Dynamics of Small Peptides: Comparison of NMR Relaxation Experiments with Molecular Dynamics Simulations

POSTER

Abstract

Understanding biological molecules from differing perspectives and obtaining results which concur with one another has been a goal of researchers for years. We applied both theoretical and experimental approaches to study the biophysics and dynamics of a small biological molecule, the dipeptide Alaninephenylalanine (Ala-Phe). For our theoretical approach we used the computer programs NAMD and VMD to place the dipeptide in a box of water and simulate atomic motions for every atom in the system for 100 nanoseconds. From these simulations we can predict correlation times for the atomic movements. Experimentally, relaxation times (T1, T2) were collected using Nuclear Magnetic Resonance (NMR). Comparing theory with experiment, we found similarities in the trends of correlation times for various atoms in the molecule.

Authors

  • Andrey Chabanov

    West Texas A\&M University, Rhodes College, Texas Woman's University, University of Texas at San Antonio, Texas A\&M University, Department of Physics, University of Texas at Arlington, Texas State University, Pajarito Scientific Corporation, Idaho National Laboratory, Duke University, UNC, Department of Chemistry, UTSA, Department of Physics and Astronomy, UTSA, The University of Texas at San Antonio, Harvar-Smithsonian Center for Astrophysics, University of New Mexico, Maria Mitchel Observatory, NRAO, University of Alabama, Trinity University, Department of Physics and Astronomy, University of Texas at San Antonio, San Antonio, Texas 78249, V. Alecsandri College, Bacau, Romania, University of Texas at Dallas, Argonne National Laboratory, Western Michigan University, Institute of Physics, UNAM, Mexico, University of North Texas - Chemistry, University of St. Thomas, SwRI San Antonio, Alan G. MacDiarmid NanoTech Institute, University of Texas at Dallas, Department of Electrical and Computer Engineering, University of Texas at Arlington, Department of Physics, University of Texas at Brownsville, SciPrint.org, The University of Texas at Austin, Georgia Tech, MIT, University of Tennessee, University of Michigan, ORNL, Texas A&M University-Commerce, University of Texas San Antonio, University of Texas at Brownsville, University of Dallas, Sternberg Astronomical Institute, SwRI, CU-Boulder, SwRI/UTSA, Southwest Research Institute, JILA, University of Colorado, Department of Physics, Texas A\&M University, Stephen F. Austin State University, Angelo State University, St. Mary's University, Physics Department, University of South Florida, CINVESTAV, Queretaro, Mexico, Department of Physics, UCSD, LANSCE, Los Alamos National Laboratory, Department of Physics and Astronomy, Texas A\&M University, Texas A\&M University: Department of Physics, Texas Christian University, Fort Worth, TX, Paschal High School, Fort Worth, TX, Tarleton State University, Stephenville, TX, Paine College, Augusta, GA, University of Houston, University of Texas at Arlington, IREAP, Department of Physics, University of Maryland, Air Force Research Laboratory, Institute for Quantum Studies and Department of Physics, Texas A\&M Universtity, College Station, Texas 77843, USA, Max-Planck Institut for Kernphysik, Saupfercheckweg 1,D-69117 Heidelberg, Germany, The National Center for Mathematics and Physics, P.O. Box 6086, KACST, Riyadh 11442, Saudi Arabia

  • David Torres

    University of St. Thomas

  • Michelle Steiger

    University of St. Thomas

  • James Clarage

    University of St. Thomas