Bulletin of the American Physical Society
2005 APS March Meeting
Monday–Friday, March 21–25, 2005; Los Angeles, CA
Session S22: Biological Physics |
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Sponsoring Units: DBP Chair: Sonya Bahar, University of Missouri-St. Louis Room: LACC 409B |
Wednesday, March 23, 2005 2:30PM - 2:42PM |
S22.00001: Visualizing interactions between Sindbis virus and cells by single particle tracking Mary Williard, Gongbo Wang, Keith Weninger Sindbis virus infects both mammalian and insect cells. Though not pathogenic in humans, Sindbis is a model for many mosquito- borne viruses that cause human disease, such as West Nile virus. We have used real-time single particle fluorescence microscopy to observe individual Sindbis virus particles as they infect living cells. Fluorescent labels were incorporated into both the viral coat proteins and the lipid envelope of the virus. Kinetics characteristic of free diffusion in solution, slower diffusion inside cells, attachment to spots on the cell surface, and motor protein transport inside cells have been observed. Dequenching of the membrane label is used to report membrane fusion events during the infection process. Tracking individual viral particles allows multiple pathways to be determined without the requirement of synchronicity. [Preview Abstract] |
Wednesday, March 23, 2005 2:42PM - 2:54PM |
S22.00002: Shape transformation of viral capsids and HIV Toan Nguyen, Robijn Bruinsma, William Gelbart We present a continuum description of the shape transformation of viral capsids. The cone-like HIV virus is shown to be an thermodynamic stable shape, intermediate between icosahedral and sphero-cylinder capsid shapes. A generalized Caspar-Klug classification is introduced to describe spherical, conical and cylinderical shapes of virus. [Preview Abstract] |
Wednesday, March 23, 2005 2:54PM - 3:06PM |
S22.00003: Fracture Toughness of Nacre Phani Nukala, Srdjan Simunovic Nacre exhibits phenomenal fracture strength and toughness properties despite the brittle nature of its constituents. For example, its work of fracture is three orders of magnitude greater than that of a single crystal of its constituent mineral. This is surprising because it is a ceramic composite made up of about 95\% brittle inorganic phase (aragonite mineral) and only a few percent of the soft organic material, and polymer-matrix composites with such high levels of ceramic fillers do not possess these exceptional combinations of stiffness, fracture strength and toughness. This study investigates the fracture properties of nacre using a simple discrete lattice model based on continuous damage random thresholds fuse network. The discrete lattice topology of the proposed model is based on nacre's unique brick and mortar microarchitecture, and the mechanical behavior of each of the bonds in the discrete lattice model is governed by the characteristic modular damage evolution of the organic matrix that includes the mineral bridges between the aragonite platelets. The numerical results obtained using this simple discrete lattice model are in excellent agreement with the previously obtained experimental results, such as nacre's stiffness, tensile strength, and work of fracture. The analysis indicates that nacre's superior toughness is a direct consequence of ductility (maximum shear strain) of the organic matrix in terms of repeated unfolding of protein molecules, and its high fracture strength is a result of its perfectly ordered brick and mortar architecture with significant overlap of the platelets, and shear strength of the organic matrix. [Preview Abstract] |
Wednesday, March 23, 2005 3:06PM - 3:18PM |
S22.00004: How do protozoa respond to intense magnetic fields? Karine Guevorkian, James M. Valles, Jr. Most microorganisms such as \textit{Paramecium Caudatum}, swim in helical paths in nature. In the absence of any external stimuli (e.g. obstacles, electric field, heat, etc.) the axes of these helical paths, which define the trajectories, are straight lines and are distributed in random directions. Our experiments reveal that these trajectories can be manipulated by applying intense DC magnetic fields of the order of several Tesla. Swimming paramecia, for example, align their trajectories with magnetic fields in excess of about 7 Tesla in fraction of a second. We will describe this phenomenon in fields up to 25 T. We will address whether this effect is an active or passive response to the magnetic torque exerted on the diamagnetically anisotropic structures in \textit{Paramecium}. In addition we will present results for other species as they are obtained. [Preview Abstract] |
Wednesday, March 23, 2005 3:18PM - 3:30PM |
S22.00005: Geometry and physics of proteins Jayanth R. Banavar, Marek Cieplak, Trinh X. Hoang, Amos Maritan, Flavio Seno, Antonio Trovato We recall some of the key lessons of protein research over the last several decades and show that they strongly suggest a new framework for understanding proteins. The unified framework is useful for understanding protein folding, amyloid formation and protein interactions and has important implications for natural selection. The experimental data and our new approach, supported by computer simulations, reveal an astonishing simplicity underlying the protein problem. \\ \\REFERENCES: Banavar, J. R. and Maritan, A. (2003). Colloquium: Geometrical approach to protein folding: A tube picture. Rev. Mod. Phys. 75, 23. \\Banavar, J. R., Hoang, T. X., Maritan, A., Seno, F. and Trovato, A., (2004). A unified perspective on proteins -- a physics approach. Phys. Rev. E 70, 041905. \\Banavar, J. R., Cieplak, M. and Maritan, A., (2004). Lattice tube model of proteins, Phys. Rev. Lett. (in press). [Preview Abstract] |
Wednesday, March 23, 2005 3:30PM - 3:42PM |
