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Linking the dynamics of molecular prime knots to topological and local structural properties

ORAL

Abstract

Molecular knots (MKs) are structures entangled into the form of knots at a molecular level. Since the synthesis of the first artificial knot in 1989, various topologies of synthetic MKs have been realized, revealing their potential applications in biomedicine and nanotechnology. MKs have shown to perform specific functions based on their dynamic behaviors. Some protein-based knots, for example, can alternate between entangled and loose states and thus act as molecular machines that trap and release other molecules as desired. In defining their dynamics, the topology of MKs is known to play an important role, as knotting reduces degrees of freedom of molecular strands. However, understanding of what specific structural factors give rise to or allow certain types of dynamics is lacking. To understand these relationships, we build a methodology for studying knot dynamics in terms of topological and local structural properties. Specifically, we explore the dynamics of prime knots---knots that cannot be decomposed into two non-trivial knots---using Molecular Dynamics simulations and relate their principal motions to knot complexity, linking numbers, curvature, and torsion. We also investigate and compare the dynamics of symmetric and asymmetric prime knots.

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Authors

  • Hyo Jung Park

    Dickinson College

  • Abdul Qadeer Rehan

    University of Tennessee, University of York, Old Dominion University, Massachusetts Institute of Technology, Old Dominion University, Massachusetts Institute of Technology, Lawrence Berkeley National Laboratory, University of California, Berkeley, Institute of Physics - University of Sao Paulo, Naval Research Laboratory, St. Cloud State University, University of Illinois at Urbana-Champaign, Space Sciences Laboratory, Virginia Polytechnic Institute and State University, Space Sciences Laboratory, University of California Berkeley, University of Maryland - Baltimore County, Sandia National Laboratories, Pacific Northwest National Laboratory, Federal University of Bahia; University of Brasília, Federal University of Bahia, Department of Applied Physics, Yale University & Department of Physics, Yale University, Theoretical Division and Center for Nonlinear Studies, Los Alamos National Laboratory, Department of Physics, University of Illinois at Urbana-Champaign & Current affiliation: Seagate Research Group, Seagate Technology, Department of Physics and Astronomy, Wayne State University, Department of Physics, University of Illinois at Urbana-Champaign, Department of Applied Physics, Yale University, Swarthmore College, Western Washington University, Departments of Chemistry and Physics and The Baruch 60 Center for Biochemical Solar Energy Research at Rensselaer Polytechnic Institute, University of Florida, Wayne State University, Vanderbilt University, University of Maryland, College Park, NASA GSFC, CfA, California Institute of Technology, Skidmore College, Durham University, University of Alberta, University of Michigan, Curtin University, Michigan State University, University of Nevada, University of Chicago, Duke University, Cornell, Pennsylvania State University, New York University Abu Dhabi, NASA Ames Research Center, Kenyon Coll, Kenyon College, University of Texas at Austin, Flatiron Institute, University of California, Los Angeles, Ohio State University, University of Pennsylvania, HERA, HERA, Rochester Institute of Technology, Howard Community College, Carleton College, California State University at Long Beach, Bishop Ireton High School, Fayetteville State University, Univ of Oklahoma, University of Massachusetts Amherst, Carnegie Observatories, San Diego State University, Associate of the National Institute of Standards and Technology, National Institute of Standards and Technology, NTT Basic Research Laboratories and NTT Research Center for Theoretical Quantum Physics, JILA, University of Colorado, 440 UCB, Boulder, CO, Department of Physics, 390 UCB University of Colorado, University of Washington, James Franck Institute, Enrico Fermi Institute, University of Chicago Department of Physics, Princeton University, Department of Physics, Arizona State University, Indiana Univ - Bloomington, National Autonomous University of Mexico, Harvard University, Nagoya University, Toyota Technological Institute, University of Tokyo, Zhejiang University, Clark University, Natl Univ of Singapore, University of Richmond

  • Anna Lappala

    Harvard University