Does the single-walled carbon nanotube affect the rate constant of binding of biotin to streptavidin? Molecular dynamics simulation perspective

IF 2.1 4区 化学 Q3 CHEMISTRY, PHYSICAL
O. Soltani, M. Bozorgmehr, M. Momen-Heravi
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引用次数: 0

Abstract

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.
单壁碳纳米管是否影响生物素与链亲和素结合的速率常数?分子动力学模拟视角
通过分子动力学模拟研究了生物素和链霉亲和素在碳纳米管存在和不存在情况下的相互作用。根据温度对链霉亲和素-生物素络合物形成(k1)和链霉亲和素-生物素络合物解离(k−1)速率常数的Arrhenius依赖性,通过分子动力学模拟轨迹计算链霉亲和素-生物素络合物形成(k1)和解离(k−1)速率常数。纳米管减少了和k1和k1的量。然而,生物素在链霉亲和素中的位置变化不大。MMPBSA计算结果表明,范德华力对两种体系(纳米管存在和不存在时)的贡献大于静电力的贡献。纳米管的存在还导致生物素与链霉亲和素相互作用中的范德华力和静电力的减少。然而,对于静电力,这种减少更大。在没有纳米管的情况下,链霉亲和素与生物素之间存在4个氢键,它们与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。
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来源期刊
CiteScore
2.10
自引率
0.00%
发文量
5
审稿时长
2.3 months
期刊介绍: The journal covers the fields of kinetics and mechanisms of chemical processes in the gas phase and solution of both simple and complex systems.
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