Computational protocol: Customized Peptide Biomaterial Synthesis via an Environment-Reliant Auto-Programmer Stigmergic Approach

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[…] The protein composition of gliadin and self-organized peptide samples were analyzed using sodium dodecyl sulfate-polyacrilamide gel electrophoresis (SDS-PAGE) performed according to conditions described by Laemmli (1970) []. Briefly, the 12% separating gels and 5% stacking gels were cast in vertical electrophoretic units (Mini-PROTEAN, Bio-Rad Laboratories, Hercules, CA, USA). Samples were diluted with the sample buffer (without β-mercaptoethanol) in a ratio of 1:2 (v/v). These samples were then heated at 90 °C for 5 min and cooled at room temperature. Gliadin fractions equivalent to 5 and 7 µg were loaded in two wells. Similarly, the self-organized peptides at 37 and 50 °C were loaded at 5, 7, and 10 µg and 5, 7, 10, and 12 µg concentrations, respectively, on separate gels. Gels were run at 100 mA for 3 h, and stained with Coomassie blue staining. The molecular weights of the peptides were estimated using ultra-low and low-range molecular-weight standards ranging from 1.1 to 26.6 kD and from 6.5 to 66 kD (Sigma-Aldrich, Cleveland, OH, USA), respectively. To analyze possible high-molecular-weight stigmergized products, bovine serum albumin (66 kD, SDS-PAGE marker from Sigma-Aldrich, Cleveland, OH, USA) was added to an ultra-low molecular-weight standard. The protein bands on the Coomassie blue stained gel were analyzed using IQuant Capture 300 software (GE Healthcare, Buckinghamshire, UK). The electrophoresis was performed in triplicate to authenticate the self-organized peptides. [...] The stigmergic self-organization of peptide fragment based on the molecular weight provided by SDS-PAGE and secondary structure provided by FTIR can be predicted using modeling software HyperChemTM 8.0.8 (Hypercube Inc., Gainesville, FL, USA) and ChemBio3D ultra 11.0 (CambridgeSoft Corporation, Cambridge, UK). The α-gliadin protein contains 266 amino acid residues with three disulfide linkages [,]. Treatment with 6M urea and DTT converted the 3D structure of the protein into a primary structure with the following amino acid sequence: This primary structure of protein was broken down to 10 possible peptide fragments by α-chymotrypsin (PeptideMass-ExPASy bioinformatics resource portal). The fragments with their molecular weight are presented in . The fragments with cysteine amino acid were then stigmergized to synthesize new peptide molecule. […]

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