NMR studies of heterocyclization and epimerization in yersiniabactin synthesis

描述（由申请人提供）：非核糖体肽合成酶（NRPSs）是在细菌和真菌中产生丰富天然产物的酶装配线。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、杆菌肽）、抗肿瘤药物（博来霉素、埃泊霉素）和免疫抑制剂（雷帕霉素）。NRPSs使用多个域，组织在连续的模块中，以装配线的方式共价加载、修改和连接基板。这个卓越的组织有希望通过交换域或模块来重新编程NRPS装配线来生产新型药物。然而，大多数NRPS结构域的相互作用仍然是未知的，重要结构域的结构和机制是未知的，人工工程的NRPS通常是非生产性的。本研究旨在揭示NRPSs中杂环形成及其立体化学改变的结构基础，并揭示相关合成过程中的结构域通讯。我们将重点关注HMWP2，这是一种参与耶尔森菌abactin （Ybt）合成的NRPS， Ybt是一种在病原体中发现的毒力因子，如鼠疫耶尔森菌（鼠疫的病原体），小肠结肠炎耶尔森菌（食物病原体）和尿路致病性大肠杆菌（负责尿路感染）。我们的结果将有助于理解这些病原体在感染过程中所采用的分子逻辑。我们将主要使用核磁共振（NMR），因为分子相互作用的瞬态性质，以及多个平衡构象的存在。核磁共振将用于确定环化和外映异构结构域的结构，确定化学和蛋白质底物的结合位点，并在分子相互作用期间表征结构域内的动力学。在协同方法中，我们将把诱变和生化分析与核磁共振实验结合起来，以提供反应机制的原子水平描述。多结构域配合物的大小达到70 kDa，这对核磁共振研究来说是一个挑战，核磁共振研究通常限制在20 kDa。在过去，我们设计了解决50 kDa蛋白质结构的方法，并从800kDa复合物中获得有用的数据。HMWP2将为进一步开发大型动态蛋白质的新NMR方法以及了解蛋白质相互作用过程中的构象重排提供一个模型系统。同时，我们的研究将使我们能够推动更大蛋白质的核磁共振研究的前沿，帮助理解生物系统中蛋白质动力学的功能，揭示关键结构域的结构，并为NRPS装配线的有效重编程提供基础，以生产新的药物。

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.