Dynamic complexity of chaotic transitions in high-dimensional classical dynamics: leu-enkephalin folding

  • Authors:

  • Dmitry Nerukh;George Karvounis;Robert C. Glen

  • Affiliations:

  • Unilever Centre for Molecular Informatics, Department of Chemistry, Cambridge University, Cambridge, UK;Unilever Centre for Molecular Informatics, Department of Chemistry, Cambridge University, Cambridge, UK;Unilever Centre for Molecular Informatics, Department of Chemistry, Cambridge University, Cambridge, UK

  • Venue:
  • CompLife'06 Proceedings of the Second international conference on Computational Life Sciences
  • Year:
  • 2006

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Abstract

Leu-Enkephalin in explicit water is simulated using classical molecular dynamics. A β-turn transition is investigated by calculating the topological complexity (in the “computational mechanics” framework [J. P. Crutchfield and K. Young, Phys. Rev. Lett., 63, 105 (1989)]) of the dynamics of both the peptide and the neighbouring water molecules. The complexity of the atomic trajectories of the (relatively short) simulations used in this study reflect the degree of phase space mixing in the system. It is demonstrated that the dynamic complexity of the hydrogen atoms of the peptide and almost all of the hydrogens of the neighbouring waters exhibit a minimum precisely at the moment of the β-turn transition. This indicates the appearance of simplified periodic patterns in the atomic motion, which could correspond to high-dimensional tori in the phase space. It is hypothesized that this behaviour is the manifestation of the effect described in the approach to molecular transitions by Komatsuzaki and Berry [T. Komatsuzaki and R.S. Berry, Adv. Chem. Phys., 123, 79 (2002)], where a “quasi-regular” dynamics at the transition is suggested. Therefore, for the first time, the less chaotic character of the folding transition in a realistic molecular system is demonstrated.