Reliability Study of Normal Mode Analysis on the BPTI Protein

POSTER

Abstract

Normal mode analysis (NMA) is a method of treating a system as a collection of spring-connected masses, with the spring constants determined by the forces acting on the system. This technique is widely used in analyzing proteins to ascertain large-scale correlated movements which may be important to the protein’s function, as well as mechanical properties such as stiffness. We wish to apply NMA to an engineered protein mesh formed by a regular lattice of fibrillar proteins as a measure of its mechanical strength and stability. In order to determine the reliability of such measurements, we use the same parameters to perform NMA on the well-studied protein Bovine Pancreatic Trypsin Inhibitor (BPTI). We use two force models: (1) a full molecular dynamics force field, which parametrizes forces between all atom types; and (2) an anisotropic network model, which couples proximal central carbon atoms to a harmonic potential. These two models are applied to both all-atom and coarse-grained representations of the protein. We obtain the frequency spectrum and root-mean-square fluctuation per residue and compare these data across models, and to simulated and experimental literature values.

Authors

  • Rachel Baarda

    University of California, Davis

  • Ethan Anderes

    UC Davis, Lawrence Berkeley National Lab - ALS, National Institute of Standards and Technology - NCNR, Univ of California - Davis, University of California, Davis, California State University, Long Beach, University of California, Irvine, University of California, Merced, UC Merced, U Central Florida, Paul Scherrer Institute, Paul Scherrer Institute in Switzerland, Hartnell Comm Coll, University of Michigan, University of Nevada, Reno, National Security Technologies LLC, Livermore, California, Humboldt State University, Stanford University, San Diego State Univ, Institute of Mathematical Problems of Biology, Eindhoven University of Technology, University Of Nevada Reno, Univ of Nevada - Reno, University of Chicago, Physics Department of the University of Nevada, Reno, NV, USA, Institute for Academic Initiatives, PPC and Graduate School of Engineering, Osaka University, Joint Institute for High Temperatures, PPC and Graduate School of Engineering, Osaka University, Institute for Academic Initiatives, Joint Institute for High Temperatures, National Institute of Standards and Technology, Gaithersburg, MD, Department of Physics, UC Davis, Department of Physics & Astronomy, Univeristy of California Irvine, 92697, Department of Chemistry and of Physics, Univeristy of California Irvine, 92697, Department of Condensed Matter Physics, Weizmann Institute of Science, Rehovot, Israel 76100, Einstein Centre for Local-Realistic Physics, Cal State Long Beach, University of nevada, Reno, Nicolaus Copernicus University, Torun, Poland, University of Maryland, CERN, Univ of California, Davis