Molecular dynamics simulations of three-strand β-sheet folding

Traditionally, the empirical force field had great difficulties in simulating P-sheet folding. In the current study, we tested molecular dynamics simulations of beta-sheet folding using a solvent-referenced potential. Three available P-sheet-forming synthetic peptides, TWIQNGSTKWYQNGSTKIYT, RGWSVQNGKYT NNGKTTEGR, and VFITS(D)PGKTYTEV(D)PGOKILQ, were simulated at their experimental temperatures. From extended initial conformations, all three peptides folded into beta-sheet conformations. The calculated ratios of the beta-structure from the 100 ns simulations were 26.5%, 17.8%, and 28.5%, respectively, for the three peptides. From different initial conformations, folding into beta-sheets was also; observed. With the same energy functions, the alanine-based peptide folded into helical conformations, demonstrating the sequence dependence of folding. During simulations, the beta-sheet folding is usually initiated by the fast formation of turns. The three-strand compact structures with favorable inter-strand side-chain interactions occur prior to backbone hydrogen bonding. The conversion of the compact structure to beta-sheet is slow, and the peptide spends most of the time in these two states. The attractive side-chain interaction is mainly due to the solvent effect,: especially the hydrophobic interactions. Without this solvent effect, beta-sheet did not form in the simulations. For the first two sequences, the simulations suggest that the experimentally observed structure may include an ensemble of beta-sheet structures. For the DP-containing peptide, one beta-sheet structure with type II' beta-turns is much more stable than other structures.