Eliminating Critical Systematic Errors In Structural Biology With Next-Generation Simulation

通过下一代模拟消除结构生物学中的关键系统误差

• 批准号: 10162611
• 负责人: James M Holton
• 金额: $ 30.95万
• 依托单位: UNIVERSITY OF CALIFORNIA, SAN FRANCISCO
• 依托单位国家: 美国
• 财政年份: 2017
• 资助国家: 美国
• 起止时间: 2017-09-01 至 2022-09-27
• 项目状态: 已结题
• 来源: https://reporter.nih.gov/project-details/10162611
• 关键词: 3-Dimensional; Accounting; Active Sites; Area; Complement; Computer software; Cone; Crystallization; Crystallography; Data; Data Collection; Data Set; Diagnosis; Diagnostic radiologic examination; Disease; Dose; Error Sources; Evolution; Generations; Geometry; Humidity; Image; In Situ; Knowledge; Ligands; Light; Lighting; Maps; Measures; Metals; Methods; Minor; Modeling; Molecular Conformation; Muramidase; Noise; Phase; Positioning Attribute; Protein Region; Protocols documentation; Radiation induced damage; Reaction; Resolution; Roentgen Rays; Sampling; Side; Signal Transduction; Solvents; Source; Spottings; Structure; Surface; Synchrotrons; Syncope; System; Technology; Update; Weight; Work; absorption; beamline; computerized tools; conformer; curve fitting; density; electron density; experimental study; improved; interest; macromolecule; method development; next generation; non-Native; novel; novel strategies; prevent; simulation; structural biology; success; three-dimensional modeling; trend; vector

PROJECT SUMMARY/ABSTRACT Data collection in macromolecular crystallography is subject to significant systematic errors that prevent successful data collection on many systems and, ultimately, limit the accuracy of resulting structures. Creating simulation technologies that can account for these errors will have significant impact on three fronts: 1) solving new structures by better accounting for radiation damage, which is responsible for 80% of failed anomalous phasing attempts, 2) improving multi-crystal averaging by simulating non-isomorphism, which will open the gateway to arbitrary gains in signal-to-noise, 3) discriminating hotly contested alternative interpretations such as the presence or absence of a bound ligand, by creating simulations with more realistic solvent models. To move towards “damage-free data” from a synchrotron, we will start by calibrating radiation damage curves on model and DBP samples. Using these curves we will incorporate realistic 3D models of radiation damage to non-cuboid crystals (RADDOSE 3D) into our diffraction image simulator (MLFSOM) to yield a 3D Dose Distribution and Illumination map along the crystal. This will result in a new generation of wavelength- dependent absorption factors for the crystal to complement existing absorption corrections. At the beamline, we will measure a 3D map of the crystal using cone beam online x-ray absorption radiography and a 2D map of the beam profile. These advances will allow us to generate zero-dose extrapolation values, in an open format, that account for experimental crystal and beam geometry. To improve multi-crystal averaging, we will begin by characterizing how non-isomorphism varies as a function of humidity, radiation damage, and functional state. By updating the classic “Crick and Magdoff” simulations of non-isomorphism with increasing complexity, we will develop a singular value decomposition approach to parameterize non-isomorphism. Using the corrections derived from this analysis, we will correct the non-isomorphism present in multi-crystal experiments, enabling the determination of novel structures, including those collected using serial crystallography at next-generation light sources. To enable enhanced simulation for robust interpretation of experimental data, we will leverage new solvent models in macromolecular crystallography and small angle X- ray scattering. Our work will create standard protocols for comparing solvent density to alternative interpretations and to quantitatively assess how likely each simulated situation is compared to the real macromolecular crystallography or SAXS data. In addition to distinguishing between different interpretations of the experimental data, improving solvent models will enhance understanding of how macromolecules influence and interact with other molecules near their surface. Collectively, we expect the benefits of eliminating these critical systematic errors be transformative to both methods development and functional studies.

项目摘要/摘要 大分子晶体学中的数据收集受到严重的系统误差的影响 在许多系统上成功收集数据，并最终限制了所得结构的准确性。创建 可以解释这些错误的仿真技术将对三个方面产生重大影响：1）解决 通过更好地考虑辐射损伤的新结构，这是80％失败偶然的造成的 阶段尝试，2）通过模拟非同构，改善多晶的平均，这将打开 在信号到噪声中任意收益的门户，3）区分激烈争议的替代解释此类解释 通过使用更真实的溶剂模型创建模拟，作为存在或不存在结合配体的存在。到 朝着同步器迈向“无损害数据”，我们将从校准辐射损伤曲线开始 模型和DBP样品。使用这些曲线，我们将结合现实的3D辐射损坏模型 进入我们的衍射图像模拟器（MLFSOM）的非蛋白晶体（Raddose 3D）以产生3D剂量 沿晶体的分布和照明图。这将导致新一代波长 - 依赖的遗憾因素使水晶完成现有的后悔更正。在梁线上， 我们将使用锥形束在线X射线抽象射线照相和2D地图测量晶体的3D图 光束轮廓的。这些进步将使我们能够在开放中生成零剂量的外推值 格式，该解释了实验晶体和光束几何形状。为了改善多晶平均，我们将 首先表征非同构的多样性与湿度，辐射损伤和 功能状态。通过更新经典的“ Crick and Magdoff”模拟非同构的模拟 复杂性，我们将开发一种奇异的值分解方法来参数化非同态。使用 从此分析中得出的校正，我们将纠正多晶中存在的非同构 实验，实现了新结构的确定，包括使用串行收集的结构 下一代光源的晶体学。启用增强的模拟，以鲁坦的解释 实验数据，我们将利用大分子晶体学和小角度x-的新溶液模型来利用新的溶液模型 射线散射。我们的工作将创建标准协议，以将溶剂密度与替代性进行比较 解释并定量评估每个模拟情况与实际情况的可能性 大分子晶体学或SAXS数据。除了区分不同的解释 实验数据，改进溶剂模型将增强对大分子如何影响的理解 并与其表面附近的其他分子相互作用。总体而言，我们期望消除这些好处 关键的系统误差是对两种方法发展和功能研究的变革性的。