Free energy landscape of the FBP28 WW domain by all-atom direct folding simulation.

Using multiplexed Q-replica exchange molecular dynamics simulation (mQ-REMD) with a modified all-atom force field (param99MOD5/GBSA), direct folding simulation at the all-atom level was performed to investigate the folding free energy landscapes of the FBP28 WW domain: a 37-residue three-stranded beta-sheet. Starting from a fully extended conformation of the FBP28 WW domain, a total of 400 ns simulation was run for each replica with this simulation protocol. Free energy analysis showed that the folding of this protein substantially proceeded through the formation of folded turn 1, followed by the partial or misfolded formation of turn 2. More importantly, the folding process of turn 2 exhibited complicated folding behaviors in the presence of several intermediate states along multiple folding routes.