Deciphering the relationship between structure, dynamics and function in helical bundle proteins

项目总结/摘要 该提案结合了病毒离子通道和从头蛋白质设计的工作。我们在M2上的工作 来自甲型流感病毒的质子通道集中在抑制和质子运动的机制， 频道。M2也是金刚烷胺类流感药物的靶点，并且大多数甲型流感病毒分离株 病毒对金刚烷胺有抗药性晶体学，计算和2D将被用来询问 机制，并有助于设计抑制金刚烷胺耐药病毒株中M2的药物。同时， 我们将扩大我们的研究，以研究传导和抑制E蛋白的机制， 冠状病毒，其结构和功能与M2很大程度上相似。 从头蛋白质设计提供了一种方法来测试和完善我们对蛋白质结构和 功能我们正在开发计算方法来设计结合小分子的蛋白质， 药物和金属卟啉。我们也在设计膜蛋白来阐明 它们折叠并发挥作用。为了探索高选择性质子传导蛋白的机制，我们 设计质子选择性通道，测试水分子网络（水线）可以 通过蛋白质中质子传导途径的非极性延伸动态和瞬时形成。的 水线将允许质子传导，但不允许大的水合碱金属离子如K+或Na+传导。我们 也从事蛋白质的设计，结合和运输营养物质，如氨基酸跨越 膜，并设计屏幕来测试它们在体内。

Project Summary/Abstract This proposal combines work on viral ion channels and de novo protein design. Our work on the M2 proton channel from influenza A virus focuses on the mechanism of inhibition and proton movement through the channel. M2 is also the target of the amantadine class of influenza drugs, and most isolates of influenza A virus are now amantadine-resistant. Crystallography, computation and 2DIR will be used to interrogate the mechanism and aid in design of drugs that inhibit M2 in amantadine-resistant strains of the virus. In parallel, we will expand our studies to examine the mechanism of conduction and inhibition of the E-proteins from coronaviruses, which have structures and functions largely similar to M2. De novo protein design provides a means to test and refine our understanding of protein structure and function. We are developing computational methods to design proteins that bind small molecules such as drugs and metalloporphyrins. We are also designing membrane proteins to elucidate the principles by which they fold and function. To probe the mechanisms of highly selective proton conduction proteins, we are designing proton-selective channels that test a hypothesis that networks of water molecules (water wires) can form dynamically and transiently through apolar stretches of the proton conduction pathway in proteins. The water wires would allow conduction of protons but not large hydrated alkali metal ions such as K+ or Na+. We also are engaged in design of proteins that bind to and transport nutrients such as amino acids across membranes, and devising screens to test them in vivo.