Theory of Protein-Protein Association

描述（由申请人提供）：蛋白质-蛋白质结合的速率在许多基本生物过程中起关键作用，从酶催化/抑制到细胞因子调节免疫应答。我们的长期目标是可靠地预测关联率，仅给出蛋白质复合物的结构，并阐明蛋白质关联的机制。我们已经完全开发了一个瞬态复杂的理论，并证明了其预测能力，在蛋白质-蛋白质协会的全面研究。瞬时复合物理论提供了独特的机会，发现蛋白质之间的关联率的广泛变化的分子基础和设计具有所需结合特性的蛋白质，我们在这个项目中利用。具体目标1是开发新的 瞬态复合理论的实现。新的发展将占疏水相互作用和构型熵的贡献，并允许在瞬态复杂的蛋白质构象采样建模。在具体目标2中，瞬时复合物理论将用于系统地设计突变，将缓慢结合的复合物转变为快速结合的复合物，并定量合理化相关蛋白质之间缔合速率的巨大差异。试验系统将包括Wiskott-Aldrich综合征蛋白与两种同源Rho GTP酶的复合物。一些设计的突变体将通过合作进行实验测试。在第三章中，我们将把瞬时复合物理论应用于蛋白质-RNA复合物。靶向用于结合核糖核酸酶抑制剂和RNA的不同位点，核糖核酸酶A的不能有效地结合前者但有效地结合后者的变体将被设计为潜在的抗癌治疗剂。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：拟议的研究将对公共卫生产生间接和有形的好处。它将促进对广泛的生物过程的基本理解，例如Wiskott-Aldrich综合征蛋白刺激肌动蛋白聚合以及同源和非同源氨酰-tRNA合成酶之间的Trna的区分（遗传密码翻译保真度的关键步骤）。这项研究也可能直接有益于哮喘和癌症治疗的设计。

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.