title: Opening and closing of a toroidal group II chaperonin revealed by a symmetry constrained elastic network model.
abstract: Recently, the atomic structures of both the closed and open forms of Group 2 chaperonin protein Mm-cpn were revealed through crystallography and cryo-electron microscopy. This toroidal-like chaperonin is composed of two eightfold rings that face back-to-back. To gain a computational advantage, we used a symmetry constrained elastic network model (SCENM), which requires only a repeated subunit structure and its symmetric connectivity to neighboring subunits to simulate the entire system. In the case of chaperonin, only six subunits (i.e., three from each ring) were used out of the eight subunits comprising each ring. A smooth and symmetric pathway between the open and closed conformations was generated by elastic network interpolation (ENI). To support this result, we also performed a symmetry-constrained normal mode analysis (NMA), which revealed the intrinsic vibration features of the given structures. The NMA and ENI results for the representative single subunit were duplicated according to the symmetry pattern to reconstruct the entire assembly. To test the feasibility of the symmetry model, its results were also compared with those obtained from the full model. This study allowed the folding mechanism of chaperonin Mm-cpn to be elucidated by SCENM in a timely manner.
authors.affiliation: School of Mechanical Engineering, Sungkyunkwan University, 2066 Seoburo, Jangan-gu, Suwon, 440-746, Republic of Korea.
authors.forename: Hoomin
authors.initials: H
authors.lastname: Lee
authors.forename: SangJae
authors.initials: S
authors.lastname: Seo
authors.forename: Minhyeok
authors.initials: M
authors.lastname: Kim
authors.forename: Jae boong
authors.initials: Jb
authors.lastname: Choi
authors.forename: Sun Min
authors.initials: SM
authors.lastname: Kim
authors.forename: Tae-Joon
authors.initials: TJ
authors.lastname: Jeon
authors.forename: Moon Ki
authors.initials: MK
authors.lastname: Kim
mesh_terms: D056385:Group II Chaperonins / Q000737:chemistry*; D011487:Protein Conformation
chemical_list: D056385:Group II Chaperonins
keywords: GroEL; chaperonin; elastic network interpolation; normal mode analysis; symmetric constrained elastic network model