Bulletin of the American Physical Society
APS March Meeting 2015
Volume 60, Number 1
Monday–Friday, March 2–6, 2015; San Antonio, Texas
Session T33: Focus Session: Conformations and Dynamics of Biopolymers II |
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Sponsoring Units: DBIO DPOLY Chair: Aniket Bhattacharya, University of Central Florida Room: 208 |
Thursday, March 5, 2015 11:15AM - 11:27AM |
T33.00001: Coupled biopolymer networks J.M. Schwarz, Tao Zhang The actin cytoskeleton provides the cell with structural integrity and allows it to change shape to crawl along a surface, for example. The actin cytoskeleton can be modeled as a semiflexible biopolymer network that modifies its morphology in response to both external and internal stimuli. Just inside the inner nuclear membrane of a cell exists a network of filamentous lamin that presumably protects the heart of the cell nucleus---the DNA. Lamins are intermediate filaments that can also be modeled as semiflexible biopolymers. It turns out that the actin cytoskeletal biopolymer network and the lamin biopolymer network are coupled via a sequence of proteins that bridge the outer and inner nuclear membranes. We, therefore, probe the consequences of such a coupling via numerical simulations to understand the resulting deformations in the lamin network in response to perturbations in the cytoskeletal network. Such study could have implications for mechanical mechanisms of the regulation of transcription, since DNA---yet another semiflexible polymer---contains lamin-binding domains, and, thus, widen the field of epigenetics. [Preview Abstract] |
Thursday, March 5, 2015 11:27AM - 11:39AM |
T33.00002: Conformations of double stranded DNA: the effect of breathing bubbles Aiqun Huang, Aniket Bhattacharya A double stranded DNA (dsDNA) is a natural semi-flexible biopolymer with persistence length $\approx$ 50 nm, while a single stranded (ss) DNA is very flexible whose persistence length is one order of magnitude smaller (3-5 nm). Depending on the temperature and sequence, the two strands in a dsDNA can locally denature into two single strands and form bubbles along the polymer chain, i.e. dsDNA exists in the form of a combination of double strands and single strands, exhibiting a heterogeneity of bending rigidity. In our study, we adopt a coarse grained model of dsDNA developed by Kim {\em et al.} [J. Y. Kim, J. H. Jeon, and W. Sung, J. Chem. Phys. {\bf 128}, 055101 2008] and further improve it by incorporating excluded volume effect and sequence heterogeneity. In this model, a dsDNA is described as two semi-flexible chains paired with each other by hydrogen bonding, the stacking interaction is designed such that the persistence length of the paired chains interpolates 3 nm and 50 nm depending on the fraction of the melted base pairs. By performing Langevin dynamics simulation we study the bubble statistics as a function of temperature and sequence and how the bubbles affect local bending rigidity and the chain conformations. We compare our results with those from WLC model. [Preview Abstract] |
Thursday, March 5, 2015 11:39AM - 11:51AM |
T33.00003: Knots along DNA Confined in Nanochannels C. Benjamin Renner, Liang Dai, Patrick Doyle We study the size distribution of spontaneous knots on semiflexible chains confined in square channels using Monte Carlo simulations. The most probable knot size is shown to vary non-monotonically with the channel size. For knotted polymers confined in channels larger than the size of a knot in bulk, our analysis reveals that the metastable knot size in weak confinement is larger than the knot size in absence of confinement because the confinement free energy gained by shrinking the knot is lessened when the chain experiences the confinement of a channel. In the case of strong confinement, the metastable knot size is smaller than the knot size in the absence of confinement because the segments in the core of the knot experience more confinement free energy, and the channels pushes the segments out of the core of the knot. We demonstrate that a simple theory can capture this non-monotonic behavior and quantitatively explain the metastable knot size as a function of the channel size. These results may have implications for tuning the channel size to either generate or screen knots. [Preview Abstract] |
Thursday, March 5, 2015 11:51AM - 12:03PM |
T33.00004: Protein dynamics from structural ensembles: Diffusive and activated contributions in a linear mode description Jeremy Copperman, Marina Guenza We have developed a coarse-grained linear Langevin equation for protein dynamics, which describes proteins as semiflexible objects collapsed into the free energy well representing the folded state of the protein. Fundamental to this approach is the inclusion of internal dissipation, absent in any rigid-body hydrodynamical modeling scheme. The normal mode analytical solution naturally separates into global modes describing the anisotropic tumbling of the object, and internal modes which contain both diffusive and activated glass-like contributions. We show how cooperativity in the dynamical modes is related to the energy barriers to mode diffusion. While molecular dynamic simulations generate the most accurate structural ensembles, we show how sets of NMR conformers can be used to generate the structural ensemble needed as input to the theory, making the approach truly predictive in nature. Results are in good agreement when compared with both nuclear magnetic resonance relaxation, and time correlation functions calculated from molecular dynamic simulations. [Preview Abstract] |
