Complete relaxation and conformational exchange matrix (CORCEMA) analysis of intermolecular saturation transfer effects in reversibly forming ligand-receptor complexes
Complete relaxation and conformational exchange matrix (CORCEMA) analysis of intermolecular saturation transfer effects in reversibly forming ligand-receptor complexes
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DOI：
10.1006/jmre.2001.2499
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发表时间：
2002-03-01
影响因子：
2.2
通讯作者：
Krishna, NR
中科院分区：
文献类型：
--
作者：
Jayalakshmi, V;Krishna, NR
分子间 NOE (INOE) 实验最近在生物分子系统中的应用包括 (i) 饱和转移差 NMR (STD-NMR) 方法和 (ii) 分子间交叉饱和 NMR (ICS-NMR) 实验。 STD-NMR 是一种很有前途的工具，可用于快速筛选大型化合物库，以识别与靶蛋白结合的生物活性配体。此外，它还可用于绘制生物活性配体与其靶蛋白的结合表位。在后一种应用中，STD-NMR 技术本质上类似于 ICS-NMR 实验，后者用于绘制复合物中蛋白质-蛋白质或蛋白质-核酸接触表面的图谱。在这项工作中，我们提出了一个完整的松弛和构象交换矩阵（CORCEMA）理论（H. N. B. Moseley 等人，J. Magn. Reson. B 108, 243-261 (1995)），适用于这两个密切相关的实验。正如我们之前的工作一样，我们表明，当弛豫率尺度上的交换速度很快时，可以使用广义平均弛豫率矩阵来制定简化的 CORCEMA 理论。其有效性范围是通过将其预测与对所有汇率都有效的确切 CORCEMA 理论的预测进行比较来确定的。使用一些理想的模型系统，我们分析了当受体蛋白上的某些质子的共振饱和时影响配体质子强度变化的因素。结果表明，分子间 NOE 实验中配体信号的强度变化很大程度上取决于：（1）饱和时间，（2）饱和受体质子相对于配体质子的位置，（3）配体-受体界面的构象，（4）分子种类的旋转相关时间，（5）可逆形成复合物的动力学，以及 (6)配体/受体比例。作为 STD-NMR 实验的典型应用示例，我们还模拟了与蛋白质结合的假设三糖的 STD 效应，INOE 的 CORCEMA 理论和相关算法可用于定量解释 STD-NMR 和 ICS-NMR 中配体的强度变化，前提是已知经历直接 RF 饱和的受体质子的身份。这里提出的形式可能有助于设计特定靶蛋白的生物活性配体，以及定量绘制复合物中分子之间的结合表位和界面。 (C) 2002 年爱思唯尔科学（美国）。
A couple of recent applications of intermolecular NOE (INOE) experiments as applied to biomolecular systems involve the (i) saturation transfer difference NMR (STD-NMR) method and (ii) the intermolecular cross-saturation NMR (ICS-NMR) experiment. STD-NMR is a promising tool for rapid screening of a large library of compounds to identify bioactive ligands binding to a target protein. Additionally, it is also useful in mapping the binding epitopes presented by a bioactive ligand to its target protein. In this latter application, the STD-NMR technique is essentially similar to the ICS-NMR experiment, which is used to map protein-protein or protein-nucleic acid contact surfaces in complexes. In this work, we present a complete relaxation and conformational exchange matrix (CORCEMA) theory (H. N. B. Moseley et al., J. Magn. Reson. B 108, 243-261 (1995)) applicable for these two closely related experiments. As in our previous work, we show that when exchange is fast on the relaxation rate scale, a simplified CORCEMA theory can be formulated using a generalized average relaxation rate matrix. Its range of validity is established by comparing its predictions with those of the exact CORCEMA theory which is valid for all exchange rates. Using some ideal model systems we have analyzed the factors that influence the ligand proton intensity changes when the resonances from some protons on the receptor protein are saturated. The results show that the intensity changes in the ligand signals in an intermolecular NOE experiment are very much dependent upon: (1) the saturation time, (2) the location of the saturated receptor protons with respect to the ligand protons, (3) the conformation of the ligand-receptor interface, (4) the rotational correlation times for the molecular species, (5) the kinetics of the reversibly forming complex, and (6) the ligand/receptor ratio. As an example of a typical application of the STD-NMR experiment we have also simulated the STD effects for a hypothetical trisaccharide bound to a protein, The CORCEMA theory for INOE and the associated algorithm are useful in a quantitative interpretation of the intensity changes in the ligand in both the STD-NMR and ICS-NMR, provided the identity of the receptor protons experiencing direct RF saturation is known. The formalism presented here is likely to be useful in the design of bioactive ligands to a specific target protein and in the quantitative mapping of binding epitopes and interfaces between molecules in complexes. (C) 2002 Elsevier Science (USA).