A mass weighted chemical elastic network model elucidates closed form domain motions in proteins

作者：Kim Min Hyeok; Seo Sangjae; Jeong Jay Il; Kim Bum Joon; Liu Wing Kam; Lim Byeong Soo; Choi Jae Boong; Kim Moon Ki

来源：Protein Science, 2013, 22(5): 605-613.

DOI：10.1002/pro.2244

• elastic network model
• normal mode analysis
• protein dynamics
• closed protein conformation

An elastic network model (ENM), usually C coarse-grained one, has been widely used to study protein dynamics as an alternative to classical molecular dynamics simulation. This simple approach dramatically saves the computational cost, but sometimes fails to describe a feasible conformational change due to unrealistically excessive spring connections. To overcome this limitation, we propose a mass-weighted chemical elastic network model (MWCENM) in which the total mass of each residue is assumed to be concentrated on the representative alpha carbon atom and various stiffness values are precisely assigned according to the types of chemical interactions. We test MWCENM on several well-known proteins of which both closed and open conformations are available as well as three -helix rich proteins. Their normal mode analysis reveals that MWCENM not only generates more plausible conformational changes, especially for closed forms of proteins, but also preserves protein secondary structures thus distinguishing MWCENM from traditional ENMs. In addition, MWCENM also reduces computational burden by using a more sparse stiffness matrix.

• 出版日期2013-5
• 单位西北大学