Bulletin of the American Physical Society
2005 APS March Meeting
Monday–Friday, March 21–25, 2005; Los Angeles, CA
Session B7: Women at the Forefront of Biological Physics |
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Sponsoring Units: DBP CSWP Chair: Aihua Xie, Oklahoma State University Room: LACC 408B |
Monday, March 21, 2005 11:15AM - 11:51AM |
B7.00001: Computational Genomics Using Graph Theory Invited Speaker: With exciting new discoveries concerning RNA's regulatory cellular roles in gene expression, structural and functional problems associated with DNA's venerable cousin have come to the forefront. RNA folding, for example, is analogous to the well-known protein folding problem, and seeks to link RNA's primary sequence with secondary and tertiary structures. As a single-stranded polynucleotide, RNA's secondary structures are defined by a network of hydrogen bonds, which lead to a variety of stems, loops, junctions, bulges, and other motifs. Supersecondary pseudoknot structures can also occur and, together, lead to RNA's complex tertiary interactions stabilized by salt and solvent ions in the natural cellular milieu. Besides folding, challenges in RNA research include identifying locations and functions of RNA genes, discovering RNA's structural repertoire (folding motifs), designing novel RNAs, and developing new antiviral and antibiotic compounds composed of, or targeting, RNAs. In this talk, I will describe some of these new biological findings concerning RNA and present an approach using graph theory (network theory) to represent RNA secondary structures. Because the RNA motif space using graphs is vastly smaller than RNA's sequence space, many problems related to analyzing and discovering new RNAs can be simplified and studied systematically. Some preliminary applications to designing novel RNAs will also be described.\newline\newline Related Reading\newline H. H. Gan, S. Pasquali, and T. Schlick, ``A Survey of Existing RNAs using Graph Theory with Implications to RNA Analysis and Design,'' Nuc. Acids Res. 31: 2926--2943 (2003). J. Zorn, H. H. Gan, N. Shiffeldrim, and T. Schlick, ``Structural Motifs in Ribosomal RNAs: Implications for RNA Design and Genomics,'' Biopolymers 73: 340--347 (2004). H. H. Gan, D. Fera, J. Zorn, M. Tang, N. Shiffeldrim, U. Laserson, N. Kim, and T. Schlick,``RAG: RNA-As-Graphs Database -- Concepts, Analysis, and Features,'' Bioinformatics 20: 1285--1291 (2004). U. Laserson, H. H. Gan, and T. Schlick, ``Searching for 2D RNA Geometries in Bacterial Genomes,'' Proceedings of the ACM Symposium on Computational Geometry, June 9--11, New York, pp. 373--377 (2004). (http://socg.poly.edu/home.htm). N. Kim, N. Shiffeldrim, H. H. Gan, and T. Schlick, ``Novel Candidates of RNA Topologies,'' J. Mol. Biol. 341: 1129--1144 (2004). Schlick, ``RAG: RNA-As-Graphs Web Resource,'' BMC Bioinformatics 5: 88--97 (2004) (http://www.biomedcentral.com/1471-2105/5/88). S. Pasquali, H. H. Gan, and T. Schlick, ``Modular RNA Architecture Revealed by Computational Analysis of Existing Pseudoknots and Ribosomal RNAs,'' Nucl. Acids Res., Submitted (2004). T. Schlick, Molecular Modeling: An Interdisciplinary Guide, Springer-Verlag, New York, 2002. [Preview Abstract] |
Monday, March 21, 2005 11:51AM - 12:27PM |
B7.00002: Crystal structures and molecular mechanism of light-induced signaling switches Invited Speaker: Since light is an important environmental variable, many organisms have evolved signalling pathways that transmit and thereby translate this stimulus into various biochemical activities. Recently, new classes of blue light photoreceptors have been identified that use flavin based photosensors. The photosensor domains are coupled to an array of other domains, including kinases and transcription factors. Recent progress in understanding the mechanism of blue-light signaling will be presented based on crystal structures of dark states and light-induced photopoducts. The structures are interpreted in the light of the spectroscopic data and used as a basis for quantum chemical calculations to obtain insight in the reaction mechanism. It will be presented and compared to previously suggested mechanisms. [Preview Abstract] |
Monday, March 21, 2005 12:27PM - 1:03PM |
B7.00003: Single Molecules Studies Using Optical Trapping and Fluorescence Techniques Invited Speaker: Biological organisms must compactly store and yet efficiently read the huge amounts of genetic information contained in their DNA. In the cell nucleus, DNA is highly compact as compared to naked DNA. The primary packing unit, the nucleosome, consists of roughly two turns of DNA wrapped around a core histone octamer. The mechanical stability of nucleosomes determines the accessibility of DNA to the cellular machinery that must decode it. We will discuss our recent progress towards understanding the mechanical stability of nucleosomes using single-molecule studies. \newline \newline Co-author: Alla Shundrovsky, Cornell University [Preview Abstract] |
Monday, March 21, 2005 1:03PM - 1:39PM |
B7.00004: Computational Studies of Proteins Invited Speaker: MultiConformation Continuum Electrostatics (MCCE), calculated acidic and basic residue ionization and sidechain positions in bacteriorhodopsin (BR) and halorhodopsin (HR). BR pumps protons out of the cell while HR pumps chlorides in. Comparison of BR ionization states in ground and late M state structures show retinal isomerization moves the protonated Schiff base away from the ionized Asp85 and 212 shifting the proton so only one acid is ionized. A proton is released from the Glu194/204 cluster because the acids separate and Arg 82 moves closer to them. In HR Asp 96 and 85 and Glu 204, important in BR proton transfers are replaced with small residues. In Monte Carlo sampling Cl- are bound near the deleted Asp 85 and Glu 204 in the ground state and released in an intermediate modeled by isomerization retinal from trans to cis and Arg movement toward the extracellular cluster. The charge shifts are similar to those found in BR. Thus, in BR H+ is the mobile charge Asp's and Glu's are fixed. In HR mobile Cl- substitutes for the deleted acids. Proton pumping in BR and chloride pumping in HR are driven by the same electrostatic forces. [Preview Abstract] |
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