Bulletin of the American Physical Society
APS March Meeting 2015
Volume 60, Number 1
Monday–Friday, March 2–6, 2015; San Antonio, Texas
Session W33: Focus Session: Conformations and Dynamics of Biopolymers III |
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Sponsoring Units: DBIO DPOLY Chair: Jeffrey Noel, Rice University Room: 208 |
Thursday, March 5, 2015 2:30PM - 2:42PM |
W33.00001: Non-Gaussian Distribution of DNA Barcode Extension In Nanochannels Using High-throughput Imaging Julian Sheats, Wesley Reinhart, Jeff Reifenberger, Damini Gupta, Abhiram Muralidhar, Han Cao, Kevin Dorfman We present experimental data for the extension of internal segments of highly confined DNA using a high-throughput experimental setup. Barcode-labeled {\it E. coli} genomic DNA molecules were imaged at a high areal density in square nanochannels with sizes ranging from 40 nm to 51 nm in width. Over 25,000 molecules were used to obtain more than 1,000,000 measurements for genomic distances between 2,500 bp and 100,000 bp. The distribution of extensions has positive excess kurtosis and is skew left due to weak backfolding in the channel. As a result, the two Odijk theories for the chain extension and variance bracket the experimental data. We compared to predictions of a harmonic approximation for the confinement free energy and show that it produces a substantial error in the variance. These results suggest an inherent error associated with any statistical analysis of barcoded DNA that relies on harmonic models for chain extension. [Preview Abstract] |
Thursday, March 5, 2015 2:42PM - 2:54PM |
W33.00002: Simulation of Microtubules: Mechanical properties Mark Stevens In order to understand microtubule assembly and the necessary monomeric properties to design artificial polymers that possess features similar to those of microtubules, we have developed a coarse-grained model of a monomer that self-assembles into tubules. In this model the monomer has a wedge shape which promotes tubule formation. There are attractive binding sites on the vertical and lateral sides of the monomer. We previously performed molecular dynamics simulations to calculate the set of structures that form upon self-assembly as we vary the lateral and vertical interaction strengths. In this talk, we will present the results of mechanical studies of the coarse-grained tubule system. The persistence length and various elastic moduli have been calculated. Microtubules have some of the largest persistence lengths of polymers. We have found that the persistence length is indeed very long for this coarse-grained model system. We calculate elastic moduli for varying the interaction strengths of the lateral and vertical interactions. We gain insight into the values that occur in microtubules, with respect to mechanical stability and stiffness. [Preview Abstract] |
Thursday, March 5, 2015 2:54PM - 3:06PM |
W33.00003: Small-angle neutron and X-ray scattering reveal conformational changes in rhodopsin activation Utsab R. Shrestha, Debsindhu Bhowmik, Suchitrhanga M.C.D. Perera, Udeep Chawla, Andrey V. Struts, Vito Graziono, Sai Venkatesh Pingali, William T. Heller, Shuo Qian, Michael F. Brown, Xiang-Qiang Chu Understanding G-protein-coupled receptor (GPCR) activation plays a crucial role in the development of novel improved molecular drugs. During photo-activation, the retinal chromophore of the visual GPCR rhodopsin isomerizes from 11-cis to all-trans conformation, yielding an equilibrium between inactive Meta-I and active Meta-II states. The principal goals of this work are to address whether the activation of rhodopsin leads to a single state or a conformational ensemble, and how protein organizational structure changes with detergent environment in solution. We use both small-angle neutron scattering (SANS) and small-angle X-ray scattering (SAXS) techniques to answer the above questions. For the first time we observe the change in protein conformational ensemble upon photo-activation by SANS with contrast variation, which enables the separate study of the protein structure within the detergent assembly. In addition, SAXS study of protein structure within detergent assembly suggests that the detergent molecules form a belt of monolayer (micelle) around protein with different geometrical shapes to keep the protein in folded state. [Preview Abstract] |
Thursday, March 5, 2015 3:06PM - 3:42PM |
W33.00004: Effects of Uniaxial Strain on Shear Moduli of Semiflexible Polymer Networks Invited Speaker: Paul Janmey |
Thursday, March 5, 2015 3:42PM - 3:54PM |
