Bulletin of the American Physical Society
2008 APS March Meeting
Volume 53, Number 2
Monday–Friday, March 10–14, 2008; New Orleans, Louisiana
Session A16: Dynamics of Nucleic Acids |
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Sponsoring Units: DBP DPOLY Chair: Igor Aronson, Argonne National Laboratory Room: Morial Convention Center 208 |
Monday, March 10, 2008 8:00AM - 8:12AM |
A16.00001: Biochemistry on a leash: A mechanism for ligand recruitment via tethered binding sites Daniel Reeves, Keith Cheveralls, Jane Kondev The diffusion limited reaction rate for ligand-receptor systems is typically estimated as the rate at which the ligand stumbles upon the receptor site by three-dimensional Brownian motion. We consider a mechanism that improves upon this limiting rate by placing a binding site on a flexible polymer. The tethered binding site explores the vicinity of the receptor site via polymer diffusion. After binding the ligand, the tether directly transfers it to the receptor site. This is in contrast with existing model mechanisms that involve non-specific binding that confines the ligand to lower-dimensional diffusion. The proposed mechanism may be relevant to the biological actin capping protein formin, which increases actin polymerization rates when bound to the growing tip of actin filaments. [Preview Abstract] |
Monday, March 10, 2008 8:12AM - 8:24AM |
A16.00002: Backtracking and error correction in DNA transcription Margaritis Voliotis, Netta Cohen, Carmen Molina-Paris, Tanniemola Liverpool Genetic information is encoded in the nucleotide sequence of the DNA. This sequence contains the instruction code of the cell - determining protein structure and function, and hence cell function and fate. The viability and endurance of organisms crucially depend on the fidelity with which genetic information is transcribed/translated (during mRNA and protein production) and replicated (during DNA replication). However, thermodynamics introduces significant fluctuations which would incur massive error rates if efficient proofreading mechanisms were not in place. Here, we examine a putative mechanism for error correction during DNA transcription, which relies on backtracking of the RNA polymerase (RNAP). We develop an error correction model that incorporates RNAP translocation, backtracking pauses and mRNA cleavage. We calculate the error rate as a function of the relevant rates (translocation, cleavage, backtracking and polymerization) and show that the its theoretical limit is equivalent to that accomplished by a multiple-step kinetic proofreading mechanism. [Preview Abstract] |
Monday, March 10, 2008 8:24AM - 8:36AM |
A16.00003: Effects of crosslinks on motor-mediated filament organization Igor Aranson, Falko Ziebert, Lev Tsimring Crosslinks and molecular motors play an important role in the organization of cytoskeletal filament networks. Here we incorporate the effect of crosslinks into our model of polar motor-filament organization, through suppressing the relative sliding of filaments in the course of motor-mediated alignment. We show that this modification leads to a nontrivial macroscopic behavior, namely the oriented state exhibits a transverse instability in contrast to the isotropic instability that occurs without crosslinks. This transverse instability leads to the formation of dense extended bundles of oriented filaments, similar to recently observed structures in actomyosin. This model also can be applied to situations with two oppositely directed motor species or motors with different processing speeds. [Preview Abstract] |
Monday, March 10, 2008 8:36AM - 8:48AM |
A16.00004: Collective alignment of polar filaments by molecular motors Falko Ziebert, Igor Aranson We study the alignment of polar biofilaments, such as microtubules and actin, subject to the action of multiple molecular motors attached simultaneously to more than one filament. Focusing on a paradigm micromechanical model of only two filaments interacting with multiple motors, we were able to investigate in detail the dynamics of the filaments' alignment. While almost no alignment occurs in the case of a single motor, we show that the filaments become perfectly aligned due to the collective action of the motors working together. Our studies revealed that the the alignment time is governed by the magnitude of the fluctuations in the motor force. [Preview Abstract] |
Monday, March 10, 2008 8:48AM - 9:00AM |
A16.00005: Detecting cooperative sequences in the binding of RNA Polymerase-II Kimberly Glass, Julian Rozenberg, Michelle Girvan, Wolfgang Losert, Ed Ott, Charles Vinson Regulation of the expression level of genes is a key biological process controlled largely by the 1000 base pair (bp) sequence preceding each gene (the promoter region). Within that region transcription factor binding sites (TFBS), 5-10 bp long sequences, act individually or cooperate together in the recruitment of, and therefore subsequent gene transcription by, RNA Polymerase-II (RNAP). We have measured the binding of RNAP to promoters on a genome-wide basis using Chromatin Immunoprecipitation (ChIP-on-Chip) microarray assays. Using all 8-base pair long sequences as a test set, we have identified the DNA sequences that are enriched in promoters with high RNAP binding values. We are able to demonstrate that virtually all sequences enriched in such promoters contain a CpG dinucleotide, indicating that TFBS that contain the CpG dinucleotide are involved in RNAP binding to promoters. Further analysis shows that the presence of pairs of CpG containing sequences cooperate to enhance the binding of RNAP to the promoter. [Preview Abstract] |
