Bulletin of the American Physical Society
2006 APS March Meeting
Monday–Friday, March 13–17, 2006; Baltimore, MD
Session Y30: Focus Session: Biopolymers I: Phase Transitions |
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Sponsoring Units: DPOLY DBP Chair: Jose Onuchic, University of California, San Diego Room: Baltimore Convention Center 327 |
Friday, March 17, 2006 8:00AM - 8:36AM |
Y30.00001: Temperature and Pressure effects on folding/unfolding of proteins Invited Speaker: High hydrostatic pressures change the energy landscape of proteins, affecting the thermodynamics and kinetics of folding. Proteins denature at high hydrostatic pressures, implying that the unfolded proteins in aqueous solution have lower volume than the folded state. A model that explains pressure unfolding requires water to penetrate the protein interior and disrupt the protein hydrophobic core. I will explore the energetics of water penetration and the effect of pressure on hydrophobic interactions. I will also describe molecular simulations of the reversible folding/unfolding equilibrium as a function of density and temperature of solvated peptides that can form alpha helices (the AK peptide) and beta hairpins (the C terminal domain of protein G). I will characterize the structural, thermodynamic and hydration changes as a function of temperature and pressure. To study protein folding equilibrium thermodynamics we use an extension of the replica exchange molecular dynamics (REMD) method that allows for density and temperature Monte Carlo exchange moves. [Preview Abstract] |
Friday, March 17, 2006 8:36AM - 9:12AM |
Y30.00002: The energy landscape for folding and function Invited Speaker: Globally the energy landscape of a folding protein resembles a partially rough funnel. The local roughness of the funnel reflects transient trapping of the protein configurations in local free energy minima. The kinetics of folding is best considered as a progressive organization of an ensemble of partially folded structures through which the protein passes through on its way to the folded structure. The folding mechanisms for several fast-folding proteins can be described using an energy landscape theory to set up the correspondence with simulations of protein minimalist models. Using these simulations together with analytical theory, we can learn about good (minimally frustrated) folding sequences and non-folding (frustrated) sequences. An important idea that emerges from this theory is that subtle features of the protein landscape can profoundly affect the apparent mechanism of folding. Experiments on the dependence of the folding/unfolding times, and the stability of these proteins to denaturant concentration and site-directed mutagenesis, and on the early events of folding allow to infer the global characteristics of the landscape. In addition to need to minimize energetic frustration, the topology of the native fold also plays a major role in the folding mechanism. Some folding motifs are easier to design than others suggesting the possibility that evolution not only selected sequences with sufficiently small energetic frustration but also selected more easily designable native structures. Several proteins (such as CI2 and SH3) have sufficiently reduced energetic frustration) that much of the heterogeneity observed in their transition state ensemble (TSE) is determined by topology. Topological effects go beyond the structure of the TSE. The overall structure of the on-route and off-route (traps) intermediates for the folding of more complex proteins is also influenced by topology. Utilizing this theoretical framework, simulations of minimalist models and computationally-expensive all-atom simulations, we are now obtaining a quantitative understanding of the folding problem, which allows for a direct comparison to a new generation of folding experiments. Connections between the folding landscape and protein function will also be discussed. [Preview Abstract] |
Friday, March 17, 2006 9:12AM - 9:24AM |
Y30.00003: RNA folding inside a virus capsid and dimensional reduction. Rouzbeh Ghafouri, Robijn Bruinsma, Joseph Rudnick As RNA folds on itself , in certain conditions, it takes the form of a branched polymer. So the problem of RNA folding in a virus capsid is essentially the problem of a branched polymer in a confined environment. In this paper we attack the problem using the technique of dimensional reduction which relates a branched polymer with self interation in D dimension to a hardcore classical gas in (D-2) dimension. We look for phase transitions and intersting physical quantities such as pressure. [Preview Abstract] |
