Advertisement

A comparison of techniques for calculating protein essential dynamics

Authors

  • D. M. F. Van Aalten,

    Corresponding author
    1. Department of Biochemistry, University of Leeds, Leeds LS2 9JT, United Kingdom
    • Department of Biochemistry, University of Leeds, Leeds LS2 9JT, United Kingdom
    Search for more papers by this author
  • B. L. De Groot,

    1. Groningen Biomolecular Sciences and Biotechnology Institut (GBB), Department of Biophysical Chemistry, University of Groningen, Nijenborgh 4, 9747 AG Groningen, The Netherlands
    Search for more papers by this author
  • J. B. C. Findlay,

    1. Department of Biochemistry, University of Leeds, Leeds LS2 9JT, United Kingdom
    Search for more papers by this author
  • H. J. C. Berendsen,

    1. Groningen Biomolecular Sciences and Biotechnology Institut (GBB), Department of Biophysical Chemistry, University of Groningen, Nijenborgh 4, 9747 AG Groningen, The Netherlands
    Search for more papers by this author
  • A. Amadei

    1. Groningen Biomolecular Sciences and Biotechnology Institut (GBB), Department of Biophysical Chemistry, University of Groningen, Nijenborgh 4, 9747 AG Groningen, The Netherlands
    Search for more papers by this author

Abstract

Recently the basic theory of essential dynamics, a method for extracting large concerted motions from protein molecular dynamics trajectories, was described. Here, we introduce and test new aspects. A method for diagonalizing large covariance matrices is presented. We show that it is possible to perform essential dynamics using different subsets of atoms and compare these to the basic C-α analysis. Essential dynamics analyses are also compared to the normal modes method. The stability of the essential space during a simulation is investigated by comparing the two halves of a trajectory. Apart from the analyses in Cartesian space, the essential dynamics in ϕ/ψ torsion angle space is discussed. © 1997 by John Wiley & Sons, Inc.

Ancillary