Thursday, March 5, 2015 12:03PM - 12:15PM |
T33.00005: Driven Polymer Translocation into a Crosslinked Gel David Sean, Gary W. Slater In a typical polymer translocation setup, a thin membrane is used to separate two chambers and a polyelectrolyte is driven by an electric field to translocate from one side of the membrane to the other via a small nanopore. However, the high translocation rate that results from the forces required to drive this process makes optical and/or electrical analysis of the translocating polymer challenging. Using coarse-grained Langevin Dynamics simulations we investigate how the translocation process can be slowed down by placing a crosslinked gel on the trans-side of the membrane. Since the driving electric field is localized in the neighborhood of the nanopore, electrophoretic migration is only achieved by a ``pushing'' action from the polymer segment residing in the nanopore. For the case of a flexible polymer we find that the polymer fills the gel pores via multiple ``herniation'' processes, whereas for a semi-flexible chain in a tight gel there are no hernias and the polymer follows a smooth curvilinear path. Moreover, for the case of a semi-flexible polymer the gel makes the translocation process more uniform by reducing the acceleration at the end of the process. [Preview Abstract] |
Thursday, March 5, 2015 12:15PM - 12:27PM |
T33.00006: Backfolded Odijk regime for semiflexible polymers confined in nanochannels Abhiram Muralidhar, Douglas Tree, Kevin Dorfman The description of properties of DNA confined in a nanochannel with size close to its persistence length has attracted significant attention recently due to its relevance to genome mapping technology. However, clear consensus between existing theories, simulations and experiments in this range of confinement is still lacking. In this talk, we show via Pruned-Enriched Rosebluth Method (PERM) simulations that Odijk's scaling theory based on hairpin formation describes the properties of confined wormlike chains when the confinement size is commensurate with the persistence length. This was made possible by our calculation of the global persistence length, which characterizes the length scale between hairpin bends in the confined molecule. We find that the range of this ``backfolded'' Odijk regime increases with the monomer anisotropy ratio $l_{\mathrm{p}}/w$, where $l_{\mathrm{p}}$ and $w$ are the persistence length and width of the molecule respectively. We are thus able to predict the experimental conditions under which one could observe these hairpins for various stiff molecules such as DNA and actin. This information can be used to engineer favorable conditions for genome mapping technology. [Preview Abstract] |
Thursday, March 5, 2015 12:27PM - 12:39PM |
T33.00007: Electrophoresis of a polyelectrolyte attached to a solid object: A strong influence of the attachment point Mykyta V. Chubynsky, Gary W. Slater In some applications of electrophoresis, a polyelectrolyte (such as the DNA) is attached to an electrically neutral object of an irregular shape (e.g., a globular protein). Because of the hydrodynamic interactions (HI) between the polymer and the object, the amount by which the polymer is slowed down should depend on the shape of the object, especially near the attachment point, and not only on its drag coefficient. To study this effect, we compute the electrophoretic mobility of a short neutral tube closed at one end with a charged polymer attached to the closed end, either inside or outside the tube. Both the polymer and the tube are represented as sets of beads and the HI are pre-averaged. For a short polymer that would occupy only a small part of the tube, the mobility is much lower when the polymer is inside than when it is outside. The mobility ratio depends exponentially on the tube length and exceeds an order of magnitude already when the length of the tube equals its width. As the polymer size is increased and the coil size approaches the tube length, the mobility in the case of inside attachment starts to grow rapidly and then quickly approaches that in the case of outside attachment. [Preview Abstract] |
Thursday, March 5, 2015 12:39PM - 12:51PM |
