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Updated: Aug 18, 2026

Analyzing Protein Architectures and Protein-Ligand Complexes by Integrative Structural Mass Spectrometry
Published on: October 15, 2018
How many dimensions are required to approximate the potential energy landscape of a model protein?
Tamiki Komatsuzaki1, Kyoko Hoshino, Yasuhiro Matsunaga
1Nonlinear Science Laboratory, Department of Earth and Planetary Sciences, Faculty of Science, Kobe University, Nada, Kobe 657-8501, Japan. tamiki@kobe-u.ac.jp
Abstract:
A scheme to approximate the multidimensional potential energy landscape in terms of a minimal number of degrees of freedom is proposed using a linear transformation of the original atomic Cartesian coordinates. For one particular off-lattice model protein the inherent frustration can only be reproduced satisfactorily when a relatively large number of coordinates are employed. However, when this frustration is removed in a Go-type model, the number of coordinates required is significantly lower, especially around the global potential energy minimum. To aid our interpretation of the results we consider modified disconnectivity graphs where a measure of the structural diversity and a metric relation between the stationary points are incorporated.
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