Release Time:2019-03-09  Hits:

Indexed by: Journal Article

Date of Publication: 2015-01-01

Journal: ADVANCE IN STRUCTURAL BIOINFORMATICS

Included Journals: Scopus、SCIE

Volume: 827

Page Number: 93-110

ISSN: 0065-2598

Key Words: Trefoil; Knot; High-temperature unfolding; Go-model; Fold

Abstract: 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 Go-model to investigate the folding mechanisms for two trefoil knot proteins. Results show that, the contacts in beta-sheet are important to the formation of knot protein, and if these contacts disappeared, the knot protein would be easy to untie. In the Go-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 beta-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.