A Conformational Search Method for Protein Systems Using Genetic Crossover and Metropolis Criterion

7th Brazilian Meeting on Simulational Physics

Sakae, Yoshitake^1,2 ; Hiroyasu, Tomoyuki^3 ; Miki, Mitsunori^4 ; Ishii, Katsuya^5 ; Okamoto, Yuko^1,5,6,7

Department of Physics, Graduate School of Science, Nagoya University, Nagoya, Aichi 464-8602, Japan^1

Computational Materials Science Initiative, Institute for Molecular Science, Okazaki, Aichi, 444-8585, Japan^2

Department of Biomedical Information, Doshisha University, Kyotanabe, Kyoto 610-0394, Japan^3

Department of Intelligent Information Engineering and Sciences, Doshisha University, Kyotanabe, Kyoto 610-0394, Japan^4

Information Technology Center, Nagoya University, Aichi 464-8601, Nagoya, Japan^5

Structural Biology Research Center, Graduate School of Science, Nagoya University, Aichi 464-8602, Nagoya, Japan^6

Center for Computational Science, Graduate School of Engineering, Nagoya University, Aichi 464-8603, Nagoya, Japan^7

关键词: Alpha-helical proteins;    Biological functions;    Conformational search;    High-energy barriers;    Metropolis criterion;    Molecular simulations;    Optimization method;    Tertiary structures;   

Others  :  https://iopscience.iop.org/article/10.1088/1742-6596/487/1/012003/pdf
DOI  :  10.1088/1742-6596/487/1/012003

来源: IOP

【 摘 要 】

Many proteins carry out their biological functions by forming the characteristic tertiary structures. Therefore, the search of the stable states of proteins by molecular simulations is important to understand their functions and stabilities. However, getting the stable state by conformational search is difficult, because the energy landscape of the system is characterized by many local minima separated by high energy barriers. In order to overcome this difficulty, various sampling and optimization methods for conformations of proteins have been proposed. In this study, we propose a new conformational search method for proteins by using genetic crossover and Metropolis criterion. We applied this method to an α-helical protein. The conformations obtained from the simulations are in good agreement with the experimental results.