S22.00006: Molecular dynamics simulations of peptides interacting with a surface: Do surfaces prevent or promote aggregation? Miriam Friedel, Joan-Emma Shea Understanding the process of protein and peptide aggregation is critical to treating and preventing debilitating diseases such as Alzheimer's. In particular, there is evidence that the aggregation process may be influenced by protein-surface or protein-membrane interactions. Nevertheless, there have been few molecular dynamics (MD) studies of proteins and peptides interacting with surfaces. Here, we present the results of an MD study of an off-lattice peptide model. Simulations of peptides both in a bulk environment and interacting with a hydrophobic surface were performed. With this simple model, we examined the impact of peptide sequence and surface hydrophobicity on the thermodynamics and kinetics of aggregation, and our results indicate that both play a significant role in determining aggregation behavior. Although interaction with a surface allows the peptides to form aggregates not easily achieved in the bulk, the kinetics of assembly is not necessarily enhanced by the presence of a surface. [Preview Abstract] |
Wednesday, March 23, 2005 3:42PM - 3:54PM |
S22.00007: Motorized adhesive particles in localized phases: A toy model for the controlling of viscoelastic phases of cytoskeletal assembly Tongye Shen, Peter Wolynes The cytoskeleton is not an equilibrium structure. To begin to investigate it, we studied a system of motorized particles that may capture the far-from-equilibrium essence of its dynamics. Variational solutions of the manybody master equation for a set of motorized spherical particles accounts for their Brownian motion as well as for motorized kickings. These approximations yield stability limits for crystalline phases and frozen amorphous structures. The methods allow one to relate the strength of nonequilibrium effects and adhesiveness (effective cross-linking of cytoskeleton) to the mechanical stability of localized phases as a function of density and/or temperature. Interestingly nonequilibrium noise does not necessarily destabilize the structures. The dynamics issues are also touched. [Preview Abstract] |
Wednesday, March 23, 2005 3:54PM - 4:06PM |
S22.00008: A Comparison Between Adaptive Integration and Path-Sampling Methods for Calculating Free Energy Differences in Molecular Systems F. Marty Ytreberg, Daniel M. Zuckerman, Robert H. Swendsen The calculation of free energy differences ($\Delta F$) is essential for the understanding of protein-ligand binding, the conformational stability of proteins and many molecular processes, yet it remains one of the most challenging tasks in computational biophysics. Here we present a study of two recently developed free energy methods, both applied to molecular systems for the first time. The first approach is an adaptive integration Monte Carlo procedure which continually updates the free energy profile connecting the two states of interest. The second method is a path-sampling implementation of the Jarzynski relation which uses a Monte Carlo procedure to generate an ensemble of non-equilibrium paths connecting the two states of interest. Both techniques are compared to the standard methods of thermodynamic integration and use of the Jarzynski relation, by calculating $\Delta F$ values for growing and for charging a simple ion in explicit SPC water. Adaptive integration is found to have the highest precision and accuracy for long simulation times. However, if very rapid $\Delta F$ estimates are the goal, the path-sampling approach is found to be the most efficient. [Preview Abstract] |
Wednesday, March 23, 2005 4:06PM - 4:18PM |
S22.00009: Effect of temperature on fd and M13 aggregation Qi Wen, Jay Tang Counterion induced aggregation of like-charged polyelectrolytes(PE) such as DNA, F-actin and fd viruses has been investigated extensively. It has been shown that the like-charge attraction is due to the correlation of counterions. The classic Oosawa model suggests that thermal fluctuations of counterions gives rise to a net attractive interaction between two paralel charged rods by inducing transient dipole moments on them. This attractive force is reminiscent of van de Waals interaction, and the interaction is expected to increase with temperature. Alternatively, positional correlations of counterions has been shown by Brownian Dynamics simulations to induce an attractive force that decreases with increasing temperature. In order to determine the dominant mechanism by which the counterions are correlated to induce attractive force, we measure the temperature dependence of threshold concentrations of divalent counterions that cause the aggregation of fd and M13 viruses. Our priliminary measurements favor the Oosawa type of mechanism, although specific chemical effects may affect the interpretation of the experimental results. [Preview Abstract] |
Wednesday, March 23, 2005 4:18PM - 4:30PM |
S22.00010: Molecular dynamics study of the Mg - AMP interaction in water Don Brugess, Ioan Kosztin The conformational states of $Mg^{++}$ complexed with adenosine monophosphate (AMP) in water solution is analyzed using classical molecular dynamics (MD) simulations. Relevant portions of the 3D \textit{potential of mean force} (PMF) of $Mg^{++}$ is reconstructed by employing two distinct methods: (1) equilibrium MD simulations using the umbrella sampling and weighted histogram analysis method, and (2) non-equilibrium steered MD simulations using a recently developed method based on the Jarzynski equality. Withing computational errors, both methods yield the same results. Two topologically distinct sets of equilibrium conformations of $Mg^{++}$ in the vicinity of the phosphate moiety are found. The free energy difference between the states within a given set is about $1~kT$, and are separated by potential barriers of $\sim 10~kT$ in height. However, the free energy difference between states from the two distinct sets are found to be unrealistically high ($\sim 10~$kcal/mol). Also, the calculated dissociation energy of Mg++ from AMP exceeds several times the corresponding experimental value. Possible sources of this discrepancy are discussed, and alternative methods to improve the accuracy of the calculations are proposed. [Preview Abstract] |
