilayers (membranes) by scanning probe techniques are ostensibly affected by the coupling of the substrate. Failure and self-healing of multilamellar lipid membranes is discussed. [Preview Abstract] |
Wednesday, March 15, 2006 3:30PM - 3:42PM |
R29.00006: A quasi-elastic neutron scattering study of the stabilization of freeze-dried cholesterol-containing DPPC liposomes by trehalose V. Garcia Sakai, M. Doxastakis, A.S. Reddy, J. de Pablo, J.K. Maranas The dissacharide trehalose has been employed extensively as a dehydroprotectant for stabilizing phospholipidic membranes, as a result of its ability to lower the gel-to-fluid phase transition temperature [Tm] of phospholipids. Upon rehydration of the membrane in the presence of trehalose, the transition is prevented and cell leakage is avoided. We use quasi-elastic neutron scattering [QENS] on selective deuterated samples to probe the dynamics of both the heads and tails of freeze-dried liposomes in the presence and absence of trehalose. The dynamics of the lipid tails are responsible for the melting transition, which is significantly lowered in the presence of the sugar. The mobility of the head-group is directly associated with the mobility of the sugar. In the current work, we add cholesterol to the liposomes. Cholesterol, abundant in mammalian cell membranes and embedded in the bilayer structure due to its hydrophobic nature, is added to the liposomes. QENS measurements on the stabilization by trehalose on cholesterol-containing liposomes are presented. At temperatures lower than Tm the mobility of the tails is greatly reduced by cholesterol, but the addition of trehalose has little effect dynamics. At temperatures above the transition though, the mobility of the tails is only slightly reduced, but the addition of trehalose leads to a large decrease in dynamics. [Preview Abstract] |
Wednesday, March 15, 2006 3:42PM - 3:54PM |
R29.00007: A Density Functional Theory Study of the Non-local Correlations between Nucleic Acid Base Pairs Valentino R. Cooper, Timo Thonhauser, David C. Langreth The interactions of nucleic acid bases are fundamentally important in determining the behavior and structure of biologically important molecules such as DNA and RNA. However, the stacking of nucleic acid bases in a strand of genetic material involves significant van der Waals forces, which are often inaccurately represented or too expensive to compute in many modern theoretical methods. In this paper, we use Density Functional Theory (DFT) with a non-local van der Waals correlation functional\footnote{M. Dion, H. Rydberg, E. Schr\"{o}der, D.~C. Langreth and B.~I. Lundqvist, {Phys. Rev. Lett.} \textbf{{92}}, {24601-1} ({2004}).} to study the stacking interactions of nucleic acid base pairs. This method correctly and seamlessly accounts for the long-range interactions present among isolated fragments through a density-density interaction formula. Since this technique is implemented within DFT it has the advantage of being able to draw on the speed, efficiency and accuracy of this \emph{ab initio} method. [Preview Abstract] |
Wednesday, March 15, 2006 3:54PM - 4:06PM |
R29.00008: Low Temperature Orbital Paramagnetism in B-DNA Michael J. Harrison A planar model of B-DNA has been developed that exhibits orbital paramagnetic properties at zero temperature. The paramagnetism is nonlinear in applied field and has a maximum several times the magnitude of diamagnetism per particle in a 2DEG. The model depends on the assumption that approximately 1{\%} of the pi-stack electrons in B-DNA are suffifiently delocalized and have wave functions that permit them to move coherently parallel to the helix axis, and extend several diameters perpendicular to its axis. The theoretical results closely represent recent experimental data [1]. 1. S. Nakamae, et. al., Phys. Rev. \underline {94}, 248102-1 (2005) [Preview Abstract] |
Wednesday, March 15, 2006 4:06PM - 4:18PM |
R29.00009: Kinetic Modelling of Transcription Elongation Daibhid O'Maoileidigh, Vasisht Tadigotla, Anirvan Sengupta, Vitaly Epshtein, Richard Ebright, Evgeny Nudler, Andrei Ruckenstein Transcription is the first step in gene expression and it is at this stage that most of genetic regulation occurs. The enzyme RNA polymerase (RNAP) walks along DNA creating an RNA transcript at a highly non-uniform rate. We discuss how many non-intuitive features of the system may be experimentally and physically motivated and present first a model, which agrees qualitatively with a host of experimental evidence. We also examine intrinsic pauses where it is thought that the RNAP will move backwards along the DNA template without changing the length of the RNA transcript. We describe a simplified kinetic scheme for the recovery of intrinsic pauses with the same degree of predictive power as our thermodynamic model (presented separately). The separation of timescales between the movement of the RNAP and global changes in the RNA secondary structure is seen to be crucial for the function of RNAP. This is essentially a model of a Brownian ratchet where RNAP executes a 1D random walk in a sequence dependent potential over a range determined by the co-transcriptional RNA fold for each transcript length [Preview Abstract] |
Wednesday, March 15, 2006 4:18PM - 4:30PM |
