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.

项目概要/摘要 大分子晶体学中的数据收集容易出现严重的系统错误，从而妨碍 在许多系统上成功收集数据，最终限制了生成结构的准确性。 能够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 更好地考虑辐射损伤的新结构，辐射损伤是造成 80% 失败异常的原因 定相尝试，2）通过模拟非同构来改进多晶平均，这将打开 通往信噪比任意增益的门户，3）区分激烈争议的替代解释，例如 通过使用更真实的溶剂模型创建模拟来确定是否存在结合配体。 从同步加速器移动“无损伤数据”，我们将从校准辐射损伤曲线开始 使用这些曲线，我们将把辐射损伤的真实 3D 模型融入到模型和 DBP 样本中。 非长方体晶体 (RADDOSE 3D) 到我们的衍射图像模拟器 (MLFSOM) 中以产生 3D 剂量 沿着晶体的分布和照明图这将产生新一代的波长- 晶体的相关吸收因子可补充光束线处的现有吸收校正。 我们将使用锥形束在线 X 射线吸收射线照相术和 2D 图来测量晶体的 3D 图 这些进步将使我们能够在开放的情况下生成零剂量外推值。 格式，考虑了实验晶体和光束几何形状，为了改进多晶体平均，我们将 首先描述非同构如何随湿度、辐射损伤和 通过更新非同构的经典“克里克和马格多夫”模拟，增加功能状态。 复杂性，我们将开发一种奇异值分解方法来参数化非同构。 根据该分析得出的修正，我们将修正多晶中存在的非同构现象 实验，能够确定新颖的结构，包括使用串行收集的结构 下一代光源的晶体学能够增强模拟以进行稳健的解释。 实验数据，我们将利用大分子晶体学和小角度X-中的新溶剂模型 我们的工作将创建用于比较溶剂密度与替代品的标准协议。 解释并定量评估每种模拟情况与真实情况相比的可能性 大分子晶体学或 SAXS 数据除了区分不同的解释之外。 根据实验数据，改进溶剂模型将增强对大分子如何影响的理解 总的来说，我们期望消除这些分子的好处。 关键的系统错误对于方法开发和功能研究来说都是变革性的。