Huizhou University, Huizhou, 516007, P. R. China.
Phys Chem Chem Phys. 2018 May 30;20(21):14587-14596. doi: 10.1039/c8cp00530c.
The Hamiltonian replica exchange Monte Carlo (H-REMC) algorithm was applied to study protein adsorption and its performance was compared with that of the temperature replica exchange Monte Carlo (T-REMC). Comparisons indicate that the simulation results are consistent but the computational efficiency is improved for H-REMC. H-REMC could accurately and efficiently identify the preferred orientations of glucose oxidase (GOx) on charged surfaces; different preferential GOx orientations on different surfaces and solution conditions could be spotted with a much fewer number of simulation runs. On positively charged surfaces, when electrostatic interactions dominate, the negatively charged GOx can be easily adsorbed with the "standing" orientation for which the substrate-binding domain is accessible to substrates. As the surface charge densities decrease and ionic strengths increase, there is an increasing contribution from the van der Waals (vdW) interactions, and thus more possible orientations appear. When the vdW interactions dominate, the unfavorable "front-lying" becomes the preferred orientation for which the substrate-binding domain is blocked by the surface. On negatively charged surfaces, though GOx has a net charge of -30 e under physiological conditions, the charged groups are unevenly distributed over the protein surface; the positive potential regions in the "back" of GOx enable the protein to be adsorbed on negatively charged surfaces with the "back-lying" orientation. The H-REMC provides an alternative method to accurately and efficiently probe the lowest-energy orientation of proteins adsorbed on surfaces for biotechnological applications.
采用哈密顿复制交换蒙卡（H-REMC）算法研究蛋白质吸附，将其性能与温度复制交换蒙卡（T-REMC）进行比较。结果表明，两种方法的模拟结果一致，但 H-REMC 的计算效率更高。H-REMC 可以准确有效地识别葡萄糖氧化酶（GOx）在带电表面上的优先取向；与使用更少的模拟运行次数，能够发现不同表面和溶液条件下 GOx 的不同优先取向。在带正电荷的表面上，当静电相互作用占主导地位时，带负电荷的 GOx 可以很容易地以“站立”取向吸附，其中底物结合域可与底物接触。随着表面电荷密度的降低和离子强度的增加，范德华（vdW）相互作用的贡献增加，出现更多可能的取向。当 vdW 相互作用占主导地位时，不利的“仰卧”取向成为首选，其中底物结合域被表面阻塞。在带负电荷的表面上，尽管 GOx 在生理条件下带有-30e 的净电荷，但带电荷的基团在蛋白质表面上分布不均匀；GOx“背面”的正电势区域使蛋白质能够以“背面”取向吸附在带负电荷的表面上。H-REMC 为生物技术应用中准确有效地探测吸附在表面上的蛋白质的最低能量取向提供了一种替代方法。
