title: Spatio-temporal hierarchy in the dynamics of a minimalist protein model.
abstract: 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.
authors: RIKEN, Advanced Institute for Computational Science, 7-1-26 Minatojima-minamimachi, Chuo-ku, Kobe, Hyogo 650-0047, Japan.
authors: Yasuhiro
authors: Y
authors: Matsunaga
authors: Akinori
authors: A
authors: Baba
authors: Chun-Biu
authors: CB
authors: Li
authors: John E
authors: JE
authors: Straub
authors: Mikito
authors: M
authors: Toda
authors: Tamiki
authors: T
authors: Komatsuzaki
authors: R Stephen
authors: RS
authors: Berry
mesh_terms: D007700:Kinetics; D056004:Molecular Dynamics Simulation; D011487:Protein Conformation; D011506:Proteins / Q000737:chemistry*
chemical_list: D011506:Proteins