Characterization of rare conformational states of proteins by combination of high-pressure X-raycrystallography with high-pressure NMR spectroscopy. Application to the small GproteinRas, its oncogenic mutants and its drug complexes.

通过高压 X 射线晶体学与高压核磁共振波谱相结合来表征蛋白质的稀有构象状态。

• 批准号: 390275479
• 负责人: Professor Dr. Hans Robert Kalbitzer
• 金额: --
• 依托单位: Lehrstuhl für Biophysik
• 依托单位国家: 德国
• 项目类别: Research Grants
• 财政年份: 2017
• 资助国家: 德国
• 起止时间: 2016-12-31 至 2020-12-31
• 项目状态: 已结题
• 来源: https://gepris.dfg.de/gepris/projekt/390275479?language=en
• 关键词: Characterization; rare; conformational; states; proteins

High pressure NMR spectroscopy (HPNMR) represents a powerful, still developing method to detect and characterize rare 'excited' conformational states. These states play an essential role in function and folding of proteins. HPNMR provides their thermodynamic parameters but gives structural information with limited resolution only. High pressure macromolecular x-ray crystallography (HPMX) is a complementary new method in protein science that basically can provide highly resolved spatial structures at high pressures. As component of an important and well-characterized signal transduction system we will concentrate on the small G-Protein Ras (rat sarcoma) protein (Ras mutations are found mutated in more than 30 % of all human cancers). It serves as a well-characterized model for method development in the proposed project, but also novel thermodynamic and structural insights are from high medical importance since they may help with the development of allosteric Ras inhibitors. By HPNMR of Ras in complex with the GTP analog GppNHp four different states 1(0), 1(T), 2(T), and 3(T) could be thermodynamically characterized that coexist at ambient pressure. Small compounds that preferentially bind to state 1(T) can allosterically inhibit the effector interaction and thus in principle can suppress the proliferative effect of oncogenic Ras mutants. The main goals of this project are (1) a thorough quantitative analysis of the rare conformational states of H- and K-Ras and their oncogenic mutants in complex with GDP and GppNHp by HPNMR supported by alternative NMR methods such as CEST and relaxation dispersion measurements, (2) to prove that HPMX can efficiently trap high-energy conformers of proteins identified in solution by high-pressure NMR spectroscopy that were identified in solution by HPNMR, (3) to correlate the observed pressure response of NMR parameters with structural changes detected by HPMX, and (4) to show that in principle the obtained high-pressure crystallographic structures can be used to design specific allosteric inhibitors binding to rare states. For showing if the thermodynamically similar state sin crystal and solution are also structurally similar, population-weighted NOESY spectra are back calculated from the X-ray structures and are compared with the experimental solution state NOESY spectra at different pressures in detail. As preliminary experiments show high pressure soaking with small state specific compounds may represent a novel method to access rare conformational states by crystallography. The dynamics under pressure of the different states will be studied by 2D transient P-jump experiments on isotope enriched Ras protein with the high-pressure jump system developed by us. The study will be complemented by relaxation dispersion and chemical exchange saturation transfer (CEST) experiments at different pressures.

高压核磁共振光谱（HPNMR）是一种强大的，仍在发展中的方法来检测和表征罕见的“激发”构象状态。这些状态在蛋白质的功能和折叠中起着至关重要的作用。HPNMR提供了它们的热力学参数，但仅以有限的分辨率给出结构信息。高压大分子X射线晶体学（HPMX）是蛋白质科学中的一种补充性新方法，基本上可以在高压下提供高分辨率的空间结构。作为一个重要的和充分表征的信号转导系统的组成部分，我们将集中在小G蛋白Ras（大鼠肉瘤）蛋白（Ras突变在超过30%的人类癌症中发现突变）。它是拟议项目中方法开发的一个充分表征的模型，而且新的热力学和结构见解具有高度的医学重要性，因为它们可能有助于开发变构Ras抑制剂。通过Ras与GTP类似物GppNHp复合的HPNMR，可以化学表征在环境压力下共存的四种不同状态1（0）、1（T）、2（T）和3（T）。优先结合状态1（T）的小化合物可以变构地抑制效应物相互作用，因此原则上可以抑制致癌Ras突变体的增殖作用。该项目的主要目标是（1）通过HPNMR对H-和K-Ras及其致癌突变体与GDP和GppNHp复合物的罕见构象状态进行彻底的定量分析，并辅之以其他NMR方法，如CEST和弛豫色散测量，（2）证明HPMX可以有效地捕获在溶液中通过高分子识别的蛋白质的高能构象异构体。通过在溶液中通过HPNMR鉴定的高压NMR光谱，（3）将观察到的NMR参数的压力响应与通过HPMX检测到的结构变化相关联，以及（4）表明原则上获得的高压晶体学结构可用于设计结合稀有状态的特定变构抑制剂。为了说明晶体和溶液的结构是否相似，从X射线结构反算了粒子数加权NOESY谱，并与不同压力下溶液态的实验NOESY谱进行了详细的比较。初步实验表明，高压浸泡与小状态特定的化合物可能代表一种新的方法，以获得罕见的构象状态的晶体学。利用自行研制的高压跳跃系统，对同位素富集的Ras蛋白进行二维瞬态P-跳跃实验，研究不同状态下的动力学行为。这项研究将补充弛豫分散和化学交换饱和转移（CEST）实验在不同的压力。