Partial Unfolding and Refolding for Structure Refinement: A Unified Approach of Geometric Simulations and Molecular Dynamics

ORAL

Abstract

The most successful protein structure prediction methods to date have been template-based modeling (TBM) or homology modeling, which predicts protein structure based on experimental structures. These high accuracy predictions sometimes retain structural errors due to incorrect templates or a lack of accurate templates in the case of low sequence similarity, making these structures inadequate in drug-design studies or molecular dynamics simulations. We have developed a new physics based approach to the protein refinement problem by mimicking the mechanism of chaperons that rehabilitate misfolded proteins. The template structure is unfolded by selectively (targeted) pulling on different portions of the protein using the geometric based technique FRODA, and then refolded using hierarchically restrained replica exchange molecular dynamics simulations (hr-REMD).

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Authors

  • Paul Campitelli

    Department of Physics and Center for Biological Physics, Arizona State University

  • Scott D. Bergesen

    Santa Fe Institute, Arizona State University, Department of Physics and Center for Biological Physics, Arizona State University, Brigham Young University Department of Physics and Astronomy, Brigham Young University, Utah Valley University, Dixie State College, Advisor, Student, Massachusetts Institute of Technology, Thomas Jefferson National Accelerator Laboratory, Colorado College, United States Air Force Academy, Georgia Institute of Technology, Utah State University, Brigham Young University - Idaho, Utah State University- Logan, National Institute of Standards and Technology, Humboldt State University, UC Santa Cruz, Institut de Chimie des Substances Naturelles, Arizona State Univ, University of Colorado at Colorado Springs, National Jewish Health, Department of Physics, The University of Texas at Austin, Department of Physics, New Mexico State University, U. S. Air Force Academy, Brigham Young Univ - Provo, University of New South Wales, University of Texas, University of Warwick, University of Louisiana, Department of Physics and Astronomy, Brigham Young University, Provo, Utah 84602, USA., Center for Materials Genomics, Department of Mechanical Engineering and Materials Science and Department of Physics, Duke University, Durham, North Ca, Duke University, Durham, North Carolina., Brigham Young University -- Provo, Utah, General Atomics -- San Diego, California, Department of Mathematics, University of British Columbia, Department of Physics, Arizona State University, UC Riverside, UMASS, STScI, NOAO, UT Austin, Texas A&M, Arizona State Univeristy, New Mexico State Univ, Los Alamos National Laboratory, Colorado State Univ, Department of Physics, Oregon State University, Colorado School of Mines, University of Alaska, Fairbanks, The Peac Institute of Multiscale Modeling, UNSW Canberra

  • Scott D. Bergesen

    Santa Fe Institute, Arizona State University, Department of Physics and Center for Biological Physics, Arizona State University, Brigham Young University Department of Physics and Astronomy, Brigham Young University, Utah Valley University, Dixie State College, Advisor, Student, Massachusetts Institute of Technology, Thomas Jefferson National Accelerator Laboratory, Colorado College, United States Air Force Academy, Georgia Institute of Technology, Utah State University, Brigham Young University - Idaho, Utah State University- Logan, National Institute of Standards and Technology, Humboldt State University, UC Santa Cruz, Institut de Chimie des Substances Naturelles, Arizona State Univ, University of Colorado at Colorado Springs, National Jewish Health, Department of Physics, The University of Texas at Austin, Department of Physics, New Mexico State University, U. S. Air Force Academy, Brigham Young Univ - Provo, University of New South Wales, University of Texas, University of Warwick, University of Louisiana, Department of Physics and Astronomy, Brigham Young University, Provo, Utah 84602, USA., Center for Materials Genomics, Department of Mechanical Engineering and Materials Science and Department of Physics, Duke University, Durham, North Ca, Duke University, Durham, North Carolina., Brigham Young University -- Provo, Utah, General Atomics -- San Diego, California, Department of Mathematics, University of British Columbia, Department of Physics, Arizona State University, UC Riverside, UMASS, STScI, NOAO, UT Austin, Texas A&M, Arizona State Univeristy, New Mexico State Univ, Los Alamos National Laboratory, Colorado State Univ, Department of Physics, Oregon State University, Colorado School of Mines, University of Alaska, Fairbanks, The Peac Institute of Multiscale Modeling, UNSW Canberra

  • Scott D. Bergesen

    Santa Fe Institute, Arizona State University, Department of Physics and Center for Biological Physics, Arizona State University, Brigham Young University Department of Physics and Astronomy, Brigham Young University, Utah Valley University, Dixie State College, Advisor, Student, Massachusetts Institute of Technology, Thomas Jefferson National Accelerator Laboratory, Colorado College, United States Air Force Academy, Georgia Institute of Technology, Utah State University, Brigham Young University - Idaho, Utah State University- Logan, National Institute of Standards and Technology, Humboldt State University, UC Santa Cruz, Institut de Chimie des Substances Naturelles, Arizona State Univ, University of Colorado at Colorado Springs, National Jewish Health, Department of Physics, The University of Texas at Austin, Department of Physics, New Mexico State University, U. S. Air Force Academy, Brigham Young Univ - Provo, University of New South Wales, University of Texas, University of Warwick, University of Louisiana, Department of Physics and Astronomy, Brigham Young University, Provo, Utah 84602, USA., Center for Materials Genomics, Department of Mechanical Engineering and Materials Science and Department of Physics, Duke University, Durham, North Ca, Duke University, Durham, North Carolina., Brigham Young University -- Provo, Utah, General Atomics -- San Diego, California, Department of Mathematics, University of British Columbia, Department of Physics, Arizona State University, UC Riverside, UMASS, STScI, NOAO, UT Austin, Texas A&M, Arizona State Univeristy, New Mexico State Univ, Los Alamos National Laboratory, Colorado State Univ, Department of Physics, Oregon State University, Colorado School of Mines, University of Alaska, Fairbanks, The Peac Institute of Multiscale Modeling, UNSW Canberra