R29.00010: Understanding spontaneous sharp bending of DNA Chongli Yuan, Elizabeth Rhoades, Lynden Archer Gene expression often requires the interplay of two distant genetic regions and thus sharp bending of DNA is essential for gene functioning. Contrary to the conventional thinking that the bending of DNA strand below its persistent length was essentially facilitated by DNA binding proteins, Widom's group recently demonstrated, using cyclization assay, that such kind of sharp bending can be spontaneously formed (\textit{Mol. Cell, 2004, 355}). Two models were referred in the original work to explain this ``enhanced'' flexibility of short DNA strand, namely, the melted single- and double-bubble models. To elucidate the detailed mechanism behind the DNA sharp bending, DNA molecules containing single- and double-melted bubbles was synthesized by introducing non Watson-Crick base pairs to the DNA backbone. Time resolved fluorescence energy transfer was used as the major tool to evaluate the bending stiffness of afore mentioned short DNA strand. The effect of bubble size, number and position on the DNA stiffness was independently evaluated. The energetic penalty of forming the locally melted structure was determined using other individual experiments. These results not only clarify the physical origin of the previously observed cyclizability of short DNA strand but also help to interpret the cyclization data of DNA molecules of wider size ranges. [Preview Abstract] |
Wednesday, March 15, 2006 4:30PM - 4:42PM |
R29.00011: The role of stacking interactions in the folding dynamics of DNA hairpins Marta Sales-Pardo, Jon Widom, Luis Amaral To gain a deeper insight into cellular processes such as transcription and translation, one needs to uncover the mechanisms controlling the configurational changes of nucleic acids. As a step toward this aim, we present here a novel mesoscopic-level computational model that provides a {\it new window} into nucleic acid dynamics. We validate the model by studying DNA hairpins, single-stranded molecules with two complementary segments (``stems'') linked by a non-complementary ``loop.'' Our model reproduces experimental observations and enables us to monitor the configurational dynamics of hairpins, providing clear evidence of a ``zipping'' process in the closing toward the native configuration. In addition, our model allows us to demonstrate that there is a preferred zipping pathway for folding which is both the most frequent and the fastest way for the hairpin to fold. Most importantly, our model allows us to tune the importance of the different interactions in the nucleotides and uncover the role of stacking interactions as the driving force in the zipping dynamics. [Preview Abstract] |
Wednesday, March 15, 2006 4:42PM - 4:54PM |
R29.00012: Thermodynamic Model of Transcription Elongation Vasisht Tadigotla, Daibhid O'Maoileidigh, Anirvan Sengupta, Vitaly Epshtein, Richard Ebright, Evgeny Nudler, Andrei Ruckenstein We present a statistical mechanics approach to the prediction of backtracked pauses in prokaryotic transcription elongation derived from structural models of the transcription elongation complex (TEC). Our algorithm is based on the thermodynamic stability of TEC along the DNA template calculated from the sequence dependent free-energy of DNA-DNA, DNA-RNA and RNA-RNA base pairing associated with (a) the translocation and size fluctuations of the transcription bubble; (b) the changes in the DNA-RNA hybrid; and (c) the changes in the RNA folding free-energy. The calculations involve no adjustable parameters apart from a cutoff used to discriminate paused from non-paused complexes. When applied to 100 experimental pauses in transcription elongation by E. coli RNA polymerase on ten DNA templates the approach produces highly statistically significant results. Transcription elongation is an inherently kinetic process and a simplified kinetic model with the same predictive power is presented separately. [Preview Abstract] |
Wednesday, March 15, 2006 4:54PM - 5:06PM |
R29.00013: The role of telomere dynamics in aging and cancer Krastan Blagoev, Edwin Goodwin Telomere length changes are far more dynamic than previously thought. In addition to a gradual loss of $\sim $100 base pairs per telomere in each cell division, losses as well as gains may occur within a single cell cycle. We are investigating how telomere exchange, extension, and deletion affect the proliferative potential of telomerase-negative somatic cells. Experimental techniques are being devised to detect dynamic telomere processes and quantify both the frequency and length changes of each. In parallel, a ``dynamic telomere model'' is being used that incorporates telomere dynamics to study how the telomere size distribution evolves with time. This is an essential step towards understanding the role that telomere dynamics play in the normal aging of tissues and organisms. The model casts light on relationships not otherwise easily explained by a deterministic ``mitotic clock,'' or to what extent the shortest initial telomere determines the onset of senescence. We also expect to identify biomarkers that will correlate with aging better than average telomere length and to shed light on the transition to unlimited growth found in telomerase-negative tumor cells having the ALT (alternative lengthening of telomeres) phenotype, and to evaluate strategies to suppress the growth of these tumors. [Preview Abstract] |
Wednesday, March 15, 2006 5:06PM - 5:18PM |
R29.00014: Optical Investigation of the Phases of Liquid Crystals of Nanoscale Duplex DNA Giuliano Zanchetta, Michi Nakata, Tommaso Bellini, Noel Clark Polymeric DNA chains are known to exhibit chiral nematic and hexagonal columnar LC phases. Recently we found that even very short duplex DNA oligomers 6-basepairs (bp) to 20-bp in length also form nematic and columnar phases depending on the concentration of DNA. To investigate the structure of those phases, we used depolarized transmission light microscopy (DTLM) to probe texture and measure birefringence, and optical interferometry to measure DNA concentration. These observations show a chiral nematic and two distinct columnar phases in the short oligomer duplexes. We will discuss the structure of these phases and present data correlating their occurance with solution conditions and with the detailed base pair configuration and the ends of the oligomers, showing that, for example, unpaired bases at the ends of the oligomers tend to suppress the LC phases. Work supported by NSF MRSEC Grant DMR 0213918 and NSF Grant 0072989. [Preview Abstract] |
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