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Latent dynamics of a protein molecule observed in dihedral angle space.

Authors
  • Omori, Satoshi
  • Fuchigami, Sotaro
  • Ikeguchi, Mitsunori
  • Kidera, Akinori
Type
Published Article
Journal
The Journal of Chemical Physics
Publisher
AIP Publishing
Publication Date
Mar 21, 2010
Volume
132
Issue
11
Pages
115103–115103
Identifiers
DOI: 10.1063/1.3360144
PMID: 20331318
Source
Medline
License
Unknown

Abstract

Dihedral angles are alternative set of variables to Cartesian coordinates for representing protein dynamics. The two sets of variables exhibit extremely different behavior. Motions in dihedral angle space are characterized by latent dynamics, in which motion induced in each dihedral angle is always compensated for by motions of many other dihedral angles, in order to maintain a rigid globular shape. Using molecular dynamics simulations, we propose a molecular mechanism for the latent dynamics in dihedral angle space. It was found that, due to the unique structure of dihedral principal components originating in the globular shape of the protein, the dihedral principal components with large (small) amplitudes are highly correlated with the eigenvectors of the metric matrix with small (large) eigenvalues. Such an anticorrelation in the eigenmode structures minimizes the mean square displacement of Cartesian coordinates upon rotation of dihedral angles. In contrast, a short peptide, deca-alanine in this study, does not show such behavior of the latent dynamics in the dihedral principal components, but shows similar behaviors to those of the Cartesian principal components, due to the absence of constraints to maintain a rigid globular shape.

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