T33.00008: Electrostatic effects on hyaluronic acid configuration John Berezney, Omar Saleh In systems of polyelectrolytes, such as solutions of charged biopolymers, the electrostatic repulsion between charged monomers plays a dominant role in determining the molecular conformation. Altering the ionic strength of the solvent thus affects the structure of such a polymer. Capturing this electrostatically-driven structural dependence is important for understanding many biological systems. Here, we use single molecule manipulation experiments to collect force-extension behavior on hyaluronic acid (HA), a polyanion which is a major component of the extracellular matrix in all vertebrates. By measuring HA elasticity in a variety of salt conditions, we are able to directly assess the contribution of electrostatics to the chain's self-avoidance and local stiffness. Similar to recent results from our group on single-stranded nucleic acids, our data indicate that HA behaves as a swollen chain of electrostatic blobs, with blob size proportional to the solution Debye length. Our data indicate that the chain structure within the blob is not worm-like, likely due to long-range electrostatic interactions. We discuss potential models of this effect. [Preview Abstract] |
Thursday, March 5, 2015 12:51PM - 1:03PM |
T33.00009: Nuclear Pore Complex Protein Sequences Determine Overall Copolymer Brush Structure and Function? David Ando, YongWoon Kim, Roya Zandi, Michael Colvin, Michael Rexach, Ajay Gopinathan Disordered proteins are an interesting class of unfolded protein biopolymers which are functionally versatile. Their sequences are unconstrained by a sequence-structure relationship, and allow for a wide range of chemical and physical polymer properties. The Nuclear Pore Complex (NPC) contains over one hundred of such proteins (FG nups), which collectively function to regulate the exchange of all materials between the nucleus and cytoplasm. We perform coarse grained simulations of both individual FG nups and grafted rings of nups mimicking the in vivo geometry of the NPC, supplemented with polymer brush modeling. Our results indicate that different regions or ``blocks'' of an individual FG nup can have distinctly different forms of disorder, and that this property appears to be a conserved feature across eukarya. Furthermore, this block structure at the individual protein level is critical to the formation of a unique higher-order polymer brush architecture. Because the interactions between FG nups may be modulated by certain forms of transport factors, our results indicate that transitions between brush morphologies could play an important role in regulating transport across the NPC, suggesting novel forms of gated transport across membrane pores with wide biomimetic applicability. [Preview Abstract] |
Thursday, March 5, 2015 1:03PM - 1:15PM |
T33.00010: When DNA Collides With Itself Zubair Azad, Robert Riehn Long range interactions in large DNA molecules are typically modeled as self-avoiding random walks. While this is useful for understanding equilibrium configurations, dynamic behavior may include more complex polymer-polymer coupling. Here we explore the possibility of internal friction within hernias of DNA under nano-confinement and fluid flow. We study the rates at which DNA hernias form and recoil at various flow speeds and hernia sizes. The formation and recoil behaviors point to possible entanglement between two genetically distant regions of DNA as they flow in the same direction. To explore internal friction between two strands moving in opposite directions, we scan the two strands comprising the hernia as well as two independent molecules against each other. From these studies, we address the drag or friction forces on two molecules under confinement and compare to the analogous system of one nano-confined molecule. [Preview Abstract] |
Thursday, March 5, 2015 1:15PM - 1:27PM |
T33.00011: Molecular Dynamics study on the Micellization of Rhamnolipids. Elango Munusamy, Steven D. Schwartz Oil spills have become one of the most serious environmental and ecological problems owing to the growth of oil exploration, production and transportation. Millions of gallons of crude oil and refined products are spilled into marine waters worldwide each year. Large volumes of surfactants are applied to the ocean as a remediation strategy. Environmental and toxicity issues arise when such a voluminous amounts of chemical surfactants are applied. One prospective solution to this problem is to use greener surfactants that possess excellent biodegradation and toxicity characteristics relative to existing classes of commonly used surfactants. In this context, we are interested in designing and developing greener surfactants that are patterned after naturally occurring glycolipids. In the present work, we concentrate on one of the more commonly studied glycolipid, rhamnolipid (Rha$_{\mathrm{1}}$C$_{\mathrm{10}}$C$_{\mathrm{10}})$. Despite the available experimental data, the molecular structure, shape and geometry of micelles formed by rhamnolipid is unknown. Molecular Dynamics (MD) simulations were performed to understand the aggregation behavior of rhamnolipids in aqueous solution and at air-water interface. All calculations were performed in NPT ensembles at 300 K using NAMD 2.8, a parallel code designed for high-performance simulation of large biological macromolecule using the CHARMM force field. The results obtained from MD simulations on the aggregation of rhamnolipids in water and at air-water interface will be presented. [Preview Abstract] |
