Folding mechanisms of Trefoil Knot proteins studied by molecular dynamics simulations and Go-model.
Most proteins need to avoid the complex topologies when folding into the native structures, but some proteins with nontrivial topologies have been found in nature. Here we used protein unfolding simulations under high temperature and all-atom Gō-model to investigate the folding mechanisms for two trefoil knot proteins. Results show that, the contacts in β-sheet are important to the formation of knot protein, and if these contacts disappeared, the knot protein would be easy to untie. In the Gō-model simulations, the folding processes of the two knot proteins are similar. The compact structures of the two knot proteins with the native contacts in β-sheet are formed in transition state, and the intermediate state has loose C-terminal. This model also reveals the detailed folding mechanisms for the two proteins.
Laboratory of Molecular Modeling and Design, State Key Laboratory of Molecular Reaction Dynamics, Dalian Institute of Chemical Physics, Chinese Academy of Science, Dalian, Liaoning, China.
Xue
X
Wu
Peijun
P
Xu
Jinguang
J
Wang
Yong
Y
Xu
Ting
T
Fu
Depeng
D
Zhang
Meixia
M
Zhao
Jiahui
J
Liu
Hujun
H
Shen
Zhilong
Z
Xiu
Guohui
G
Li
D008958:Models, Molecular; D056004:Molecular Dynamics Simulation; D010455:Peptides / Q000737:chemistry / Q000378:metabolism*; D017510:Protein Folding; D000071164:Trefoil Factor-2
D010455:Peptides; D000071164:Trefoil Factor-2