Open Access

ARTICLE

A 3-D Coarser-Grained Computational Model for Simulating Large Protein Dynamics

by Jae-In Kim¹, Hyoseon Jang², Jeong-Hee Ahn³, Sungsoo Na⁵

1 Graduate student, Dept. of Mechanical Eng., Korea University, Anam-dong, Seongbuk-gu, Seoul136-713, Korea (email: jay414@korea.ac.kr)
2 Graduate student, Dept. of Mechanical Eng., Korea University, Anam-dong, Seongbuk-gu, Seoul136-713, Korea (email: hsjang@korea.ac.kr)
3 Graduate student, Dept. of Mechanical Eng., Korea University, Anam-dong, Seongbuk-gu, Seoul136-713, Korea (email: shibuya@korea.ac.kr)
4 Research Professor, Corresponding author, Dept. of Mechanical Eng., Korea University, Anam-dong, Seongbuk-gu, Seoul 136-713, Korea (email:Kilhoeom@gmail.com)
5 Professor, Corresponding author, Dept. of Mechanical Eng., Korea University, Anam-dong, Seongbuk-gu, Seoul 136-713, Korea (email:nass@korea.ac.kr)

Computers, Materials & Continua 2009, 9(2), 137-152. https://doi.org/10.3970/cmc.2009.009.137

Abstract

Protein dynamics is essential for gaining insight into biological functions of proteins. Although protein dynamics is well delineated by molecular model, the molecular model is computationally prohibited for simulating large protein structures. In this work, we provide the three-dimensional coarser-grained anisotropic model (CGAM), which is based on model reduction applicable to large protein structures. It is shown that CGAM achieves the fast computation on low-frequency modes, quantitatively comparable to original structural model such as elastic network model (ENM). This indicates that the CGAM by model reduction method enable us to understand the functional motion of large proteins with remarkable computational efficiency.

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Keywords

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