How the all-atom simulation and the Ising-based theory reconcile with each other on the helix-coil transition

M. Takano, K. Nagayama, A. Suyama

Research output: Contribution to journalArticle

3 Citations (Scopus)

Abstract

In this report, we addressed a somewhat basic question about how the two extreme models, the all-atom model and the Ising-based model, can be consistent with each other regarding the polypeptide helix-coil transition. Comparisons of several physical properties were made between the results of the all-atom simulations and those of the Ising-based theories. From the equilibrium point of view, the two models were found to exhibit a qualitatively similar trend, which is significant considering the extreme difference in precision between the two models. On the other hand, from the kinetic viewpoint, there appeared a difference in relaxation behavior between the two models; i.e., so-called stretched exponential relaxation was observed in the all-atom simulation whereas the kinetic Ising model showed simple exponential relaxation. A plausible source of the observed difference is briefly discussed.

Original languageEnglish
Pages (from-to)155-161
Number of pages7
JournalJournal of Biological Physics
Volume28
Issue number2
DOIs
Publication statusPublished - 2002 Sep 23
Externally publishedYes

Keywords

  • Glauber dynamics
  • Helix-coil transition
  • Ising model
  • Kinetics
  • Molecular dynamics simulation
  • Relaxation
  • Statistical mechanics
  • Stretched exponential

ASJC Scopus subject areas

  • Biophysics
  • Atomic and Molecular Physics, and Optics
  • Molecular Biology
  • Cell Biology

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