Fs-21 Peptides Can Form Both Single Helix and Helix−Turn−Helix

Detailed folding processes and mechanisms of two alanine-based peptides (Fs-21 and MABA-Fs) were investigated by all atom molecular dynamic simulation with a new AMBER force field and Generalized Born continuum solvent model. Both peptides showed multiphase folding processes. Much like what has been envisaged by the folding funnel theory, the number of accessible conformations descended quickly as folding progresses. Interestingly, MABA-Fs and Fs-21 peptides exhibited notably different folding kinetics; the Fs-21-folding was a two-phase process while MABA-Fs went through three phases and folded more slowly than the Fs-21 peptide by four times. These difference highlights the contribution of the bulky N-terminal MABA group. Furthermore, it is found that helix -turn -helix conformation was the most stable state at 300 K, instead of the expected full helix conformation. At 273 K, however, the full helix became the most stable state. The turn structure was found to be stabilized mainly by the hydrophobic interactions. Statistical analysis of high-resolution PDB structures indicated that most helices are shorter than 16 amino acids. Taken together, we suo-est that the intrinsic property of polypeptide chain dictates the formation of short helices in proteins.