Temperature evolution of Trp-cage folding pathways: An analysis by dividing the probability flux field into stream tubes.

ABSTRACT: Owing to its small size and very fast folding rate, the Trp-cage miniprotein has become a benchmark system to study protein folding. Two folding pathways were found to be characteristic of this protein: pathway I, in which the hydrophobic collapse precedes the formation of α-helix, and pathway II, in which the events occur in the reverse order. At the same time, the relative contribution of these pathways at different temperatures as well as the nature of transition from one pathway to the other remain unclear. To gain insight into this issue, we employ a recently proposed hydrodynamic description of protein folding, in which the process of folding is considered as a motion of a "folding fluid" (Chekmarev et al., Phys. Rev. Lett. 100(1), 018107 2008). Using molecular dynamics simulations,

SUBMITTER: Andryushchenko VA 

PROVIDER: S-EPMC5696308 | biostudies-literature | 2017 Dec

REPOSITORIES: biostudies-literature