Monday, March 10, 2008 9:00AM - 9:12AM |
A16.00006: Dynamic self-assembly of nanocomposite ring structures through the interaction of thermodynamic and energy-dissipating processes Haiqing Liu, Erik Spoerke, Marlene Bachand, Steven Koch, Bruce Bunker, George Bachand Self-assembly of nanostructured materials occurs in thermodynamic and energy-dissipating systems. We've described a unique self-assembly scheme in which non-equilibrium nanocomposites are formed by the interaction of energy dissipation and thermodynamics. Three distinct composite structures (mobile linear, rotating circular and immobile aggregated composites) are formed when streptavidin-coated quantum dots are introduced to biotinylated microtubules that are being transported by kinesin. The circular nanocomposites occur only in a delicately balanced regime when thermodynamic and energy-dissipating components interact cooperatively. Linear translation and axial rotation of microtubules drive the formation of mechanical strain within the composites, which ultimately defines the structural shape and rotational direction. Disassembly of these composites occurs spontaneously, as well as induced by the addition of free biotin. Exploitation of dynamic self-assembly promises nanostructured materials with revolutionary behaviors that are unattainable through conventional self-assembly. \newline *Sandia is a multiprogram laboratory operated by Sandia Corporation, a Lockheed Martin Company, or the United States Department of Energy's National Nuclear Security Administration under contract DE-AC04-94AL85000. [Preview Abstract] |
Monday, March 10, 2008 9:12AM - 9:24AM |
A16.00007: How Large are Cooperative Effects in Hydrogen Bonded Molecular Chains? Martin Fuchs, Matthias Scheffler, Joel Ireta Intermolecular hydrogen bonds play an eminent role in a wide range of materials. In particular, they are critical for the secondary structure stabilization of biopolymers like proteins and nucleic acids. Arrays of hydrogen bonds (hbs), such as in chains or helices, often display a cooperative strengthening of the individual hbs. This cooperativity is crucial for understanding the stability and properties of hydrogen bonded materials. Here we investigate the hb cooperativity in model chains of HCl, HF, HCN, formamide, and 4-pyridone, i.e. molecules forming weak to strong hbs. We calculate the hb strength of infinitely long chains using density-functional theory (DFT) with the Perdew-Burke-Ernzerhof generalized gradient approximation (PBE-GGA). We show that for large intermolecular separations, the hbs in the infinite chain strengthen by 20\% over the respective molecular dimers, consistent with dipolar electrostatics [1]. At the equilibrium separation, the hbs strengthen significantly further (up to 260\% for HF), with additional stabilization from induced dipolar interactions. Comparing with results from higher-level calculations (MP2 and quantum Monte Carlo) we find that DFT faithfully describes the cooperativity in these systems in which the hbs are close to linear. [1] P.B. Allen, J. Chem. Phys. {\bf 120}, 2951 (2004) [Preview Abstract] |
Monday, March 10, 2008 9:24AM - 9:36AM |
A16.00008: Single stranded DNA hairpin loop kinetics: A Brownian dynamics study Martin Kenward, Kevin Dorfman The dynamics of single stranded DNA (ssDNA) molecules play a role in a number of biological functions and have a found uses in several microfluidic applications. In particular, ssDNA having complementary sequences at their ends can form hairpin loops in which the complementary sections bind to one another. The appearance of these loops and fluctuations between {\it open} and {\it closed} states depend on a number of variables including: the degree of complementarity of the end sequences, temperature and strength of hydrogen bonding and base stacking. In this study, we present a Brownian dynamics model which is used to examine the kinetics of the hairpin loop formation. We present results for the melting behavior of hairpins as a function of temperature and other system parameters. We also present results for the kinetic rate constants $k_{-}$ and $k_{+}$ corresponding to the open-closed and closed-open transitions respectively. [Preview Abstract] |
Monday, March 10, 2008 9:36AM - 9:48AM |
