Simonson Thomas, Carlsson Jens, Case David A
Laboratoire de Biochimie (UMR7654 du CNRS), Department of Biology, Ecole Polytechnique, 91128 Palaiseau, France.
J Am Chem Soc. 2004 Apr 7;126(13):4167-80. doi: 10.1021/ja039788m.
Ionizable residues play important roles in protein structure and activity, and proton binding is a valuable reporter of electrostatic interactions in these systems. We use molecular dynamics free energy simulations (MDFE) to compute proton pKa shifts, relative to a model compound in solution, for three aspartate side chains in two proteins. Simulations with explicit solvent and with an implicit, dielectric continuum solvent are reported. The implicit solvent simulations use the generalized Born (GB) model, which provides an approximate, analytical solution to Poisson's equation. With explicit solvent, the direction of the pKa shifts is correct in all three cases with one force field (AMBER) and in two out of three cases with another (CHARMM). For two aspartates, the dielectric response to ionization is found to be linear, even though the separate protein and solvent responses can be nonlinear. For thioredoxin Asp26, nonlinearity arises from the presence of two substates that correspond to the two possible orientations of the protonated carboxylate. For this side chain, which is partly buried and has a large pKa upshift, very long simulations are needed to correctly sample several slow degrees of freedom that reorganize in response to the ionization. Thus, nearby Lys57 rotates to form a salt bridge and becomes buried, while three waters intercalate along the opposite edge of Asp26. Such strong and anisotropic reorganization is very difficult to predict with Poisson-Boltzmann methods that only consider electrostatic interactions and employ a single protein structure. In contrast, MDFE with a GB dielectric continuum solvent, used for the first time for pKa calculations, can describe protein reorganization accurately and gives encouraging agreement with experiment and with the explicit solvent simulations.
可电离残基在蛋白质结构和活性中发挥着重要作用，质子结合是这些系统中静电相互作用的重要报告分子。我们使用分子动力学自由能模拟（MDFE）来计算相对于溶液中模型化合物的质子pKa位移，该位移针对两种蛋白质中的三个天冬氨酸侧链。本文报告了使用显式溶剂和隐式介电连续介质溶剂的模拟结果。隐式溶剂模拟使用广义玻恩（GB）模型，该模型为泊松方程提供了近似的解析解。对于显式溶剂，在一种力场（AMBER）下，所有三种情况的pKa位移方向都是正确的；在另一种力场（CHARMM）下，三种情况中有两种是正确的。对于两个天冬氨酸，发现电离的介电响应是线性的，尽管单独的蛋白质和溶剂响应可能是非线性的。对于硫氧还蛋白的天冬氨酸26，非线性源于存在两种亚状态，它们对应于质子化羧酸盐的两种可能取向。对于这个部分埋藏且pKa大幅上移的侧链，需要非常长的模拟来正确采样几个响应电离而重新排列的慢自由度。因此，附近的赖氨酸57旋转形成盐桥并被埋藏，同时三个水分子沿着天冬氨酸26的相对边缘插入。这种强烈且各向异性的重新排列很难用仅考虑静电相互作用并采用单一蛋白质结构的泊松-玻尔兹曼方法来预测。相比之下，首次用于pKa计算的带有GB介电连续介质溶剂的MDFE能够准确描述蛋白质的重新排列，并与实验以及显式溶剂模拟结果取得了令人鼓舞的一致性。
