Shanghai Key Laboratory of Molecular Catalysis and Innovative Materials, Department of Chemistry, Fudan University, Shanghai 200433, People's Republic of China.
J Phys Chem B. 2010 Dec 2;114(47):15663-72. doi: 10.1021/jp1048869. Epub 2010 Nov 9.
Dynein light chain LC8 is a highly conserved, dimeric protein involved in a variety of essential cellular events. Phosphorylation at Ser88 was found to promote mammalian cell survival and regulate the dimer to monomer transition at physiological pH. Combining molecular dynamics (MD) simulation and free energy calculation methods, we explored the atomistic mechanism of the phosphorylation-induced dimer dissociation. The MD simulation revealed that phosphorylation/phosphomimetic mutation at Ser88 opens an entrance into the dimer interface for water molecules, which disturb the hydrogen bond network around His55 and is expected to raise the pK(a) value and protonation ratio of His55 as well. The free energy calculations showed that the S88E mutation destabilized the dimer by 6.6 kcal/mol, in good agreement with the experimental value of 8.1 kcal/mol. The calculated destabilization upon phosphorylation is 50.8 kcal/mol, showing that phosphorylation definitely prevents dimer formation under physiological conditions. Further analysis of the calculated free energy changes demonstrated that the electrostatic contribution dominates the impact of phosphorylation on dimer dissociation.
动力蛋白轻链 LC8 是一种高度保守的二聚体蛋白，参与多种重要的细胞事件。研究发现，丝氨酸 88 的磷酸化可促进哺乳动物细胞存活，并调节生理 pH 下二聚体向单体的转变。我们结合分子动力学 (MD) 模拟和自由能计算方法，探索了磷酸化诱导二聚体解离的原子机制。MD 模拟表明，丝氨酸 88 的磷酸化/磷酸模拟突变在二聚体界面上打开了水分子进入的入口，破坏了围绕 His55 的氢键网络，预计会提高 His55 的 pK(a) 值和质子化比率。自由能计算表明，S88E 突变使二聚体不稳定，降低了 6.6 kcal/mol，与实验值 8.1 kcal/mol 非常吻合。磷酸化引起的去稳定化计算为 50.8 kcal/mol，表明磷酸化在生理条件下肯定会阻止二聚体的形成。对计算得到的自由能变化的进一步分析表明，静电贡献主导了磷酸化对二聚体解离的影响。
