The structural characteristics of Bombyx mori silk fibroin before spinning as studied with molecular dynamics simulation

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.