Multi-Resolution Docking Methods for Electron Microscopy

电子显微镜的多分辨率对接方法

• 批准号: 10120245
• 负责人: WILLY R WRIGGERS
• 金额: $ 31.36万
• 依托单位: OLD DOMINION UNIVERSITY
• 依托单位国家: 美国
• 财政年份: 2001
• 资助国家: 美国
• 起止时间: 2001-04-01 至 2024-08-31
• 项目状态: 已结题
• 来源: https://reporter.nih.gov/project-details/10120245
• 关键词: 3-Dimensional; Algorithms; Architecture; Area; Biological; Cells; Characteristics; Chemoreceptors; Chimera organism; Collaborations; Communities; Complement; Complex; Computational algorithm; Computer Models; Computer software; Computing Methodologies; Crowding; Cryo-electron tomography; Cryoelectron Microscopy; Cytoskeletal Filaments; Data; Databases; Deposition; Detection; Development; Docking; Dose; Drug Design; Drug Targeting; Educational workshop; Electron Microscopy; Electrons; Elements; Environment; Equilibrium; Exhibits; Feedback; Filament; Freezing; Funding; Goals; Grant; Hair Cells; Health; Human; Hybrids; Hydration status; Internet; Laboratories; Least-Squares Analysis; Link; Machine Learning; Manuals; Maps; Mathematics; Measures; Medical; Methods; Microscope; Modeling; Modernization; Molecular Motors; Molecular Structure; Morphologic artifacts; Nature; Noise; Organelles; Organism; Pattern; Plant Roots; Research; Resolution; Sampling; Shapes; Specimen; Structure; Techniques; Technology; Tissues; Tomogram; Training; Validation; Variant; Visualization software; Work; algorithmic methodologies; automated segmentation; base; beta pleated sheet; computer code; cryogenics; data warehouse; deep learning; denoising; density; electron tomography; experience; feature detection; fitness; flexibility; fundamental research; heuristics; high standard; image reconstruction; improved; interest; learning network; macromolecular assembly; novel; particle; prevent; process optimization; programs; reconstruction; structured data; theories; tool

Summary In the past decade, we have witnessed a revolutionary progress in camera technology and the attainable resolution of macromolecular assemblies via cryogenic electron microscopy (cryo-EM) and in the development of computational algorithms that relate the resulting 3D maps to atomic resolution structures. Whereas single- particle cryo-EM today is capable of directly solving atomic structures of biomolecular assemblies in isolation, electron tomography (ET) in unstained frozen-hydrated samples is widely used to capture the 3D organization of supramolecular complexes in their native (organelle, cell, or tissue) environments. We have identified three inter-related research areas where our computational modeling experience (historically rooted in pre-revolution multi-scale approaches) offers the biggest value to today's post-revolution EM community: (1) medium resolution cryo-EM modeling, (2) the segmentation and denoising of cryo-ET data, and (3) the validation of atomic models and their corresponding maps. The first aim is an extension of promising new ideas in flexible fitting as well as secondary structure prediction for medium resolution maps, which have been our key research areas in the past. medium resolution (5-10Å) maps are still widely used in EM and can be of significant biological importance. This is particularly true in the case of cryo-ET maps, which are harder to read than single particle cryo-EM maps because they often exhibit considerable noise, anisotropic resolution, and anisotropic density variations due to the low dose requirements and the missing wedge in the Fourier space. In the case of tightly packed or crowded macromolecular structures, the fusion of nearby biomolecular densities prevents an automated segmentation of geometric shapes, requiring a labor-intensive manual tracing by human experts. We are currently developing novel computational approaches to provide a more objective strategy for missing wedge correction in homogeneous specimen areas of tomograms. Our hybrid approach combines deconvolution and denoising with template matching in a unified mathematical framework that allows modeling constraints to be imposed in a least-squares optimization process. Our approach can also be extended to the flexible refinement of atomic structures using our damped dynamics flexible fitting approach by tuning the internal point-spread functions to the missing wedge of the ET data. To support these aims, we will quantitatively measure the fitness of an atomic model in local density regions and characterize the fitness of maps with reliable reference structures. The collaborative efforts supported by this grant will include the refinement of cytoskeletal filaments, molecular motors, bacterial chemoreceptor arrays, and hair cell stereocilia. The algorithmic and methodological developments will be distributed freely through the established Internet-based mechanisms used by the Situs and Sculptor packages and as plugins for the popular UCSF Chimera graphics program.

总结 在过去的十年里，我们见证了相机技术的革命性进步， 通过低温电子显微镜（cryo-EM）解析大分子组装体， 计算算法，将产生的3D地图与原子分辨率结构联系起来。而单身- 粒子冷冻EM如今能够直接解决孤立的生物分子组件的原子结构， 在未染色的冷冻水化样品中的电子层析成像（ET）被广泛用于捕获3D组织 超分子复合物在其天然（细胞器，细胞或组织）环境中的作用。我们已经确定了三个 相互关联的研究领域，我们的计算建模经验（历史上植根于革命前 多尺度方法）为当今革命后的新兴市场社区提供了最大的价值：（1）中等 分辨率cryo-EM建模，（2）cryo-ET数据的分割和去噪，以及（3） 原子模型及其对应的地图。第一个目标是将有前途的新想法扩展到灵活的 拟合以及中等分辨率图的二级结构预测，这一直是我们的关键 过去的研究领域。中等分辨率（5- 10厘米）地图仍然广泛用于EM， 重要的生物学意义。这在低温ET图的情况下尤其如此，因为低温ET图更难阅读 比单粒子低温电磁图，因为它们往往表现出相当大的噪音，各向异性的分辨率， 由于低剂量要求和傅立叶空间中的楔形缺失，导致各向异性密度变化。在 紧密堆积或拥挤的大分子结构、附近生物分子密度的融合 防止几何形状的自动分割，需要劳动密集型手动跟踪， 人类专家我们目前正在开发新的计算方法，以提供更客观的 断层图像均匀样本区域中缺失楔形校正策略。我们的混合方法 将去卷积和去噪与模板匹配结合在统一的数学框架中， 在最小二乘优化过程中要施加的建模约束。我们的方法也可以是 扩展到原子结构的灵活细化使用我们的阻尼动力学灵活的拟合方法， 将内部点扩散函数调谐到ET数据的缺失楔形。为了实现这些目标，我们将 定量测量局部密度区域中原子模型的适应性，并表征 具有可靠参考结构的地图。这项赠款支持的合作努力将包括 细胞骨架丝、分子马达、细菌化学感受器阵列和毛细胞的精细化 静纤毛算法和方法的发展将通过既定的 Situs和Sculptor软件包使用的基于Internet的机制，以及流行的UCSF的插件 奇美拉图形程序。