Ramakrishnan Sathish Kumar, Martin Marta, Cloitre Thierry, Firlej Lucyna, Gergely Csilla
Université Montpellier 2 , Laboratoire Charles Coulomb UMR 5221, F-34095 Montpellier, France.
J Chem Inf Model. 2014 Jul 28;54(7):2117-26. doi: 10.1021/ci500260v. Epub 2014 Jun 17.
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.
尽管近期对材料特异性肽进行了广泛的研究，但有待探索的基本问题是肽与无机表面之间的分子相互作用。在此，我们使用计算机模拟（密度泛函理论和经典分子动力学）来研究硅结合肽的吸附机制以及单个氨基酸在肽对n型硅（n(+)-Si）半导体亲和力中的作用。研究了先前使用噬菌体展示技术精心设计的三种与硅结合的12聚体肽。确定了肽靠近表面的构象，并鉴定了最佳结合氨基酸。吸附能计算解释了实验观察到的肽对n(+)-Si不同程度的亲和力。我们的残基扫描分析表明，结合亲和力既取决于氨基酸的身份，也取决于其在肽序列中的位置。