Friday, March 17, 2006 9:24AM - 9:36AM |
Y30.00004: On the Melting Transition of RNA David Schwab, Robijn Bruinsma The secondary structure of RNA can undergo a phase transition from a designed native state to a branched molten-globule. This melting transition is continuous, neglecting excluded volume. We study the effect of excluded volume interactions in good solvent on the melting transition. First, we calculate the effect of a constant external tension on the melting transition in the ideal polymer case and then, in the context of Flory theory, equate the tension with what would be generated by excluded volume. We find that, with excluded volume, the continuous melting transition is still second order but with a different exponent. [Preview Abstract] |
Friday, March 17, 2006 9:36AM - 9:48AM |
Y30.00005: Trapping and Condensing DNA at the Air/Water Interface Jaime Ruiz-Garcia DNA is a highly charged polyelectrolite and as such it is considered to be completely soluble in pure water. Surprisingly, we found that DNA can be trapped at the air/water interface and does not go back into a pure water subphase. Once at the interface, DNA molecules condense to form different two-dimensional mesostructures such as foams, giant rings, disks and rods at low density. This condensation occurs without the presence of multivalent cationic ions, as it is required in bulk, for example in condensing DNA toroids. At high density, the molecules form a regular monomolecular network. At the interface, DNA is only partially immersed in water, which originates that the chains get only partially charged, but the charges are of the same sign. Therefore, this can be considered another case of like-charge attraction, similar to those found in colloids trapped between glass plates and at the air/water interface. However, the origin of the attractive part of the interaction potential is unknown. In addition, we found that DNA at the air/water interface can form 2D smectic-like domains tens of microns in size, which are interesting from a theoretical and application standpoints. [Preview Abstract] |
Friday, March 17, 2006 9:48AM - 10:00AM |
Y30.00006: Insight into the Helix-to-Coil Transition in DNA Boualem Hammouda Dissolved DNA is known to undergo a helix-to-coil transition when temperature is increased. For a solution of 4{\%} DNA in water, the transition temperature is around 94$^{o}$C. UV absorption spectroscopy was performed to characterize such a transition. The 260 nm absorption line is a good monitor of the un-stacking of the DNA amine bases. Small-Angle Neutron Scattering was also performed to investigate structural changes that accompany the transition. A characteristic DNA cross section correlation length was found to increase from 9A to 15A and the Porod exponent was found to decrease from close to 4 to around 2 across the transition. The average sugar-sugar inter-distance is larger in the open molecule coil phase. The helix phase is characterized by a cylindrical structure with well-defined interface whereas melted DNA macromolecules behave like Gaussian coils. Jump in the scattered (solvation) intensity was also observed across the transition. A hysteresis cycle was observed upon a subsequent temperature decrease. Once DNA melts, it does not reform the helix phase easily. DNA solvation (interaction of DNA and solvent molecules) has also been investigated. When solvent mixtures (for example water/alcohol mixtures) are used, ideal solvent mixing is observed for the helix phase but a highly non-ideal mixing behavior is observed for the coil phase. [Preview Abstract] |
Friday, March 17, 2006 10:00AM - 10:12AM |
Y30.00007: Diffusion of Isolated DNA molecules: dependence on length and topology Rae M. Robertson, Stephan Laib, Douglas E. Smith Diffusion coefficients (D) for relaxed circular and linear DNA molecules ranging in length (L) from 5.9 to 287.1 kilobasepairs were measured by tracking the Brownian motion of single molecules. A topology independent scaling law, D$\sim $L$^{-0.58+/-0.016}$, was observed, in good agreement with the --0.588 exponent predicted by renormalization group theory. The measured ratio D$_{Circular}$/D$_{Linear}$ = 1.32+/-0.014 fell between predictions of 1.18 for Kirkwood hydrodynamic theory and 1.45 for renormalization group theory and agreed best with a value 1.31 predicted using the Zimm model and an expression for the radius of gyration proposed by Bensafi, Maschke, and Benmouna. Measurements on supercoiled DNA molecules were also made and qualitatively compared to theoretical predictions. [Preview Abstract] |
Friday, March 17, 2006 10:12AM - 10:24AM |