A16.00009: Statistical Analysis of the Chemotactic Motility Cycle of Amoeboid Cells. Baldomero Alonso-Latorre, Juan C. del Alamo, Ruedi Meili, Richard A. Firtel, Juan C. Lasheras Amoeboid motility results from the repetition of stereotypic steps that produce quasi-periodic oscillations of cell length and speed. We characterize the steps of the motility cycle of \textit{Dictyostelium }cells crawling on elastic substrates by analyzing their traction forces. Using a high-resolution force cytometry method for wild type cells and mutants with contractility and adhesion defects, we find that the time evolution of the traction forces is quasi-periodic, with a period (T) that correlates strongly with the cell speed (V) according to a simple law VT=L. The constant L is the distance traveled per cycle. The magnitude of the traction forces exerted by the cells does not correlate with the cell speed, suggesting that the speed of migration is determined by the ability of the cell to rapidly repeat the phases of the motility cycle. Phase average statistics allow us to combine time sequences of force maps derived from different cells to obtain a spatio-temporal representation of a canonical motility cycle divided into four steps: protrusion, contraction, retraction and relaxation. We find that myosin II-dependent contraction is present in all the steps of the wild-type motility cycle,including protrusion. [Preview Abstract] |
Monday, March 10, 2008 9:48AM - 10:00AM |
A16.00010: Force generated by polymerization of actin filaments Coraline Brangbour, Olivia du Roure, Emmanuele Helfer, Marc Fermigier, Marie-France Carlier, Jerome Bibette, Jean Baudry Actin polymerization drives protrusions at the cell surface and leads to cell motility. Using magnetic colloids, we measure how the chemical reaction of polymerization generates mechanical forces. We detail in particular the force-velocity relation of growing actin filaments; and discuss how the stalling force is affected by the mean number of filaments between two beads. [Preview Abstract] |
Monday, March 10, 2008 10:00AM - 10:12AM |
A16.00011: Probing Brownian Motion of an Ellipsoid with an External Force Shao-Qing Zhang, Wu-Pei Su Brownian motion has translational and rotational degrees of freedom. Anisotropy in the shape of a Brownian particle leads to dissipative coupling between transitional and rotational motion. However, the coupling effects, which depend on the initial orientation of an ellipsoid, cannot be detected by most typical experimental techniques. To surmount the hurdle between theoretical predictions and experimental measurements, we present a theoretical scheme for uncovering the translation- rotation coupling by applying a constant external force to an ellipsoid in a two-dimensional suspension. The geometry of the ellipsoid can be determined using the first two cumulants. An anisotropy-isotropy alternation is found in the cumulant series. We also discuss the probability distribution function (PDF) of lab-frame displacements to gain insight into the significance of anisotropy of a Brownian particle in diverse environments. [Preview Abstract] |
Monday, March 10, 2008 10:12AM - 10:24AM |
A16.00012: Probing Protein Conformations at the Oil-water Interface Using Single-Molecule Force Spectroscopy Ahmed Touhami, Marcela Alexander, Milena Corredig , John Dutcher The present work aims at a deeper understanding of the conformational changes in Beta-lactoglobulin (BLG) protein adsorbed onto the oil-in-water emulsion interfaces due to variations in pH. Mechanical unfolding of BLG using AFM-single-molecule force spectroscopy (AFM-SMFS) was performed on single oil droplets that were mechanically trapped in a polycarbonate filter. 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. Our results show clearly that at pH 2.5 BLG exists as a dimer in which each monomer is similar to two Immunoglobulin domains. At pH 6.8 BLG on the oil droplets adopts a conformation consisting of domains with a contour length of 11 nm. Furthermore, at pH 9 the interactions between the AFM tip and the BLG layer on the oil droplet surface are dominated by a huge repulsion due to the highly negatively charged BLG layer. This study demonstrates a novel application of AFM-SMFS to investigate the underlying mechanisms by which proteins can be used to stabilize food products. [Preview Abstract] |
Monday, March 10, 2008 10:24AM - 10:36AM |
A16.00013: Structural motifs of biomolecules Hoang Trinh, Jayanth Banavar, Amos Maritan, Chiara Poletto, Antonio Trovato, John Maddocks, Andrzej Stasiak Biomolecular structures are assemblies of emergent anisotropic building modules such as uniaxial helices or biaxial strands. We provide an approach to understanding a marginally compact phase of matter that is occupied by proteins and DNA. This phase, which is in some respects analogous to the liquid crystal phase for chain molecules, stabilizes a range of shapes that can be obtained by sequence-independent interactions occurring intra- and intermolecularly between polymeric molecules. We present a singularity free self-interaction for a tube in the continuum limit and show that this results in the tube being positioned in the marginally compact phase. Our work provides a unified framework for understanding the building blocks of biomolecules. [Preview Abstract] |
Monday, March 10, 2008 10:36AM - 10:48AM |
A16.00014: Instabilities of ordered chiral active suspensions Tapan Adhyapak, Davide Marenduzzo, Sriram Ramaswamy Suspensions of actively contractile or tensile filaments with simple orientational order are hydrodynamically unstable. Here we study, analytically as well as numerically, the manner in which the presence of cholesteric order competes with this instability. [Preview Abstract] |
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