Wednesday, March 23, 2005 4:30PM - 4:42PM |
S22.00011: Predictive filtering in the phototransduction cascade Ilya Nemenman Animals gather sensory information to guide their actions. But acting takes time, and sense data are useful only to the extent that they carry predictive information, that is, information about the state of the world at the time of the actions. We suggest that efficient maximization, extraction, and transmission of such predictive information, rather than maximization of the overall channel capacity, may be the correct optimization principle responsible for designs of some sensory systems. We support these arguments by analyzing information transmission in the enzymatic amplifier in the phototrandusction cascade, were maximization of predictive information seems to explain various experimentally observed properties, such as time scale and gain adaptation. Further, we emphasize that some standard filters used in signal processing can be viewed as (implicitly) maximizing predictive information as well. [Preview Abstract] |
Wednesday, March 23, 2005 4:42PM - 4:54PM |
S22.00012: Theoretical Study on the Influence of Solvent on Subtilisin Catalysis Yiming Zhang, Lu Yang, Jonathan Dordick, Shekhar Garde, Saroj Nayak Using a hybrid quantum mechanical and molecular mechanical (QM/MM) approach we have studied subtilisin catalysis in water and tetrahydrofuran (THF). Extensive classical molecular dynamics simulations have been carried out in order to obtain the solvent structure around the protein, while hybrid QM/MM method is used to provide the reaction energy profile for the enzymatic reaction. The reaction energy barrier for the formation of the enzyme's tetrahedral intermediate in water is found to be about 7 kcal/mol lower than formation of the tetrahedral intermediate in THF. This result is in good agreement with experimental data where the reactivity of subtilisin is up to four orders of magnitude lower in THF than in water. The lower reaction barrier in water is related to the enhanced stabilization of the enzyme's transition state (TS) in water through hydrogen bonding between solvent water molecules and the TS complex. In addition, we find that the role of Asp32 in stabilizing the tetrahedral intermediate state abates in THF. [Preview Abstract] |
Wednesday, March 23, 2005 4:54PM - 5:06PM |
S22.00013: Dynamical and Mechanical Behavior of Associating Protein Hydrogels Darina Danova, James L. Harden, David R. Heine, Gary S. Grest Molecular dynamics simulation is used to study the dynamical and mechanical properties of hydrogels made from synthetic associating proteins. These proteins are triblock architectures composed of a central soluble, unstructured block flanked by associating helical ends. The ends are amphiphilic leucine zippers designed to reversibly assemble into trimeric bundles. Solutions of the triblock proteins reversibly self-assemble into hydrogels with predominantly trifunctional crosslinks. The hydrogel formation may be controlled by changes in temperature and pH, thus providing a switchable material with potential application in biomedical and environmental engineering. A coarse-grained model which mimics the alpha-helical secondary structure and amphiphilic properties of the leucine zipper domains is developed in order to accurately describe the structure and dynamics of the self-assembling hydrogel. Then, mechanical properties of the hydrogel under uniaxial and shear strain are presented and related to changes in the molecular level structure of the hydrogel in an effort to relate the protein structure to the hydrogel material properties. [Preview Abstract] |
Wednesday, March 23, 2005 5:06PM - 5:18PM |
S22.00014: Encapsidation of Linear Polyelectrolyte in a Viral Nanocontainer Yufang Hu, Roya Zandi, Charles Knobler, William Gelbart We present the results from a combined experimental and theoretical study on the self-assembly of a model icosahedral virus, Cowpea Chlorotic Mottle Virus (CCMV). The formation of native CCMV capsids is believed to be driven primarily by the electrostatic interactions between the viral RNA and the positively charged capsid interior, as well as by the hydrophobic interactions between capsid protein subunits. To probe these molecular interactions, \textit{in vitro} self-assembly reactions are carried out using the CCMV capsid protein and a synthetic linear polyelectrolyte, sodium polystyrene sulfonate (NaPSS), which functions as the analog of viral RNA. Under appropriate solutions conditions, NaPSS is encapsidated by the viral capsid. The molecular weight of NaPSS is systematically varied and the resulting average capsid size, size distribution, and particle morphology are measured by transmission electron microscopy. The correlation between capsid size and packaged cargo size, as well as the upper limit of capsid packaging capacity, are characterized. To elucidate the physical role played by the encapsidated polyelectrolyte in determining the preferred size of spherical viruses, we have used a mean-field approach to calculate the free energy of the virus-like particle as a function of chain length (and of the strength of chain/capsid attractive interaction). We find good agreement with our analytical calculations and experimental results. [Preview Abstract] |
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