title: On the roles of the alanine and serine in the β-sheet structure of fibroin.
abstract: 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.
authors.affiliation: Department of Chemistry and Chemical Engineering, "Babes-Bolyai" University, 11 Arany Janos Str, Cluj-Napoca RO-400028, Romania. Electronic address: carrascoza@chem.ubbcluj.ro.
authors.forename: Juan Francisco
authors.initials: JF
authors.lastname: Carrascoza Mayen
authors.affiliation: Department of Chemistry and Chemical Engineering, "Babes-Bolyai" University, 11 Arany Janos Str, Cluj-Napoca RO-400028, Romania.
authors.forename: Alexandru
authors.initials: A
authors.lastname: Lupan
authors.affiliation: Department of Chemistry and Chemical Engineering, "Babes-Bolyai" University, 11 Arany Janos Str, Cluj-Napoca RO-400028, Romania.
authors.forename: Ciprian
authors.initials: C
authors.lastname: Cosar
authors.affiliation: Department of Chemistry and Chemical Engineering, "Babes-Bolyai" University, 11 Arany Janos Str, Cluj-Napoca RO-400028, Romania.
authors.forename: Attila-Zsolt
authors.initials: AZ
authors.lastname: Kun
authors.affiliation: Department of Chemistry and Chemical Engineering, "Babes-Bolyai" University, 11 Arany Janos Str, Cluj-Napoca RO-400028, Romania.
authors.forename: Radu
authors.initials: R
authors.lastname: Silaghi-Dumitrescu
mesh_terms: D000409:Alanine / Q000032:analysis*; D000595:Amino Acid Sequence; D004151:Dipeptides / Q000737:chemistry; D005349:Fibroins / Q000737:chemistry*; D008958:Models, Molecular; D056004:Molecular Dynamics Simulation; D017433:Protein Structure, Secondary; D012694:Serine / Q000032:analysis*
chemical_list: D004151:Dipeptides; C000589855:glycylserine; D012694:Serine; D005349:Fibroins; C065992:N-glycylalanine; D000409:Alanine
keywords: DFT; Fibroin; Molecular modeling; Semiempirical; Silk II; β-sheet