Molecular Modeling Laboratory, Department of Chemistry, Indian Institute of Technology Kharagpur, Kharagpur 721302, India.
J Phys Chem B. 2023 Aug 24;127(33):7251-7265. doi: 10.1021/acs.jpcb.3c03223. Epub 2023 Aug 13.
Ionic liquids (ILs) are known to stabilize protein conformations in aqueous medium. Importantly, ILs can also act as refolding additives in urea-driven denaturation of proteins. However, despite the importance of the problem, detailed microscopic understanding of the counteraction effects of ILs on urea-induced protein denaturation remains elusive. In this work, atomistic molecular dynamics (MD) simulations of the protein α-lactalbumin have been carried out in pure aqueous medium, in 8 M binary urea-water solution and in ternary urea-IL-water solutions containing ammonium-based ethyl ammonium acetate (EAA) as the IL at different concentrations (1-4 M). Attempts have been made to quantify detailed molecular-level understanding of the origin behind the counteraction effects of the IL on urea-induced partial unfolding of the protein. The calculations revealed significant conformational changes of the protein with multiple free energy minima due to its partial unfolding in binary urea-water solution. The counteraction effect of the IL was evident from the enhanced structural rigidity of the protein with propensity to transform into a single native free energy minimum state in ternary urea-IL-water solutions. Such an effect has been found to be associated with preferential direct binding of the IL components with the protein and simultaneous expulsion of urea from the interface, thereby providing additional stabilization of the protein in ternary solutions. Most importantly, modified rearrangement of the hydrogen bond network at the interface due to the formation of stronger protein-cation (PC) and protein-anion (PA) hydrogen bonds by breaking relatively weaker protein-urea (PU) and protein-water (PW) hydrogen bonds has been recognized as the microscopic origin behind the counteraction effects of EAA on urea-induced partial unfolding of the protein.
离子液体（ILs）已知可在水介质中稳定蛋白质构象。重要的是，ILs 还可以作为尿素驱动的蛋白质变性的复性添加剂。然而，尽管这个问题很重要，但对于 ILs 对尿素诱导的蛋白质变性的拮抗作用的详细微观理解仍然难以捉摸。在这项工作中，对纯水溶液中的蛋白质α-乳白蛋白、8 M 二元尿素-水溶液中和含有铵基乙基氯化铵（EAA）的三元尿素-IL-水溶液中的蛋白质进行了原子分子动力学（MD）模拟。在不同浓度（1-4 M）的情况下。试图量化对 IL 对尿素诱导的蛋白质部分展开的拮抗作用的起源的详细分子水平理解。计算结果表明，由于在二元尿素-水中的部分展开，蛋白质发生了显著的构象变化，出现了多个自由能最小值。IL 的拮抗作用明显体现在蛋白质的结构刚性增强上，蛋白质倾向于在三元尿素-IL-水中转化为单个天然自由能最小状态。这种效应与 IL 成分与蛋白质的优先直接结合以及从界面逐出尿素有关，从而在三元溶液中为蛋白质提供了额外的稳定性。最重要的是，由于形成了更强的蛋白质-阳离子（PC）和蛋白质-阴离子（PA）氢键，打破了相对较弱的蛋白质-尿素（PU）和蛋白质-水（PW）氢键，界面处的氢键网络发生了改
