Hybrid Methods for Dynamic Structure Analysis of Proteins from Pathogenic Microorganisms

项目摘要 本研究计划将探讨一般假设，了解构象多样性 蛋白质的研究将为它们的生物学提供新的见解，并使医学研究成为可能。它是针对两个 系统分类：整合膜蛋白（IMP）和病毒-宿主相互作用。IMP发挥着关键作用， 看门人、受体、转运蛋白、体内平衡调节剂和药物靶点。这些功能是通过 IMP在膜环境中的构象可塑性。IMP的制备具有挑战性，并且 在适当的膜模拟环境中重构甚至更具挑战性。成本效益 浓缩体积中同位素富集的技术，NMR与 进化协变（EC），接触预测的新方法，以及创新的建模方法， 蛋白质结构预测社区，将被应用于结构功能研究的IMP。这些IMP， 选自重要的人类病原体，包括E. coli、克雷伯氏菌（K.肺炎，和铜绿假单胞菌，是潜在的 抗生素发现的目标。EC还将与NMR数据相结合，以确定多种化合物的结构。 蛋白质的“自然状态”。我们计划的第二部分是针对病毒宿主生物分子 复合物和抗病毒药物发现。我们将利用创新的顺磁NMR方法， 小角X射线散射（SAXS）、电子-电子双共振光谱（DEER）和Förster 共振能量转移（FRET），严格定义动态域间结构分布赋予 通过鼠莫洛尼白血病病毒（MLV）整合酶（IN）的部分有序接头。这些数据将 在最大占用概率（MaxOcc）的上下文中解释，并用于探测此 G-逆转录病毒基因整合机制的灵活性。结构域间接头还起到提供 约束伴侣滥交所需的灵活性。我们还将确定结构域间连接序列 流感病毒非结构蛋白1（NS 1）的表达赋予了适当的可塑性，以确定其特异性和亲和力， 宿主蛋白和RNA。这种结构和功能混杂是NS 1的机制的基础， 抑制对流感感染的细胞先天免疫应答，并对其进行严格表征。 动态结构基础将为减毒活病毒疫苗的研制提供基础信息。 我们还将利用我们的平台研究通过结合SARS-CoV 2病毒的主要蛋白酶来抑制其的药物 （Mpro）。我们已经确定了三种药物，这些药物已被批准用于人类，最初旨在抑制 丙型肝炎病毒的NSP 3/4A蛋白酶，在病毒复制试验中也能在低浓度下抑制SARS-CoV 2， 微摩尔浓度。我们的计算对接研究还确定了其他几个FDA- 可能抑制Mpro的批准药物。酶动力学、生物物理化学和X射线晶体学研究 将用于表征这些蛋白酶抑制剂药物和Mpro之间形成的复合物， 开发其作为COVID-19治疗剂或作为新治疗开发的先导化合物的潜力。

PROJECT SUMMARY This research program will investigate the general hypothesis that understanding the conformational diversity of proteins will provide new insights into their biology, and enable medical research. It is directed to two classes of systems: Integral Membrane Proteins (IMPs) and viral-host interactions. IMPs play critical roles as gate keepers, receptors, transporters, homeostasis regulators, and drug targets. These functions are mediated by the conformational plasticity of the IMP in the membrane environment. IMPs are challenging to prepare, and even more challenging to reconstitute in appropriate membrane mimicking environments. Cost-effective technologies for isotope-enrichment in condensed volumes, hybrid approaches combining NMR with evolutionary co-variation (ECs), novel methods of contact prediction, and innovative modeling methods from the protein structure prediction community, will be applied to structure-function studies of IMPs. These IMPs, chosen from important human pathogens, including E. coli, K. pneumoniae, and P. aeruginosa, are potential targets for antibiotic discovery. ECs will also be combined with NMR data to determine structures of multiple “native states” of proteins. The second component of our program is directed to viral – host biomolecular complexes, and antiviral drug discovery. We will utilize innovative paramagnetic NMR methods, together with small angle X-ray scattering (SAXS), electron-electron double resonance spectroscopy (DEER), and Förster resonance energy transfer (FRET), to rigorously define dynamic interdomain structural distributions conferred by the partially-ordered linkers of the murine Moloney Leukemia Virus (MLV) integrase (IN). These data will be interpreted in the context of maximum occupancy probabilities (MaxOcc), and used to probe the role(s) of this flexibility in the gene integration mechanisms of g-retroviruses. Interdomain linkers also function to provide flexibility needed for binding partner promiscuity. We will also determine how the interdomain linker sequences of influenza Non-Structural Protein 1 (NS1) confer appropriate plasticity to define its specificity and affinity for host proteins and RNAs. This structural and functional promiscuity underlies NS1’s mechanisms for suppressing the cellular innate immune response to influenza infection, and rigorous characterization of its dynamic structural basis will provide fundamental information for live-attenuated virus vaccine development. We will also apply our platform to investigate drugs that inhibit SARS-CoV2 virus by binding its main protease (Mpro). We have identified three drugs, already approved for use in humans, originally designed to inhibit the NSP3/4A protease of hepatitis C virus, that also inhibit SARS-CoV2 in viral replication assays at low micromolar concentrations. Our computational docking studies have also identified several other FDA- approved drugs that may inhibit Mpro. Enzyme kinetic, biophysical chemistry, and X-ray crystallography studies will be used to characterize complexes formed between these protease inhibitor drugs and Mpro, and to develop their potential as COVID-19 therapeutics, or as lead compounds for new therapeutic development.