Department of Chemistry, Texas Materials Institute, and Interdisciplinary Life Sciences Program, The University of Texas at Austin, 105 E 24th St. STOP A5300, Austin, Texas 78712, United States.
Department of Biomedical Engineering, The University of Texas at Austin, Austin, Texas 78712, United States.
J Phys Chem B. 2023 Jun 29;127(25):5609-5619. doi: 10.1021/acs.jpcb.3c02060. Epub 2023 Jun 20.
Precisely quantifying the magnitude and direction of electric fields in proteins has long been an outstanding challenge in understanding biological functions. Nitrile vibrational Stark effect probes have been shown to be minimally disruptive to the protein structure and can be better direct reporters of local electrostatic field in the native state of a protein than other measures such as p shifts of titratable residues. However, interpretations of the connection between measured vibrational energy and electric field rely on the accurate molecular understanding of interactions of the nitrile group and its environment, particularly from hydrogen bonding. In this work, we compared the extent of hydrogen bonding calculated in two common force fields, the fixed charge force field Amber03 and polarizable force field AMOEBA, at 10 locations of cyanocysteine (CNC) in staphylococcal nuclease (SNase) against the experimental nitrile absorption frequency in terms of full width at half-maximum (FWHM) and frequency temperature line slope (FTLS). We observed that the number of hydrogen bonds correlated well in AMOEBA trajectories with respect to both the FWHM ( = 0.88) and the FTLS ( = -0.85), whereas the correlation of Amber03 trajectories was less reliable because the Amber03 force field predicted more hydrogen bonds in some mutants. Moreover, we demonstrated that contributions from the interactions between CNC and nearby water molecules were significant in AMOEBA trajectories but were not predicted by Amber03. We conclude that although the nitrile absorption peak shape could be qualitatively predicted by the fixed charge Amber03 force field, the detailed electrostatic environment measured by the nitrile probe in terms of the extent of hydrogen bonding could only be accurately observed in the AMOEBA trajectories, where the permanent dipole, quadrupole, and dipole-induced-dipole polarizable interactions were all taken into account. The significance of this finding to the goal of accurately predicting electric fields in complex biomolecular environments is discussed.
精确量化蛋白质中电场的大小和方向一直是理解生物功能的一个突出挑战。腈基振动斯塔克效应探针对蛋白质结构的干扰最小，并且可以比其他测量方法（如可滴定残基的 p 位移）更好地直接报告蛋白质天然状态下的局部电场。然而，对测量的振动能量与电场之间的关系的解释依赖于对腈基基团及其环境相互作用的准确分子理解，特别是氢键。在这项工作中，我们比较了在固定电荷力场 Amber03 和极化力场 AMOEBA 中的 10 个位置计算的氰基半胱氨酸（CNC）在金黄色葡萄球菌核酸酶（SNase）中的氢键程度，以实验腈基吸收频率的半峰全宽（FWHM）和频率温度线斜率（FTLS）为指标。我们观察到，在 AMOEBA 轨迹中，氢键的数量与 FWHM（ = 0.88）和 FTLS（ = -0.85）都很好地相关，而 Amber03 轨迹的相关性不太可靠，因为 Amber03 力场在某些突变体中预测了更多的氢键。此外，我们证明了 CNC 与附近水分子之间的相互作用的贡献在 AMOEBA 轨迹中很重要，但 Amber03 力场没有预测到。我们的结论是，尽管固定电荷 Amber03 力场可以定性地预测腈基吸收峰的形状，但腈基探针测量的氢键程度的详细静电环境只能在 AMOEBA 轨迹中准确观察到，其中考虑了永久偶极矩、四极矩和偶极诱导偶极极化相互作用。讨论了这一发现对准确预测复杂生物分子环境中电场的目标的意义。