W33.00005: Emergence of attraction in simulations of coarse-grained double stranded DNA Shahzad Ghanbarian, Joerg Rottler DNA condensation induced by multivalent counterions is believed to play an important role in DNA bundling and packing into the cell nucleus. We present a coarse-grained, implicit solvent representation of rigid ds-DNA molecules in the presence of divalent counterions. In order to include solvation effects arising from the discrete nature of the water molecules, short-ranged corrections are added to the pairwise interaction potentials such that the structure of counterions is consistent with results from corresponding explicit solvent simulations. The effective force between two DNA strands generated by these potentials provides an excellent match to that observed in the explicit solvent model. Importantly, this interaction features multiple minima and reproduces the like-charge attraction effect between DNA molecules observed in full atomistic simulations at significantly reduced computational expense. This result proves that it is possible to capture complex multibody interactions between polyelectrolyte strands with two-body potentials. [Preview Abstract] |
Thursday, March 5, 2015 3:54PM - 4:06PM |
W33.00006: Capturing Transition Paths and Transition States for Conformational Rearrangements in the Ribosome Jeffrey Noel, Jorge Chahine, Vitor Leite, Paul Whitford To reveal the molecular determinants of biological function, one seeks to characterize the interactions that are formed in conformational and chemical transition states. In other words, what interactions govern the molecule's energy landscape? To accomplish this, it is necessary to determine which degrees of freedom can unambiguously identify each transition state. Here, we perform simulations of large-scale aminoacyl-tRNA (aa-tRNA) rearrangements during accommodation on the ribosome and project the dynamics along experimentally-accessible atomic distances. From this analysis, we obtain evidence for which coordinates capture the correct number of barrier-crossing events and accurately indicate when the aa-tRNA is on a transition path. While a currently-used coordinate in single-molecule experiments performs poorly, this study implicates alternative coordinates along which rearrangements are accurately described as diffusive movements across a one-dimensional free-energy profile. From this, we provide the theoretical foundation required for single-molecule techniques to uncover the energy landscape governing aa-tRNA selection by the ribosome. More details can be found at doi:10.1529/biophysj.106.090944. [Preview Abstract] |
Thursday, March 5, 2015 4:06PM - 4:18PM |
W33.00007: Study on the stability of the DNA hairpin d(ATCCAT-GTTA-TAGGAT) employing molecular dynamics simulation Sangwook Wu DNA hairpin plays a critical role in the regulation of gene expression and DNA recombination. We studied the conformation of the DNA hairpin, d(ATCCAT-GTTA-TAGGAT) (PDB id:1AC7), employing molecular dynamics (MD) simulation. Despite the non-canonical Watson-Crick base pair (G:A) in the tetraloop (GTTA), MD simulation reveals that the conformation of the DNA hairpin is remarkably stable. In this study, we discuss about the physical/chemical origin of the stability of the DNA hairpin. [Preview Abstract] |
Thursday, March 5, 2015 4:18PM - 4:30PM |
W33.00008: Effect of solvent viscosity on driven translocation of a semi-flexible polymer through a nanopore Ramesh Adhikari, Aniket Bhattacharya We study the effect of solvent viscosity and pore diameter on the driven translocation of a semi-flexible chain using Langevin dynamics simulation. We observe that for a given chain stiffness the mean first passage time (MFPT) has a nonmonotonic dependence on the solvent viscosity. For moderate external biases, the MFPT decreases at very low solvent viscosity exhibiting a minimum before it increases linearly as a function of high solvent viscosity. We demonstrate a stiffer chain translocates faster than a flexible chain of same length at the low viscosity regime while the opposite is true at high viscosity regime. The effect of pore size on the translocation dynamics is more acute at low solvent viscosity (pore friction dominating regime), but has almost negligible effect at the high viscosity regime for the parameters used in our studies. [Preview Abstract] |
Thursday, March 5, 2015 4:30PM - 4:42PM |
