NMR studies of heterocyclization and epimerization in yersiniabactin synthesis

描述(申请人提供)：非核糖体多肽合成酶(NRPS)是一种酶流水线，能在细菌和真菌中产生丰富的天然产物。这些产品赋予病原体毒力，通常是有价值的治疗药物，包括抗生素(青霉素、杆菌素)、抗肿瘤药物(博莱霉素、埃博西隆)和免疫抑制剂(雷帕霉素)。NRPS使用组织在连续模块中的多个域，以装配线方式共价加载、修改和连接衬底。这个非凡的组织拥有通过交换结构域或模块来重新编程NRPS装配线来生产新型药物的承诺。然而，大多数NRPS结构域的相互作用仍然没有表征，重要结构域的结构和机制尚不清楚，人工工程的NRPS通常是无效的。这一建议旨在揭示NRPS中杂环形成及其立体化学变化的结构基础，并揭示相关合成过程中的结构域通讯。我们将重点关注HMWP2，一种参与合成耶尔森巴菌素(Ybt)的NRPS，Ybt是一种在病原体中发现的毒力因子，如腺鼠疫的病原体鼠疫耶尔森氏菌，一种食品病原体小肠结肠炎耶尔森氏菌，以及导致尿路感染的泌尿系致病性大肠杆菌。我们的结果将有助于理解这些病原体在感染过程中使用的分子逻辑。我们将主要使用核磁共振(核磁共振)，因为分子相互作用的瞬变性质，以及平衡时存在多个构象。核磁共振将用于确定环化和异构化结构域的结构，确定化学和蛋白质底物的结合位置，并表征分子相互作用过程中结构域内的动力学。在一种协同的方法中，我们将结合诱变和生化分析与核磁共振实验，提供反应机理的原子水平描述。多结构域复合体的大小达到70 kDa，这对通常限制在20 kDa的核磁共振研究是一个挑战。在过去，我们设计了解决50 kDa蛋白质结构的方法，并从800 kDa的复合体中获得了有用的数据。HMWP2将提供一个模型系统，进一步开发用于大型动态蛋白质的新的核磁共振方法，并从总体上理解蛋白质相互作用过程中的构象重排。我们的研究将同时使我们能够推动更大蛋白质的核磁共振研究的前沿，帮助了解蛋白质动力学在生物系统中的功能，揭示关键结构域的结构，并为有效地重新编程NRPS装配线以生产新的药物提供基础。

DESCRIPTION (provided by applicant): Non-ribosomal peptide synthetases (NRPSs) are enzymatic assembly lines that produce a wealth of natural products in bacteria and fungi. These products confer virulence to pathogens and often are valuable therapeutics, including antibiotics (penicillin, bacitracin), antitumor agents (bleomycin, epothilone), and immunosuppressants (rapamycin). NRPSs use multiple domains, organized in contiguous modules, to covalently load, modify, and join substrates in an assembly line fashion. This remarkable organization holds the promise of producing novel pharmaceuticals by swapping domains or modules to reprogram the NRPS assembly line. However, most NRPS domain interactions remain uncharacterized, the structure and mechanism of important domains are unknown, and artificially engineered NRPSs are generally unproductive. This proposal aims to reveal the structural basis for heterocycle formation and alteration of their stereochemistry in NRPSs, and unravel domain communication during related synthesis. We will focus on HMWP2, an NRPS that participates in the synthesis of yersiniabactin (Ybt), a virulence factor found in pathogens such as Yersinia pestis, the causative agent of the bubonic plague, Y. enterocolitica, a food pathogen, and uropathogenic E. coli, responsible for urinary tract infections. Our results will contribute to understanding the molecular logic employed by these pathogens during infections. We will primarily use Nuclear Magnetic Resonance (NMR) because of the transient nature of molecular interactions, as well as the existence of multiple conformers in equilibrium. NMR will be used to determine the structures of cyclization and epimerization domains, identify binding sites of chemical and protein substrates, and characterize dynamics within domains during molecular interactions. In a synergistic approach, we will combine mutagenesis and biochemical assays with NMR experiments to provide an atomic level description of reaction mechanisms. The size of the multi-domain complexes reaches 70 kDa and is a challenge for NMR studies, which are typically limited to 20 kDa. In the past we designed methods to solve structures of 50 kDa proteins and obtain useful data from 800kDa complexes. HMWP2 will provide a model system to further develop new NMR methods for large dynamic proteins and to understand conformational rearrangements during protein interactions in general. Our research will simultaneously enable us to push the frontier in NMR studies of larger proteins, help understand the function of protein dynamics in biological systems, reveal the structure of critical domains, and provide a basis for efficient reprogramming of NRPS assembly lines to produce new pharmaceuticals.