School of Chemistry and Molecular Engineering, Shanghai Engineering Research Center of Molecular Therapeutics and New Drug Development, East China Normal University , Shanghai, 200062, China.
Department of Chemistry, University of Florida , Gainesville, Florida 32611, United States.
J Am Chem Soc. 2018 Feb 7;140(5):1639-1648. doi: 10.1021/jacs.7b08569. Epub 2018 Jan 27.
Ionizable residues in the interior of proteins play essential roles, especially in biological energy transduction, but are relatively rare and seem incompatible with the complex and polar environment. We perform a comprehensive study of the internal ionizable residues on 21 variants of staphylococcal nuclease with internal Lys, Glu, or Asp residues. Using pH replica exchange molecular dynamics simulations, we find that, in most cases, the pK values of these internal ionizable residues are shifted significantly from their values in solution. Our calculated results are in excellent agreement with the experimental observations of the Garcia-Moreno group. We show that the interpretation of the experimental pK values requires the study of not only protonation changes but also conformational changes. The coupling between the protonation and conformational equilibria suggests a mechanism for efficient pH-sensing and regulation in proteins. This study provides new physical insights into how internal ionizable residues behave in the hydrophobic interior of proteins.
蛋白质内部的可离子化残基起着至关重要的作用，特别是在生物能量转导中，但它们相对较少，似乎与复杂的极性环境不兼容。我们对具有内部赖氨酸、谷氨酸或天冬氨酸残基的 21 种葡萄球菌核酸酶变体的内部可离子化残基进行了全面研究。使用 pH 复制交换分子动力学模拟，我们发现，在大多数情况下，这些内部可离子化残基的 pK 值与它们在溶液中的值有显著的偏移。我们的计算结果与加西亚-莫雷诺小组的实验观察结果非常吻合。我们表明，对实验 pK 值的解释不仅需要研究质子化变化，还需要研究构象变化。质子化和构象平衡之间的耦合为蛋白质中高效的 pH 感应和调节提供了一种机制。这项研究为我们提供了关于内部可离子化残基在蛋白质疏水环境中行为的新的物理见解。
