Multi-basin dynamics of a protein in aqueous solution

  • A. E. García
Part of the Centre de Physique des Houches book series (LHWINTER, volume 2)


A molecular dynamics simulation of crambin in aqueous solution shows that motions are characteristic of non-linear systems. We describe typical non-linear excitations, such as intermittency, for various representations of the protein dynamics and structure. The protein backbone dihedral angles show fast correlated transitions from one minimum well to another. Each transition is followed by small overdamped oscillations. Equal-time cross correlations of all (φ, ψ) angles show that correlations are extended along the backbone chain. An analysis based on a generalized least squares fitting of the protein fluctuations along vectors show that a small set of molecule optimal dynamic coordinates (MODC) describe most of the protein fluctuations. In addition, the MODC describe a trajectory where the protein conformation jumps from one minimum well to another. An extension of the MODC describing 2- and 3- dimensional cuts of the protein configurational space clearly shows a trajectory around multiple basins of attraction.


Molecular Dynamic Dihedral Angle Configurational Space Molecular Dynamic Trajectory Helical Region 
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Copyright information

© Springer-Verlag Berlin Heidelberg 1995

Authors and Affiliations

  • A. E. García
    • 1
  1. 1.Theoretical Biology and Biophysics GroupT10, MSK710, Los Alamos National LaboratoryLos AlamosUSA

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