Theory of Protein-Protein Association

描述(由申请人提供)：蛋白质-蛋白质结合的速度在许多基本的生物过程中起着关键作用，从酶的催化/抑制到细胞因子对免疫反应的调节。我们的长期目标是在给定蛋白质复合体结构的情况下可靠地预测缔合率，并阐明蛋白质缔合的机制。我们已经充分发展了瞬变-复合体理论，并在蛋白质-蛋白质结合的综合研究中展示了它的预测能力。瞬变络合物理论提供了独特的机会来发现蛋白质之间结合率的广泛差异的分子基础，并设计具有所需结合特性的蛋白质，我们在这个项目中利用了这一点。具体目标1是开发一种新的 瞬变-复变理论的实现。新的发展将考虑疏水相互作用和构象熵的贡献，并允许在瞬时复合体中对蛋白质构象采样进行建模。在具体目标2中，瞬变-复合体理论将被用来系统地设计突变，将慢结合的复合体转变为快结合的复合体，并定量地合理地解释相关蛋白质之间结合率的巨大差异。测试系统将包括Wiskott-Aldrich综合征蛋白与两个同源Rho GTP酶的复合体。一些设计的突变体将通过合作进行实验测试。在具体目标3中，我们将把瞬变络合物理论应用于蛋白质-RNA复合体。以核糖核酸酶抑制剂和RNA结合的不同部位为靶点，核糖核酸酶A的变体无效地结合前者，但后者有效地结合，将被设计为潜在的抗癌治疗药物。总之，这些应用将展示通过操纵蛋白质相互作用来控制蛋白质功能的能力，并对蛋白质结合率的生物学作用产生有价值的见解。公共卫生相关性：拟议的研究对公共卫生既有间接的好处，也有有形的好处。它将促进对广泛生物学过程的基本理解，例如Wiskott-Aldrich综合征蛋白对肌动蛋白聚合的刺激，以及tRNA在同源和非同源氨基酰tRNA合成酶之间的区分(这一步骤对于遗传密码翻译的保真度至关重要)。这项研究还可能直接有益于哮喘和癌症治疗药物的设计。

DESCRIPTION (provided by applicant): The rate of protein-protein association plays critical roles in many fundamental biological processes ranging from enzyme catalysis/inhibition to regulation of immune response by cytokines. Our long-term objectives are to reliably predict association rates given just the structures of protein complexes and elucidate the mechanisms of protein association. We have fully developed a transient-complex theory and demonstrated its predictive power in a comprehensive study of protein-protein association. The transient-complex theory presents unique opportunities to uncover molecular bases for wide variations in association rates among proteins and design proteins with desired binding properties, which we exploit in this project. Specific Aim 1 is to develop a new implementation of the transient-complex theory. The new developments will account for contributions of hydrophobic interactions and configurational entropy and allow for modeling of protein conformational sampling in the transient complex. In Specific Aim 2, the transient-complex theory will be used to systematically design mutations that will turn slow-binding complexes into fast-binding ones and to quantitatively rationalize large differences in association rate between related proteins. Test systems will include complexes of the Wiskott-Aldrich Syndrome protein with two homologous Rho GTPases. Some of the designed mutants will be tested experimentally through collaboration. In Specific Aim 3 we will apply the transient-complex theory to protein-RNA complexes. Targeting distinct sites for binding ribonuclease inhibitor and RNA, variants of ribonuclease A that bind the former ineffectively but the latter efficiently will be designed as potential anti-cancer therapeutics. Together, these applications will demonstrate the ability to control protein functions by manipulating protein interactions and yield valuable insight on the biological roles of protein association rates. PUBLIC HEALTH RELEVANCE: The proposed research will have both indirect and tangible benefits to public health. It will advance fundamental understanding of a broad range of biological processes, such as the stimulation of actin polymerization by the Wiskott-Aldrich Syndrome protein and the discrimination of Trna between cognate and non-cognate aminoacyl-tRNA synthetases (a step critical for the fidelity of the translation of the genetic code). The research may also benefit directly the design of asthma and cancer therapeutics.