Deep Topological Sampling of Protein Structures

蛋白质结构的深度拓扑采样

• 批准号: 9304913
• 负责人: Bruce R. Donald
• 金额: $ 29.55万
• 依托单位: DUKE UNIVERSITY
• 依托单位国家: 美国
• 财政年份: 2017
• 资助国家: 美国
• 起止时间: 2017-09-18 至 2021-07-31
• 项目状态: 已结题
• 来源: https://reporter.nih.gov/project-details/9304913
• 关键词: Adopted; Algorithmic Software; Algorithms; Binding; Biological; Capsid Proteins; Cell physiology; Complement 3a; Complex; Computer software; Computing Methodologies; Crystallization; Data; Diacylglycerol Kinase; Dimerization; Drug Design; Environment; Enzymes; Epitopes; Flavivirus; HIV; HIV-1; Homo; Ice; Immune response; Integral Membrane Protein; Laboratories; Lead; Measurement; Membrane; Methodology; Methods; Molecular Conformation; Nuclear Magnetic Resonance; Pathogenicity; Pharmaceutical Preparations; Prevalence; Problem Solving; Proteins; Protocols documentation; Publishing; Resistance; Resolution; Sampling; Specificity; Structural Biologist; Structure; System; Techniques; Testing; Time; Transmembrane Domain; Validation; Viral; Zika Virus; base; design; dimer; env Gene Products; enzyme structure; experimental study; global health; glycoprotein 41; immunogenic; immunogenicity; insight; lipid biosynthesis; nanodisk; neutralizing antibody; novel; open source; pathogen; prospective; protein complex; protein folding; protein structure; public health relevance; response; stem; theories; therapeutic target; three dimensional structure; tool

Project Summary. Most proteins are symmetric oligomeric complexes. Despite their prevalence and biomedical importance, such complexes are vastly underrepresented in the PDB, and determining their structures presents daunting challenges for NMR structural biologists. In particular, simulated annealing (SA), a widely-used technique for structure determination of homo-oligomers, is vulnerable to significant structural errors. Due to assignment ambiguity, SA converges to local minima rather than to the optimal structure or structural ensemble indicated by the data. Fold Operator Theory overcomes these errors, using a systematic search algorithm shown to identify biologically important assignments and structures that SA does not find. For example, the published NMR and crystal structures of the enzyme Diacylglycerol Kinase (DAGK) have very different topologies. Our systematic search techniques not only showed that both published folds are supported by the NMR data, but also found a novel fold that satisfies the data better than either published fold. We propose to develop novel algorithms and software enabling global and systematic search for NMR structure determination, building on our preliminary results showing that our methods can solve problems where traditional stochastic NMR methods struggle. These new tools will dramatically increase the accuracy of NMR structure determination with assignment ambiguity, which unavoidably arises for higher-order symmetric homo-oligomers. The proposed Deep Topological Sampling (DTS) has two primary modules: Fold Operator Theory (FOT); and DISCO (which we recently used to solve the structure of a membrane-associated MPER homo-trimer designed to probe immunogenic responses to the HIV-1 viral coat protein gp41). Aim 1: We will implement a general FOT in software, to compute all the protein folds consistent with the NMR data. FOT will search globally over folds, and avoid being trapped in local minima, to find all satisfying structures. Aim 2: We will develop our DISCO algorithm to search within each viable fold generated by FOT to find all feasible low-energy structures. DISCO and FOT will exploit novel geometric and topological algorithms to perform automated assignments accurately and efficiently, thus alleviating the most time-consuming and potentially error-prone step in multimeric structure determination. Aim 3: We will apply our FOT/DTS software (developed in Aims 1-2) prospectively to important systems. (A) We will perform experiments to determine the true functional structure DAGK adopts in its native environment. (B) We will use our methods to determine the structure of a larger HIV-1 membrane-associated pre-fusion gp41 trimer construct exposing transient, intermediate epitopes that bind broadly neutralizing antibodies, but are structurally invisible in larger laboratory constructs. (C) We will solve the hemifusion intermediate structures of the antigenic, symmetric homo- oligomeric domains of the Zika virus envelope protein, an emerging global health threat. Our novel open- source software can be applied to a vast array of symmetric protein targets in viral and bacterial pathogens.

项目摘要。大多数蛋白质是对称寡聚复合物。尽管它们很流行并且 生物医学重要性，此类复合物在 PDB 中的代表性严重不足，并决定了它们的 结构给核磁共振结构生物学家带来了艰巨的挑战。特别是模拟退火（SA）， 一种广泛使用的同源低聚物结构测定技术，容易受到显着结构影响 错误。由于分配模糊性，SA 收敛到局部最小值而不是最优结构或 数据表明的结构整体。折叠算子理论克服了这些错误，使用系统的 搜索算法可识别 SA 未找到的生物学上重要的分配和结构。为了 例如，已发表的二酰基甘油激酶 (DAGK) 的 NMR 和晶体结构具有非常重要的意义。 不同的拓扑。我们的系统搜索技术不仅表明两个已发表的折叠都是 NMR 数据支持，但也发现了一种新的折叠，比任何已发布的折叠都更好地满足数据。 我们建议开发新的算法和软件，实现 NMR 的全局和系统搜索 结构确定，基于我们的初步结果表明我们的方法可以解决问题 传统的随机核磁共振方法在这方面举步维艰。这些新工具将大大提高预测的准确性 核磁共振结构测定具有分配模糊性，这对于高阶对称结构来说是不可避免的 同质低聚物。拟议的深度拓扑采样 (DTS) 有两个主要模块： 折叠运算符 理论（FOT）；和 DISCO（我们最近用它来解决膜相关 MPER 的结构） 设计用于探测对 HIV-1 病毒外壳蛋白 gp41 的免疫原性反应的同源三聚体。 目标 1：我们将在软件中实现一个通用的 FOT，以计算与 核磁共振数据。 FOT将全局搜索折叠，避免陷入局部极小值，找到所有满足的 结构。目标 2：我们将开发 DISCO 算法，在 FOT 生成的每个可行折叠内进行搜索，以 找到所有可行的低能结构。 DISCO 和 FOT 将利用新颖的几何和拓扑算法 准确高效地执行自动化分配，从而减轻最耗时和 多聚体结构测定中可能容易出错的步骤。目标 3：我们将应用我们的 FOT/DTS 软件 （在目标 1-2 中制定）前瞻性地针对重要系统。 (A) 我们将进行实验以确定 DAGK 在其原生环境中采用真正的功能结构。 (B) 我们将使用我们的方法来确定 更大的 HIV-1 膜相关融合前 gp41 三聚体构建体的结构，暴露瞬时， 广泛结合中和抗体的中间表位，但在较大的实验室中结构上不可见 构造。 (C) 我们将解决抗原性、对称同源体的半融合中间体结构 寨卡病毒包膜蛋白的寡聚结构域是一种新兴的全球健康威胁。我们的小说开放—— 源软件可应用于病毒和细菌病原体中的大量对称蛋白质靶标。