Bulletin of the American Physical Society
2017 Annual Meeting of the APS Mid-Atlantic Section
Volume 62, Number 19
Friday–Sunday, November 3–5, 2017; Newark, New Jersey
Session H1: Proteins and DNA I |
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Chair: Luis Cruz, Drexel University Room: 235, Campus Center, NJIT |
Saturday, November 4, 2017 2:00PM - 2:36PM |
H1.00001: Magnesium regulates the circadian oscillator in cyanobacteria. Invited Speaker: Yong-Ick Kim The circadian clock is a 24-hour biological rhythm in our body, which controls many of our time related activities, such as sleep and awake. The cyanobacterial circadian clock is the simplest clock and its oscillator is composed of KaiA, KaiB, and KaiC proteins, which generate the self-sustained circadian oscillation of phosphorylation and dephosphorylation on KaiC. KaiA activates the phosphorylation of KaiC by binding A-loop in KaiC while KaiB attenuates it by sequestering KaiA from A-loop. The structural analysis revealed that the magnesium regulates the phosphorylation and dephosphorylation of KaiC by association or dissociation on the catalytic Glu, which activates the phosphorylation. High magnesium concentration made KaiC dephosphorylate though low magnesium concentration made KaiC phosphorylate without KaiA. The magnesium concentration was altered by light in cyanobacteria and KaiC alone behaved as an hourglass type oscillator by altering magnesium concentration. Our findings suggested that the circadian oscillator has evolved from an hourglass to a self-sustained oscillator. [Preview Abstract] |
Saturday, November 4, 2017 2:36PM - 3:12PM |
H1.00002: Progress and challenges in the atomistic simulation of nucleic acids Invited Speaker: Stefano Piana Molecular dynamics (MD) simulation has become a powerful tool for characterizing at an atomic level of detail the conformational changes undergone by proteins. The application of such simulations to RNA structures, however, has proven more challenging, due in large part to the fact that the physical models (``force fields'') available for MD simulations of RNA molecules are substantially less accurate in many respects than those currently available for proteins. Here, I will present a revision of a widely used RNA force field in which the parameters have been modified, based on quantum mechanical (QM) calculations and existing experimental information, to more accurately reflect the fundamental forces that stabilize RNA structures. We evaluated these revised parameters through long-timescale MD simulations of a set of RNA molecules that covers a wide range of structural complexity, including single-stranded RNAs, RNA duplexes, RNA hairpins, and riboswitches. The structural and thermodynamic properties measured in these simulations exhibited dramatically improved agreement with experimentally determined values. Based on the comparisons we performed, this new RNA force field appears to achieve a level of accuracy comparable to that of state-of-the-art protein force fields. Although it represents an improvement in various respects, the force field is still based on rather crude approximations of the physics, and outstanding issues will be discussed. [Preview Abstract] |
Saturday, November 4, 2017 3:12PM - 3:24PM |
H1.00003: Kinetics of (un)binding between DNA-functionalized particles using a coarse-grained model with explicit nucleotide representation Tiara Maula, Jeetain Mittal Advances in technology have made necessary the manufacture of materials at increasingly precise scales. However, developing materials with finely ordered structures up to the nanometer scale is infeasible using traditional top-down methods. This has prompted interest in self-assembling materials like DNA-functionalized particles (DFPs). In this research, we use a coarse-grained DFP model which preserves key chemical and structural properties of DNA while explicitly representing nucleotide bases in order to study the kinetics between two complementary particles. Specifically, we explore the effect of temperature, DNA grafting density, and length of the linker sequence on the rates binding and unbinding, with a particular focus on how these factors could be used as tuning parameters for the design of materials which can assemble into desired ordered structures. Our results should help tune assembly conditions and obtain desired crystal lattices unhindered by kinetically arrested amorphous or undesired structures. [Preview Abstract] |
Saturday, November 4, 2017 3:24PM - 4:00PM |
H1.00004: DNA is an Active Force-Generating Element in a Viral Molecular Motor Invited Speaker: Stephen Harvey Double-stranded DNA (dsDNA) bacteriophages have a protein coat (the capsid) surrounding a dsDNA genome. During viral assembly, an ATP-driven motor forces the DNA into the preformed capsid. These motors are among the strongest of all biological motors. We proposed that the DNA is an active component in the translocation machinery. This "scrunchworm hypothesis" argues that the portal proteins drive dsDNA through a cycle of shortening and lengthening, and that the DNA shortening-lengthening cycle is coupled to a protein-DNA grip-and-release cycle to rectify the motion and drive the DNA forward. We have recently completed computer simulations on the DNA-portal complexes from phages phi29, T4 and P22. We also examined the patterns of electrostatic potential in all the structures. We conclude that (1) conformational changes in the portal proteins drive lengthening and shortening motions in dsDNA in the portal's channel; (2) these DNA conformational changes are driven by protein-DNA electrostatic interactions; and (3) DNA shortening and lengthening motions play an active role in translocation. The challenges ahead include (1) identification of the conformational changes in the ATPase during the biochemical cycle; and (2) determining how these drive conformational changes in the portal. [Preview Abstract] |
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