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Updated: Jun 14, 2026

Investigating Protein Sequence-structure-dynamics Relationships with Bio3D-web
Published on: July 16, 2017
Latent dynamics of a protein molecule observed in dihedral angle space
Satoshi Omori1, Sotaro Fuchigami, Mitsunori Ikeguchi
1Department of Supramolecular Biology, Yokohama City University, Yokohama 230-0045, Japan.
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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