The Folding of de Novo Designed Protein DS119 via Molecular Dynamics Simulations.

ABSTRACT: As they are not subjected to natural selection process, de novo designed proteins usually fold in a manner different from natural proteins. Recently, a de novo designed mini-protein DS119, with a βαβ motif and 36 amino acids, has folded unusually slowly in experiments, and transient dimers have been detected in the folding process. Here, by means of all-atom replica exchange molecular dynamics (REMD) simulations, several comparably stable intermediate states were observed on the folding free-energy landscape of DS119. Conventional molecular dynamics (CMD) simulations showed that when two unfolded DS119 proteins bound together, most binding sites of dimeric aggregates were located at the N-terminal segment, especially residues 5-10, which were supposed to form β-sheet with its own C-termina

SUBMITTER: Wang M 

PROVIDER: S-EPMC4881441 | biostudies-literature | 2016 Apr

REPOSITORIES: biostudies-literature