Investigation of bacterial adhesion pili via novel Brownian dynamics simulations

通过新颖的布朗动力学模拟研究细菌粘附菌毛

• 批准号: 7483423
• 负责人: Adam Wayne Van Wynsberghe
• 金额: $ 4.68万
• 依托单位: UNIVERSITY OF CALIFORNIA, SAN DIEGO
• 依托单位国家: 美国
• 财政年份: 2008
• 资助国家: 美国
• 起止时间: 2008-05-01 至 2011-04-30
• 项目状态: 已结题
• 来源: https://reporter.nih.gov/project-details/7483423
• 关键词: Adhesions; Algorithms; Bacteria; Bacterial Adhesion; Biological Process; Catalysis; Cells; Class; Computational Technique; Computer Simulation; Data; Decompression Sickness; Diffuse; Docking; Escherichia coli; Human; Infection; Investigation; Membrane; Methods; Modeling; Molecular; Molecular Conformation; Molecular Motors; Motion; Mutation; Neutrons; Pilum; Play; Pliability; Proteins; Public Health; Role; Signal Transduction; Standards of Weights and Measures; Structure; System; Taq Polymerase; Techniques; Tertiary Protein Structure; Testing; millisecond; nanosecond; novel; prevent; simulation

DESCRIPTION (provided by applicant): Intramolecular motions play an important role in a variety of biological processes including signal transduction, catalysis, and molecular motors. Unfortunately, these motions have proven difficult to study both experimentally and computationally. Standard computational techniques are limited to the nanosecond regime while the above motions occur in micro- to milliseconds. Alternatively, Brownian dynamics (BD) algorithms can reach the necessary timescales, but have traditionally been limited to rigid structures. Therefore, to investigate intramolecular motions from a computational perspective, novel techniques must be developed. In this proposal, we will develop and implement computational strategies to include intramolecular motions in BD simulations. Our approach involves: identifying protein domains, treating them as separate rigid bodies in a BD framework, and tethering them via an empirical energy function. The method, Tethered Brownian dynamics (TBD), will allow long timescale simulations that include intramolecular flexibility of multi-domain proteins. TBD will be initially tested against computational data such as normal mode analysis but then refined by utilizing neutron scattering spectra of Taq DNA polymerase. We will then apply these techniques to study the formation of class I adhesion pili in pyelonephritic E. coli. These structures are necessary and sufficient for adhesion, an important step towards infection. The techniques we will develop are necessary for investigating pili formation because it has been hypothesized that after the monomeric units diffuse through an usher protein in the bacterial outer membrane an internal hinge-bending motion is required to effectively dock the protein in its proper conformation. After validating our TBD algorithm for this system, we will test this docking hypothesis and attempt to identify the molecular mechanism for the structural effects of several mutations. Our simulations will describe an atomic scale model for pilus assembly that may enable the identification of pharmacologic targets for the inhibition of pilus formation and infection. PUBLIC HEALTH RELEVANCE In this study, computational models that allow the study of flexible proteins will be developed and used to investigate the formation of class I pili, structures that bacteria produce to enable adhesion to human host cells. By elucidating the molecular mechanism of the formation of these structures, we hope to inform strategies to disrupt pili assembly, thus preventing or disabling adhesion and infection.

描述（由申请人提供）：分子内运动在各种生物学过程中起着重要作用，包括信号转导，催化和分子电机。不幸的是，这些动作被证明很难在实验和计算上研究。标准计算技术仅限于纳秒制度，而上述动作发生在微秒至毫秒中。另外，布朗动力学（BD）算法可以达到必要的时间标准，但传统上仅限于刚性结构。因此，为了从计算角度研究分子内运动，必须开发新技术。在此提案中，我们将制定并实施计算策略，以在BD模拟中包括分子内运动。我们的方法涉及：识别蛋白质结构域，将其视为BD框架中的独立刚体，并通过经验能量函数束缚它们。该方法是束缚的布朗动力学（TBD），将允许长时间模拟，包括多域蛋白的分子内柔韧性。 TBD最初将针对计算数据（例如正常模式分析）进行测试，然后通过利用TAQ DNA聚合酶的中子散射光谱进行完善。然后，我们将应用这些技术研究pyelonephritic E. Coli中I类粘附的形成。这些结构是必要的，足以进行粘附，这是迈向感染的重要一步。我们将开发的技术对于研究pili形成是必要的，因为已经假设在单体单位通过细菌外膜中的usher蛋白扩散后，需要内部铰链弯曲运动以有效地对抗其适当构象中的蛋白质。在验证了该系统的TBD算法后，我们将测试该对接假设，并试图确定几种突变的结构效应的分子机制。我们的仿真将描述一个用于菌毛组装的原子量表模型，该模型可以鉴定出抑制菌毛形成和感染的药理学靶标。在这项研究中，将开发允许研究柔性蛋白质的计算模型，并用于研究I类PILI的形成，细菌产生的结构可以使人类宿主细胞粘附。通过阐明这些结构形成的分子机制，我们希望告知破坏pili组装的策略，从而防止或禁用粘附和感染。