The interaction of biotin and streptavidin in the presence and absence of a carbon nanotube was studied by molecular dynamics simulation. With respect to the Arrhenius dependence of the rate constants with temperature, those of streptavidin–biotin complex formation ( k 1 ) and streptavidin–biotin complex dissociation ( k − 1 ) were calculated from molecular dynamics simulation trajectories. Nanotube has reduced the amount of and k1 and k1. However, the biotin position in streptavidin does not change much. The results obtained from MMPBSA calculations show that the contribution of the van der Waals forces to both systems (in the absence and presence of the nanotube) was greater than that of electrostatic forces. The presence of the nanotube also led to the reduction of van der Waals and electrostatic forces in the interaction of biotin with streptavidin. However, this reduction was greater for electrostatic forces. In the absence of a nanotube, there are four hydrogen bonds between streptavidin and biotin, which are related to the residues Ser27, Tyr43, Ser45 and Ser88. In the presence of the nanotube, the hydrogen bonding of biotin with Ser45 is removed.

中文翻译：

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单壁碳纳米管会影响生物素与链霉亲和素结合的速率常数吗？分子动力学模拟视角

通过分子动力学模拟研究了存在和不存在碳纳米管时生物素和链霉亲和素的相互作用。关于速率常数随温度的 Arrhenius 依赖性，链霉亲和素-生物素复合物形成 (k 1 ) 和链霉亲和素-生物素复合物解离 (k - 1 ) 的速率常数由分子动力学模拟轨迹计算。Nanotube减少了k1和k1的量。然而，链霉亲和素中的生物素位置变化不大。从 MMPBSA 计算获得的结果表明，范德华力对两个系统的贡献（在不存在和存在纳米管的情况下）大于静电力的贡献。纳米管的存在还导致生物素与链霉亲和素相互作用中范德华力和静电力的降低。然而，静电力的这种降低更大。在没有纳米管的情况下，链霉亲和素和生物素之间有四个氢键，分别与 Ser27、Tyr43、Ser45 和 Ser88 残基有关。在纳米管的存在下，生物素与 Ser45 的氢键被去除。