School of Chemistry and Chemical Engineering, Guangdong Provincial Key Lab for Green Chemical Product Technology, South China University of Technology , Guangzhou, Guangdong, 510640, People's Republic of China.
Langmuir. 2013 Sep 10;29(36):11366-74. doi: 10.1021/la401171v. Epub 2013 Aug 28.
The orientation of an antibody plays an important role in the development of immunosensors. Protein G is an antibody binding protein, which specifically targets the Fc fragment of an antibody. In this work, the orientation of prototypical and mutated protein G B1 adsorbed on positively and negatively charged self-assembled monolayers was studied by parallel tempering Monte Carlo and all-atom molecular dynamics simulations. Both methods present generally similar orientation distributions of protein G B1 for each kind of surface. The root-mean-square deviation, DSSP, gyration radius, eccentricity, dipole moment, and superimposed structures of protein G B1 were analyzed. Moreover, the orientation of binding antibody was also predicted in this work. Simulation results show that with the same orientation trends, the mutant exhibits narrower orientation distributions than does the prototype, which was mainly caused by the stronger dipole of the mutant. Both kinds of proteins adsorbed on charged surfaces were induced by the competition of electrostatic interaction and vdW interaction; the electrostatic interaction energy dominated the adsorption behavior. The protein adsorption was also largely affected by the distribution of charged residues within the proteins. Thus, the prototype could adsorb on a negatively charged surface, although it keeps a net charge of -4 e. The mutant has imperfect opposite orientation when it adsorbed on oppositely charged surfaces. For the mutant on a carboxyl-functionalized self-assembled monolayer (COOH-SAM), the orientation was the same as that inferred by experiments. While for the mutant on amine-functionalized self-assembled monolayer (NH2-SAM), the orientation was induced by the competition between attractive interactions (led by ASP40 and GLU56) and repulsive interactions (led by LYS10); thus, the perfect opposite orientation could not be obtained. On both surfaces, the adsorbed protein could retain its native conformation. The desired orientation of protein G B1, which would increase the efficiency of binding antibodies, could be obtained on a negatively charged surface adsorbed with the prototype. Further, we deduced that with the packing density of 12,076 protein G B1 domain per μm(2), the efficiency of the binding IgG would be maximized. The simulation results could be applied to control the orientation of protein G B1 in experiments and to provide a better understanding to maximize the efficiency of antibody binding.
抗体的取向在免疫传感器的发展中起着重要作用。蛋白 G 是一种抗体结合蛋白，它专门针对抗体的 Fc 片段。在这项工作中，通过平行温度蒙特卡罗和全原子分子动力学模拟研究了原型和突变体蛋白 G B1 在带正电荷和带负电荷的自组装单层上的吸附取向。这两种方法对于每种表面都呈现出一般相似的蛋白 G B1 取向分布。分析了蛋白 G B1 的均方根偏差（DSSP）、回转半径、偏心率、偶极矩和叠加结构。此外，在这项工作中还预测了结合抗体的取向。模拟结果表明，在具有相同取向趋势的情况下，突变体比原型具有更窄的取向分布，这主要是由于突变体的偶极矩更强所致。两种蛋白在带电荷的表面上的吸附都是静电相互作用和 vdW 相互作用竞争的结果；静电相互作用能主导吸附行为。蛋白质的吸附也受到蛋白质内带电残基分布的很大影响。因此，尽管原型带有-4 个电子的净电荷，但它可以吸附在带负电荷的表面上。当突变体吸附在带相反电荷的表面上时，其取向并不完全相反。对于在羧酸功能化自组装单层（COOH-SAM）上的突变体，其取向与实验推断的取向相同。然而，对于在胺功能化自组装单层（NH2-SAM）上的突变体，其取向是由吸引相互作用（由 ASP40 和 GLU56 引起）和排斥相互作用（由 LYS10 引起）之间的竞争引起的；因此，无法获得完美的相反取向。在这两种表面上，吸附的蛋白质都可以保留其天然构象。通过在带负电荷的表面上吸附原型，可以获得提高结合抗体效率的理想蛋白 G B1 取向。进一步推断，在 12,076 个蛋白 G B1 结构域/μm(2)的堆积密度下，结合 IgG 的效率将最大化。模拟结果可应用于控制实验中蛋白 G B1 的取向，并提供更好的理解以最大化抗体结合效率。
