Relaxation Mode Analysis for a Peptide

Abstract

Biopolymers have flexible structures and several varieties of functions. The functions are derived from not only structures but also the structural fluctuations. Therefore, the properties of structural fluctuations of biopolymers are important for understanding the interrelationship between its movement and functions. Principle component analysis is one of the most popular methods for analyzing the static properties of structural fluctuations. The method treats “static” information although it is applied in many simulations of protein systems. Relaxation mode analysis developed to investigate “dynamic” properties of polymer, homo-polymer, systems [1,2]. In the case of liner polymers, the relaxation phenomena have been studied systematically in terms of the relaxation modes and rates.In RMA, the time correlation matrices of structural fluctuations for two different times are calculated. Then, by solving a generalized eigenvalue problem for these matrices, the relaxation rates and modes are estimated from the eigenvalues and eigenvectors, respectively. Recently, relaxation mode analysis has been applied to protein, hetero-polymer, systems to investigate dynamic properties of structural fluctuations[3,4]. In this poster, we explain relaxation mode analysis for hetero-polymer systems and show the obtained results.[1] H. Takano and S. Miyashita, J. Phys. Soc. Jpn. 64, 3688 (1995).[2] H. Hirao, S. Koseki, H. Takano, J. Phys. Soc. Jpn. 66, 3399 (1997).[3] A. Mitsutake, H. Iijima, H. Takano, J. Chem. Phys.135, 164102 (2011).[4] T. Nagai, A. Mitsutake, and H. Takano, J. Phys. Soc. Jpn. 82, 023803 (2013); T. Nagai, A. Mitsutake, H. Takano, Seibutsu Butsuri (Biophysics), 49, Supplement S75, (Abstracts for the 47st annual meeting, The Biophysical Society of Japan) (2009).