Journal of Physical Chemistry B, Vol.116, No.23, 6916-6922, 2012
Folding Models of Mini-Protein FSD-1
We have carried out all-atom action-derived molecular dynamics (ADMD) folding simulations of the full-size FSD-1. FSD-1 is a designed mini-protein of 28 residues containing both a and beta secondary structure elements. Multiple folding pathways are found for FSD-1, which is consistent with existing computational studies. Hydrophobic collapse is observed first, and then subsequent folding events proceeds by forming either alpha-helix or beta-hairpin. Concurrent formation of the full tertiary structure and the secondary structure elements of alpha-helix and beta-hairpin is observed. The folding pathway of FSD-1 elucidated by ADMD simulations does not follow the scenario of the framework model. ADMD simulations provide significant insights for the general mechanisms of protein folding and conformational changes.