title: Molecular mechanism of selective binding of peptides to silicon surface.
abstract: Despite extensive recent research efforts on material-specific peptides, the fundamental problem to be explored yet is the molecular interactions between peptides and inorganic surfaces. Here we used computer simulations (density functional theory and classical molecular dynamics) to investigate the adsorption mechanism of silicon-binding peptides and the role of individual amino acids in the affinity of peptides for an n-type silicon (n(+)-Si) semiconductor. Three silicon binding 12-mer peptides previously elaborated using phage display technology have been studied. The peptides' conformations close to the surface have been determined and the best-binding amino acids have been identified. Adsorption energy calculations explain the experimentally observed different degrees of affinity of the peptides for n(+)-Si. Our residual scanning analysis demonstrates that the binding affinity relies on both the identity of the amino acid and its location in the peptide sequence.
authors.affiliation: Université Montpellier 2 , Laboratoire Charles Coulomb UMR 5221, F-34095 Montpellier, France.
authors.forename: Sathish Kumar
authors.initials: SK
authors.lastname: Ramakrishnan
authors.forename: Marta
authors.initials: M
authors.lastname: Martin
authors.forename: Thierry
authors.initials: T
authors.lastname: Cloitre
authors.forename: Lucyna
authors.initials: L
authors.lastname: Firlej
authors.forename: Csilla
authors.initials: C
authors.lastname: Gergely
mesh_terms: D000327:Adsorption; D000595:Amino Acid Sequence; D056004:Molecular Dynamics Simulation; D009842:Oligopeptides / Q000737:chemistry*; D011487:Protein Conformation; D011789:Quantum Theory; D012666:Semiconductors; D012825:Silicon / Q000737:chemistry*; D012997:Solvents / Q000737:chemistry; D013379:Substrate Specificity; D013499:Surface Properties; D013816:Thermodynamics; D014618:Vacuum; D014867:Water / Q000737:chemistry
chemical_list: D009842:Oligopeptides; D012997:Solvents; D014867:Water; D012825:Silicon