W33.00009: Spontaneous curvature in chiral polar filaments near interfaces Peter D. Olmsted, Emily E. Riley, Sophia Jordens, Ivan Usov, Lucio Isa, Raffaele Mezzenga Chiral filaments (actin, DNA, alpha helical strands, $\ldots$) are ubiquitous in biology, and they frequently come into contact with interfaces or inhomogeneous environments, either in biology (e.g. actin on membranes) or use and processing of biomaterials (fibrils at solvent boundaries or nanoparticle surfaces). Recent experiments\footnote{S Jordens, \textit{et al.}, ``Adsorption at liquid interfaces induces amyloid fibril bending and ring formation'', \textit{ACS Nano} (2014) \texttt{http://pubs.acs.org/doi/pdf/10.1021/nn504249x}.} have shown that amyloid fibrils can develop unusual curvatures at the air-water interface. Here we show that spontaneous curvature follows, on symmetry grounds, for chiral polar filaments placed in inhomgeneous environments such as near surfaces. We demonstrate this for simple model surface-fibril interactions, and discuss some of the implications. [Preview Abstract] |
Thursday, March 5, 2015 4:42PM - 4:54PM |
W33.00010: Adsorption of Helical Polymers on a Substrate Matthew Williams Formation of tertiary structures made up of helical polymer segments is modified by the introduction of a substrate on which the polymer is adsorbed. The effect of a substrate on biological systems such as helical structures may be important in the formation of early life. We perform replica-exchange Monte Carlo simulations to study the effect of a substrate on formation of helical structures, comparing the structural phase space for both adsorbed and non-adsorbed helical polymers. For this purpose a generic, hybrid coarse-grained model for polymer adsorption has been employed. [Preview Abstract] |
Thursday, March 5, 2015 4:54PM - 5:06PM |
W33.00011: ABSTRACT WITHDRAWN |
Thursday, March 5, 2015 5:06PM - 5:18PM |
W33.00012: Elasticity of 3D networks with rigid filaments and compliant crosslinks Knut M. Heidemann, Abhinav Sharma, Florian Rehfeldt, Christoph F. Schmidt, Max Wardetzky Disordered filamentous networks with compliant crosslinks exhibit a low linear elastic shear modulus at small strains, but stiffen dramatically at high strains. Here, we perform an analytical and numerical study on model networks in three dimensions. Our model consists of a collection of randomly oriented rigid filaments connected by flexible crosslinks that are modeled as wormlike chains. Under the assumption of affine deformations in the limit of \emph{infinite} crosslink density, we show analytically that the nonlinear elastic regime in 1- and 2-dimensional networks is characterized by power-law scaling of the elastic modulus with the stress. In contrast, 3-dimensional networks show an exponential dependence of the modulus on stress. Independent of dimensionality, if the crosslink density is \emph{finite}, we show that the only persistent scaling exponent is that of the single wormlike chain. Consequently, unlike suggested in prior work, the model system studied here cannot provide an explanation for the experimentally observed linear scaling of the modulus with the stress in filamentous networks. [Preview Abstract] |
Thursday, March 5, 2015 5:18PM - 5:30PM |
W33.00013: Molecular Dynamics Investigations of the alpha-helix to Beta-barrel Conformational Transformation in RfaH Jeevan GC, Yuba Bhandari, Bernard Gerstman, Prem Chapagain We used combination of replica exchange molecular dynamics simulations with implicit solvent and detailed all-atom simulations with explicit solvent to investigate the $\alpha $-helix to $\beta $-structure transformation of RfaH-CTD. While interacting with the N-terminal domain (NTD), the C-terminal domain (CTD) of~RfaH folds to a $\alpha $-helix bundle but it undergoes an all-$\alpha $ to all-$\beta $ conformational transformation when it does not interact with the NTD. The RfaH-CTD in the all-$\alpha $ topology is involved in regulating transcription whereas in the all-$\beta $ topology it is involved in stimulating translation by recruiting a ribosome to an mRNA. Calculations of free-energy landscape and transfer entropy elucidate the details of the RfaH-CTD transformation process. The importance of interfacial interactions between the two domains of RfaH is highlighted by the compromised structural integrity of the helical form of the CTD in the absence NTD. We also studied interdomain and intradomain interactions in RfaH using Steered Molecular Dynamics Simulations. We investigated the role of the interdomain salt-bridge interaction in the domain stability Potential mean force was calculated to obtain free energy profile using Jarzynski Equality. [Preview Abstract] |
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