Structural information content and lyapunov exponent calculation in protein unfolding Article

Gerstman, B, Garbourg, Y. (1998). Structural information content and lyapunov exponent calculation in protein unfolding . JOURNAL OF POLYMER SCIENCE PART B-POLYMER PHYSICS, 36(15), 2761-2769. 10.1002/(SICI)1099-0488(19981115)36:15<2761::AID-POLB10>3.0.CO;2-5

cited authors

  • Gerstman, B; Garbourg, Y

authors

abstract

  • A lattice model with Monte Carlo dynamics is used to carry out computer simulations of protein dynamics on a four α-helix bundle. The interaction energies in the model can be set so that either the helix bundle structure remains relatively stable or changed so that it unfolds. The computer model produces output that simulates experimental measurements relating to the structure. We show how this output can be used with analytical techniques of nonlinear dynamics to obtain important information about the complex underlying protein dynamics. Time-delay reconstruction plots of structural parameters of unfolding bundles resemble strange attractors in a space of dimension 3-4. We calculate Lyapunov exponents for these unfolding runs and find positive Lyapunov exponents implying chaotic dynamics. For stable runs the Lyapunov exponents are close to zero. We use these Lyapunov exponents to calculate the rate of loss of structural information during the unfolding process and show how the approach may be useful for investigating the folding dynamics of proteins. © 1998 John Wiley & Sons, Inc.

publication date

  • November 15, 1998

published in

start page

  • 2761

end page

  • 2769

volume

  • 36

issue

  • 15