Thursday, March 5, 2015 1:27PM - 1:39PM |
T33.00012: Combining Protein Dynamics and Aggregation Measurements Curtis Meuse Infrared spectroscopy has long been used to deduce concentration and structural descriptions of proteins in a variety of static and time resolved experiments. We have developed an infrared order parameter to describe protein conformation variations around the average molecular values. Here, we combine our order parameter measurements with circular dichroism, light scattering and atomic force microscopy measurements to clarify the characterization of protein structure and aggregation. By combining the information from our suite of methods, we explore the relationship between protein stability, dynamics and aggregation. Our focus is on developing new methods to compare the structure, dynamics and function of nearly identical biopharmaceutical protein ensembles. Examples include lysozyme, albumin cytochrome $c$ and the characterization of amyloid beta during aggregation. [Preview Abstract] |
Thursday, March 5, 2015 1:39PM - 1:51PM |
T33.00013: Wide Field Spectroscopy of Diffusing and Interacting DNA Using Tunable Nanoscale Geometries Shane Scott, Jason Leith, Hugo Brandao, Simon Sehayek, Alexander Hofkirchner, Jill Laurin, Daniel Berard, Alexander Verge, Paul Wiseman, Sabrina Leslie It remains an outstanding challenge to directly image interacting and diffusing biomolecules under physiological conditions. Many biochemical questions can be posed in the form: Does A interact with B? What are the energetics, kinetics, stoichiometry, and cooperativity of this interaction? To tackle this challenge, we use tunable nanoscale confinement to perform wide-field imaging of interacting DNA molecules in free solution, under an extended range of reagent concentrations and interaction rates. We present the integration of ``Convex Lens-induced Confinement (CLiC)'' microscopy with image correlation analysis, simultaneously suppressing background fluorescence and extending imaging times. The measured DNA-DNA interactions would be inaccessible to standard techniques but are important for developing a mechanistic understanding of life-preserving processes such as DNA transcription. [Preview Abstract] |
Thursday, March 5, 2015 1:51PM - 2:03PM |
T33.00014: Observation of DNA dynamics near silicon nanopores by controlling the ultraviolet light spot Hirohito Yamazaki, Shintaro Ito, Keiko Esashika, Toshiharu Saiki Biopolymer translocation through a nanopore is an attractive phenomenon in the field of biophysics. When the voltage is applied through a nanopore, DNA coils thread into a nanopore by deforming its coil structure and recoil after translocation through a nanopore. Because DNA coil structure is relative with DNA translocation, DNA dynamics near a nanopore have a correlation with DNA translocation. To investigate DNA dynamics, we developed the optical nanopore detection system, which has a capability to observe DNA dynamics near nanopore at sub-100-nm and sub-millisecond resolutions. Here, we report our experimental results of DNA dynamics near nanopores by controlling position of light spots. Because silicon have high refractive index and extinction coefficient at ultraviolet light, the ultraviolet light creates z- and x-polarized light spot, which locate on nanopores and 50 nm apart from nanopores, respectively. By controlling light polarization, we observed different fluorescence intensity traces between z- and x-polarized light spot. The experimental results showed that fluorescence intensity trance of z-polarized light spot decayed faster than that of x-polarized light spot, which explain DNA dynamics near nanopores change by position from nanopores. [Preview Abstract] |
Thursday, March 5, 2015 2:03PM - 2:15PM |
T33.00015: Tension-induced binding of semiflexible biopolymers Panayotis Benetatos, Alice von der Heydt, Annette Zippelius We investigate theoretically the effect of polymer tension on the collective behaviour of reversible cross-links. We use a model of two parallel-aligned, weakly-bending wormlike chains with a regularly spaced sequence of binding sites subjected to a tensile force. Reversible cross-links attach and detach at the binding sites with an affinity controlled by a chemical potential. In a mean-field approach, we calculate the free energy of the system and we show the emergence of a free energy barrier which controls the reversible (un)binding. The tension affects the conformational entropy of the chains which competes with the binding energy of the cross-links. This competition gives rise to a sudden increase in the fraction of bound sites as the polymer tension increases. The force-induced first-order transition in the number of cross-links implies a sudden force-induced stiffening of the effective stretching modulus of the polymers. This mechanism may be relevant to the formation and stress-induced strengthening of stress fibers in the cytoskeleton. [Preview Abstract] |
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