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Updated: Jun 6, 2026

Study of Protein Dynamics via Neutron Spin Echo Spectroscopy
Published on: April 13, 2022
Detecting coupled collective motions in protein by independent subspace analysis
Shun Sakuraba1, Yasumasa Joti, Akio Kitao
1Graduate School of Frontier Sciences, The University of Tokyo, Tokyo 113-0032, Japan.
Abstract:
Protein dynamics evolves in a high-dimensional space, comprising aharmonic, strongly correlated motional modes. Such correlation often plays an important role in analyzing protein function. In order to identify significantly correlated collective motions, here we employ independent subspace analysis based on the subspace joint approximate diagonalization of eigenmatrices algorithm for the analysis of molecular dynamics (MD) simulation trajectories. From the 100 ns MD simulation of T4 lysozyme, we extract several independent subspaces in each of which collective modes are significantly correlated, and identify the other modes as independent. This method successfully detects the modes along which long-tailed non-Gaussian probability distributions are obtained. Based on the time cross-correlation analysis, we identified a series of events among domain motions and more localized motions in the protein, indicating the connection between the functionally relevant phenomena which have been independently revealed by experiments.
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