Analysis of motion features for molecular dynamics simulation of proteins

Recently, a new method for time series analysis using the wavelet transformation has been proposed by Sakurai et al. We apply it to molecular dynamics simulation of Thermomyces lanuginosa lipase (TLL). Introducing indexes to characterize collective motion of the protein, we have obtained the following two results. First, time evolution of the collective motion involves not only the dynamics within a single potential well but also takes place wandering around multiple conformations. Second, correlation of the collective motion between secondary structures shows that collective motion exists involving multiple secondary structures. We discuss future prospects of our study involving 'disordered proteins'. (C) 2010 Elsevier B.V. All rights reserved.