open access

https://hdl.handle.net/2115/54747

Spatio-temporal hierarchy in the dynamics of a minimalist protein model

英語

2013-12-07

American Institute of Physics

Journal of chemical physics

139(21)

215101-1-215101-13

A method for time series analysis of molecular dynamics simulation of a protein is presented. In this approach, wavelet analysis and principal component analysis are combined to decompose the spatio-temporal protein dynamics into contributions from a hierarchy of different time and space scales. Unlike the conventional Fourier-based approaches, the time-localized wavelet basis captures the vibrational energy transfers among the collective motions of proteins. As an illustrative vehicle, we have applied our method to a coarse-grained minimalist protein model. During the folding and unfolding transitions of the protein, vibrational energy transfers between the fast and slow time scales were observed among the large-amplitude collective coordinates while the other small-amplitude motions are regarded as thermal noise. Analysis employing a Gaussian-based measure revealed that the time scales of the energy redistribution in the subspace spanned by such large-amplitude collective coordinates are slow compared to the other small-amplitude coordinates. Future prospects of the method are discussed in detail.

学術雑誌論文

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Copyright 2013 American Institute of Physics. This article may be downloaded for personal use only. Any other use requires prior permission of the author and the American Institute of Physics. The following article appeared in Journal of Chemical Physics 139, 215101 (2013) and may be found at http://scitation.aip.org/content/aip/journal/jcp/139/21/10.1063/1.4834415.

0021-9606

AA00694991