Determining anion-quadrupole interactions among protein, DNA, and ligand molecules

Harris, Jenkins, Reyles Jonathan, Rickett Stephanie, Utley, Howell, Baudry Jerome, Hinde

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Harris et al. BMC Bioinformatics 2011, 12(Suppl 7):A5 http://www.biomedcentral.com/1471-2105/12/S7/A5 MEETING ABSTRACT Open Access Determining anion-quadrupole interactions among protein, DNA, and ligand molecules 1,4* 2 1 2 1 1,3Jason B Harris , David D Jenkins , Jonathan Reyles , Stephanie Rickett , Jordan M Utley , Elizabeth E Howell , 1,3,4 5Jerome Baudry , Robert J Hinde thFrom 10 Annual UT-ORNL-KBRIN Bioinformatics Summit 2011 Memphis, TN, USA. 1-3 April 2011 Background molecular dynamics simulations in buried and solvent An extensive search through the Protein Databank exposed environments to observe non-static behavioral (about 4500 nonredundant structures) was previously traits as well as the reproducibility of AQ interactions completed within our lab to analyze the energetic and by force field parameters. 4. Building an online database geometric characteristics of an understudied molecular for public access to our data and search program. interaction known as an anion-quadrupole (AQ) interac- tion. Such an interaction occurs when the positively Acknowledgments charged edge of an aromatic ring, resulting from a quad- We would like to acknowledge the NSF-IGERT traineeship, Scalable ruple moment (i.e., a dual dipole moment), renders the Computing and Leading Edge Innovative Technologies (SCALE-IT), for providing the resources for this project.aromatic molecule noncovalently bound to a nearby anionic molecule.

Informations

• Publié par: biomed
• Publié le: 01 janvier 2011
• Nombre de lectures: 3
• Langue: English

Extrait

Harriset al.BMC Bioinformatics2011,12(Suppl 7):A5 http://www.biomedcentral.com/14712105/12/S7/A5

M E E T I N GA B S T R A C TOpen Access Determining anionquadrupole interactions among protein, DNA, and ligand molecules 1,4* 2 12 11,3 Jason B Harris, David D Jenkins , Jonathan Reyles , Stephanie Rickett , Jordan M Utley , Elizabeth E Howell, 1,3,4 5 Jerome Baudry, Robert J Hinde th From10 AnnualUTORNLKBRIN Bioinformatics Summit 2011 Memphis, TN, USA. 13 April 2011

Background An extensive search through the Protein Databank (about 4500 nonredundant structures) was previously completed within our lab to analyze the energetic and geometric characteristics of an understudied molecular interaction known as an anionquadrupole (AQ) interac tion. Such an interaction occurs when the positively charged edge of an aromatic ring, resulting from a quad ruple moment (i.e., a dual dipole moment), renders the aromatic molecule noncovalently bound to a nearby anionic molecule. The study considered a very limited scenario of molecules that can participate in AQ inter actions, consisting of the phenyl group of a phenylala nine (phe) amino acid as the aromatic participant and the carboxylate group of an aspartate (asp) or glutamate (glu) amino acid as the anionic participant. The results revealed anionquadrupole pairs to be prevalent within most of the protein structures. It was also observed that the interaction energy for AQ pairs was heavily depen dent on the angle between the anion and plane of the aromatic ring, favoring a more planar interaction. In light of these critical observations being made from such a limited scenario, only pheglu and pheasp pairs and in a reduced sample set of the PDB, we are now continuing this work of identifying AQ interactions using a greatly expanded strategy. We are following these four aims: 1. Optimizing the AQsearch program to run in a semiparallel fashion and on a large cluster of processors in order to handle larger analyses, 2. Add ing to our search additional anionic participants which will include nonprotein structures such as DNA and small ligands, 3. Studying a subset of the AQ pairs with

* Correspondence: [e-mail] 1 Graduate School of Genome Science and Technology, University of Tennessee, Knoxville, TN, 37996, USA Full list of author information is available at the end of the article

molecular dynamics simulations in buried and solvent exposed environments to observe nonstatic behavioral traits as well as the reproducibility of AQ interactions by force field parameters. 4. Building an online database for public access to our data and search program.

Acknowledgments We would like to acknowledge the NSFIGERT traineeship, Scalable Computing and Leading Edge Innovative Technologies (SCALEIT), for providing the resources for this project.

Author details 1 Graduate School of Genome Science and Technology, University of 2 Tennessee, Knoxville, TN, 37996, USA.Department of Electrical Engineering and Computer Science, University of Tennessee, Knoxville, TN, 37996, USA. 3 Department of Biochemistry, Cellular, and Molecular Biology, University of 4 Tennessee, Knoxville, TN, 37996, USA.Center for Molecular Biophysics, Oak 5 Ridge National Laboratory, TN, 37831, USA.Department of Chemistry, University of Tennessee, Knoxville, TN, 37996, USA.

Published: 5 August 2011

doi:10.1186/1471210512S7A5 Cite this article as:Harriset al.:Determining anionquadrupole interactions among protein, DNA, and ligand molecules.BMC Bioinformatics201112(Suppl 7):A5.

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