On the roles of the alanine and serine in the β-sheet structure of fibroin

- Semiempirical MP6, DFT calculations and molecular dynamics calculations on fibroin type models are provided.
- These results show how alanine and serine impact the rigidity of β-sheet structures.
- Alanine adds stability to the rigidity of the sheet, allowing it to maintain a properly pleated structure even in a single β-sheet.
- The role of the serine is proposed to involve modulation of the hydrophobicity.

In its silk II form, fibroin is almost exclusively formed from layers of β-sheets, rich in glycine, alanine and serine. Reported here are computational results on fibroin models at semi-empirical, DFT levels of theory and molecular dynamics (MD) for (Gly)10, (Gly-Ala)5 and (Gly-Ser)5 decapeptides. While alanine and serine introduce steric repulsions, the alanine side-chain adds to the rigidity of the sheet, allowing it to maintain a properly pleated structure even in a single β-sheet, and thus avoiding two alternative conformations which would interfere with the formation of the multi-layer pleated-sheet structure. The role of the serine is proposed to involve modulation of the hydrophobicity in order to construct the supramolecular assembly as opposed to random precipitation due to hydrophobicity.