氨基酸
肽
分子动力学
化学
硅
分子结合
肽序列
氨基酸残基
机制(生物学)
组合化学
立体化学
生物物理学
生物化学
计算化学
分子
生物
有机化学
基因
物理
量子力学
作者
Sathish Ramakrishnan,Marta Martin,Thierry Cloître,Lucyna Firlej,Csilla Gergely
摘要
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.
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