Y30.00008: Mobility of DNA on supported lipid bilayers Chakradhar Padala, Richard Cole, Sanat Kumar, Ravi Kane Extensive theoretical ideas have been developed to understand the transport properties of transmembrane proteins in the lipid bilayer. However, of late, there has been a rising interest in understanding the transport properties of non-compact macromolecules strongly adsorbed ``on'' and not incorporated into lipid bilayers in light of the relevance for designing improved DNA separation strategies and for gene therapy. Previously, researchers like Radler \textit{et al}. have suggested that such strongly adsorbed polymers can be treated similar to a polymer in a two-dimensional fluid, but there exists no experimental proof to date. In order to test this hypothesis and also to gain a better understanding of polymer dynamics in two dimensions, we studied the lateral transport of a short, single stranded DNA oligonucleotide adsorbed on a supported cationic lipid bilayer. Fluorescence Recovery After Photobleaching (FRAP) analysis reveals that diffusivity of the adsorbed DNA quantitatively tracks that of the underlying lipid. These results, along with the comparison between our results for short, non-compact adsorbed biopolymers and those reported for globular proteins incorporated into the lipid bilayer will be discussed. [Preview Abstract] |
Friday, March 17, 2006 10:24AM - 10:36AM |
Y30.00009: Electrophoresis of DNA on a disordered two-dimensional substrate Cynthia J. Olson Reichhardt, Charles Reichhardt We propose a new method for electrophoretic separation of DNA in which adsorbed polymers are driven over a disordreed two-dimensional substrate which contains attractive sites for the polymers. Using simulations of a model for long polymer chains, we show that the mobility increases with polymer length, in contrast to gel electrophoresis techniques, and that separation can be achieved for a range of length scales. We demonstrate that the separation mechanism relies on excluded volume interactions between polymer segments. [Preview Abstract] |
Friday, March 17, 2006 10:36AM - 10:48AM |
Y30.00010: Kinetic Modeling of Designed Signaling DNA Aptamers Issei Nakamura, Razvan Nutiu, Jasmine Yu, Yingfu Li, An-Chang Shi Aptamers are recently developed molecular biosensors made of single functionalized DNA molecules. They can bind a protein target specifically or a complementary DNA sequence. The binding kinetics can be studied based on the principle of fluorescence quenching, which in turn provides an understanding of the binding mechanism and the conformational structure of DNA during the binding reaction. Despite many experimental studies, an understanding of the binding reaction is still lacking. In our study, we constructed kinetic models for the aptamer binding reaction, and showed that the theoretical models can be studied to describe experimental observations. Determined parameters for the rate constant for the reaction provided us with an understanding of the binding mechanism of aptamers. We will discuss the numerical solutions to them in comparison with the experiment and show how the binding reaction of aptamers occurs as time proceeds. [Preview Abstract] |
Friday, March 17, 2006 10:48AM - 11:00AM |
Y30.00011: AFM Imaging of Counterion-Induced Phase Transition of Biological Polyelectrolyte Network on a Photopolymer Containing Azo-Dye Taiji Ikawa, Osamu Watanabe, Youli Li, Cyrus Safinya We present a new method for direct imaging of protein assembly based on atomic force microscopy and a protein immobilization technique using a nonionic photopolymer containing azo-dye; the photopolymer was found to be capable of holding proteins in an aqueous solution by exposure to blue-wavelength light. As a model system, we examine the association of actin filament in the presence of divalentcation. We find the method clearly represents phase transitions of the filament network as a function of both cation concentration and filament length. Longer filaments (up to 10 $\mu $m) shows an isolated single filament phase (0 mM of Mg$^{2+})$ transforms to a web-like network phase (5-10 mM) and finally condenses into a close-packed bundled phase (20-80 mM). Meanwhile, shorter filaments (up to 200 nm) form a co-existing nematic-like raft phase at intermediate cation concentration (5-40 mM), coinciding with the previous result obtained by small-angle x-ray scattering study. From angular analysis, the longer filament is shown to prefer wider angular configuration, suggesting the interaction between filaments is dependent on their length such that longer filaments are more repulsive than shorter one. [Preview Abstract] |
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