First Jeremy T, Novelli Elisa T, Webb Lauren J
Department of Chemistry, Texas Materials Institute, and Institute for Cell and Molecular Biology The University of Texas at Austin 105 East 24th Street STOP A5300, Austin, Texas 78712-1224, United States.
J Phys Chem B. 2020 Apr 23;124(16):3387-3399. doi: 10.1021/acs.jpcb.0c00747. Epub 2020 Apr 10.
Electric fields are fundamentally important to biological phenomena, but are difficult to measure experimentally or predict computationally. Changes in p of titratable residues have long been used to report on local electrostatic fields in proteins. Alternatively, nitrile vibrational probes are potentially less disruptive and more direct reporters of local electrostatic field, but quantitative interpretation is clouded by the ability of the nitrile to accept a hydrogen bond. To this end, we incorporated nitrile probes into 10 locations of staphylococcal nuclease (SNase) where p shifts had already been determined. We characterized the local environment of each nitrile probe experimentally, through temperature-dependent spectroscopy, and computationally, through molecular dynamics simulations, and show that hydrogen bonding interactions dominate the spectral line shapes. We demonstrate that the information provided by the line shape of the nitrile spectra, compared to scalar values of p shift or nitrile frequency shift, better describes local environments in proteins in a manner that will be useful for future computational efforts to predict electrostatics in complex biological systems.
电场对生物现象至关重要，但难以通过实验测量或通过计算预测。可滴定残基的p值变化长期以来一直用于报告蛋白质中的局部静电场。另外，腈振动探针可能干扰较小，并且是局部静电场更直接的报告物，但由于腈接受氢键的能力，定量解释变得模糊不清。为此，我们将腈探针整合到葡萄球菌核酸酶（SNase）的10个位置，这些位置的p值变化已经确定。我们通过温度相关光谱实验表征了每个腈探针的局部环境，并通过分子动力学模拟进行了计算，结果表明氢键相互作用主导了光谱线形。我们证明，与p值变化或腈频移的标量值相比，腈光谱线形提供的信息能以一种对未来预测复杂生物系统静电学的计算工作有用的方式，更好地描述蛋白质中的局部环境。
