Department of Biophysics, Johns Hopkins University, 3400 N. Charles Street, Baltimore, MD 21218, USA.
Structure. 2012 Jun 6;20(6):1071-85. doi: 10.1016/j.str.2012.03.023. Epub 2012 May 25.
Structural consequences of ionization of residues buried in the hydrophobic interior of proteins were examined systematically in 25 proteins with internal Lys residues. Crystal structures showed that the ionizable groups are buried. NMR spectroscopy showed that in 2 of 25 cases studied, the ionization of an internal Lys unfolded the protein globally. In five cases, the internal charge triggered localized changes in structure and dynamics, and in three cases, it promoted partial or local unfolding. Remarkably, in 15 proteins, the ionization of the internal Lys had no detectable structural consequences. Highly stable proteins appear to be inherently capable of withstanding the presence of charge in their hydrophobic interior, without the need for specialized structural adaptations. The extent of structural reorganization paralleled loosely with global thermodynamic stability, suggesting that structure-based pK(a) calculations for buried residues could be improved by calculation of thermodynamic stability and by enhanced conformational sampling.
系统研究了 25 个含有内部赖氨酸残基的蛋白质中，残基离子化对蛋白质疏水环境的影响。晶体结构表明，可离子化基团被埋藏在内部。NMR 光谱表明，在所研究的 25 个案例中，有 2 个内部赖氨酸残基的离子化导致蛋白质整体展开。在 5 个案例中，内部电荷引发了局部结构和动力学变化，在 3 个案例中，它促进了部分或局部展开。值得注意的是，在 15 个蛋白质中，内部赖氨酸残基的离子化没有检测到结构后果。高度稳定的蛋白质似乎天生能够承受其疏水环境中存在的电荷，而无需特殊的结构适应。结构重组的程度与整体热力学稳定性大致平行，这表明可以通过计算热力学稳定性和增强构象采样来改进基于结构的埋藏残基 pKa 计算。
