Department of Chemistry, University of Pittsburgh, PA, 15260, USA.
Department of Chemistry, University of Washington, WA, 98195, USA.
Phys Chem Chem Phys. 2024 Feb 22;26(8):6806-6816. doi: 10.1039/d3cp05951k.
The bifunctional spin label double-histidine copper-(II) capped with nitrilotriacetate [dHis-Cu(II)-NTA], used in conjunction with electron paramagnetic resonance (EPR) methods can provide high-resolution distance data for investigating protein structure and backbone conformational diversity. Quantitative utilization of this data is limited due to a lack of rapid and accurate dHis-Cu(II)-NTA modeling methods that can be used to translate experimental data into modeling restraints. Here, we develop two dHis-Cu(II)-NTA rotamer libraries using a set of recently published molecular dynamics simulations and a semi-empirical meta-dynamics-based conformational ensemble sampling tool for use with the recently developed chiLife bifunctional spin label modeling method. The accuracy of both the libraries and the modeling method are tested by comparing model predictions to experimentally determined distance distributions. We show that this method is accurate with absolute deviation between the predicted and experimental modes between 0.0-1.2 Å with an average of 0.6 Å over the test data used. In doing so, we also validate the generality of the chiLife bifunctional label modeling method. Taken together, the increased structural resolution and modeling accuracy of dHis-Cu(II)-NTA over other spin labels promise improvements in the accuracy and resolution of protein models by EPR.
双功能自旋标记双组氨酸铜（II）与氮川三乙酸（NTA）配位[ dHis-Cu（II）-NTA]，与电子顺磁共振（EPR）方法结合使用，可以提供高分辨率的蛋白质结构和骨架构象多样性的距离数据。由于缺乏快速准确的 dHis-Cu（II）-NTA 建模方法，无法将实验数据转换为建模约束，因此限制了对这些数据的定量利用。在这里，我们使用一组最近发表的分子动力学模拟和一种基于半经验元动力学的构象集合采样工具，开发了两种 dHis-Cu（II）-NTA 构象文库，用于最近开发的 chiLife 双功能自旋标记建模方法。通过将模型预测与实验确定的距离分布进行比较，测试了文库和建模方法的准确性。结果表明，该方法的预测与实验模式之间的绝对偏差在 0.0-1.2 Å 之间，平均偏差为 0.6 Å，在使用的测试数据上。这样，我们还验证了 chiLife 双功能标签建模方法的通用性。综上所述，dHis-Cu（II）-NTA 比其他自旋标记具有更高的结构分辨率和建模精度，有望通过 EPR 提高蛋白质模型的准确性和分辨率。
