title: A mass weighted chemical elastic network model elucidates closed form domain motions in proteins.
abstract: An elastic network model (ENM), usually Cα 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 α-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.
authors: SKKU Advanced Institute of Nanotechnology-SAINT, Sungkyunkwan University, Suwon 440-746, Korea.
authors: Min Hyeok
authors: MH
authors: Kim
authors: Sangjae
authors: S
authors: Seo
authors: Jay Il
authors: JI
authors: Jeong
authors: Bum Joon
authors: BJ
authors: Kim
authors: Wing Kam
authors: WK
authors: Liu
authors: Byeong Soo
authors: BS
authors: Lim
authors: Jae Boong
authors: JB
authors: Choi
authors: Moon Ki
authors: MK
authors: Kim
mesh_terms: D004548:Elasticity; D008956:Models, Chemical; D056004:Molecular Dynamics Simulation; D009038:Motion; D011487:Protein Conformation; D017434:Protein Structure, Tertiary; D011506:Proteins / Q000737:chemistry*
chemical_list: D011506:Proteins