In an initial attempt to understand the structural organization of Bombyx mori silk fibroin stored in the silk gland using several solid-state NMR techniques, we recently reported the conformation of the crystalline form of silk I (The unprocessed conformation of the silk fibroin before spinning in the solid state) as a repeated type II beta-turn structure (Ala, (phi,psi) = (-60degrees,130degrees), and Gly, (phi,psi) = (70degrees,30degrees)) in a model peptide (Ala-Gly)(15) (Asakura et al. J. Mol. Biol. 2001, 306, 291-305). To examine the favorable secondary structure(s) associated with silk fibroin molecules, we analyzed the results of molecular dynamic (MD) simulations of three model dipeptides of the type Ac-YXX-NHMe (where Xxx = Gly, Ala and Ser) in explicit water because the concentration of the silk fibroin before spinning in the middle silk gland is about 30% in water. The conformational probability maps constructed for these dipeptides indicate that the torsion angles of Gly, Ala, and Ser residues in the type II beta-turn structure are in the stable state even in water, and only our model among silk I models proposed previously can satisfy the stable state for these residues simultaneously. The high possibility of the appearance of beta-turn structure is pointed out by the MD simulation of Ac-(Ala-GlY)(8)-NHMe molecule in water. There is also a high possibility to form intramolecular hydrogen bonding involving the ith Ser (OH)-H-gamma functionality as a donor and the (i - 3)th Gly C=O group as an acceptor when the side chain conformation of the Ser residue, X, = -60degrees. This is derived from the molecular mechanics simulation of Ac-(Ala-Gly-Ser)-NHMe without water and will further stabilize the type II beta-turn conformation.