Laboratory of Chemical Physics, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, Maryland 20892-0520, United States.
J Am Chem Soc. 2020 May 6;142(18):8281-8290. doi: 10.1021/jacs.0c00747. Epub 2020 Apr 24.
Protein-small cosolute molecule interactions are ubiquitous and known to modulate the solubility, stability, and function of many proteins. Characterization of such transient weak interactions at atomic resolution remains challenging. In this work, we develop a simple and practical NMR method for extracting both energetic and dynamic information on protein-cosolute interactions from solvent paramagnetic relaxation enhancement (sPRE) measurements. Our procedure is based on an approximate (non-Lorentzian) spectral density that behaves exactly at both high and low frequencies. This spectral density contains two parameters, one global related to the translational diffusion coefficient of the paramagnetic cosolute, and the other residue specific. These parameters can be readily determined from sPRE data, and then used to calculate analytically a concentration normalized equilibrium average of the interspin distance, ⟨⟩, and an effective correlation time, τ, that provide measures of the energetics and dynamics of the interaction at atomic resolution. We compare our approach with existing ones, and demonstrate the utility of our method using experimental H longitudinal and transverse sPRE data recorded on the protein ubiquitin in the presence of two different nitroxide radical cosolutes, at multiple static magnetic fields. The approach for analyzing sPRE data outlined here provides a powerful tool for deepening our understanding of extremely weak protein-cosolute interactions.
蛋白质-小分子协同分子相互作用普遍存在,已知可调节许多蛋白质的溶解度、稳定性和功能。在原子分辨率下对这种瞬时弱相互作用进行特征描述仍然具有挑战性。在这项工作中,我们开发了一种简单实用的 NMR 方法,可从溶剂顺磁弛豫增强 (sPRE) 测量中提取蛋白质-协同物相互作用的能量和动态信息。我们的程序基于一个近似(非洛伦兹)的谱密度,在高频和低频下都能准确表现。该谱密度包含两个参数,一个与顺磁协同物的平移扩散系数相关的全局参数,另一个与残基特异性相关。这些参数可以从 sPRE 数据中轻松确定,然后用于分析计算自旋间距离的归一化平衡平均值 ⟨⟩ 和有效相关时间 τ,它们以原子分辨率提供相互作用的能量和动力学的度量。我们将我们的方法与现有方法进行了比较,并使用在不同静态磁场下存在两种不同的氮氧自由基协同物的蛋白质泛素的 H 纵向和横向 sPRE 实验数据演示了我们方法的实用性。这里概述的分析 sPRE 数据的方法为深入了解极其微弱的蛋白质-协同物相互作用提供了有力工具。