GORGON

戈尔贡

• 批准号: 7953791
• 负责人: MARC L BAKER
• 金额: $ 3.48万
• 依托单位: BAYLOR COLLEGE OF MEDICINE
• 依托单位国家: 美国
• 财政年份: 2008
• 资助国家: 美国
• 起止时间: 2008-12-01 至 2009-11-30
• 项目状态: 已结题
• 来源: https://reporter.nih.gov/project-details/7953791
• 关键词: Amino Acids; Bacteriophages; Cartoons; Computer Retrieval of Information on Scientific Projects Database; Electron Microscopy; Elements; Funding; Generations; Grant; Institution; Manuals; Maps; Modeling; Pear; Process; Research; Research Personnel; Resolution; Resources; Shapes; Source; Structural Models; Structure; United States National Institutes of Health; Vertebral column; X-Ray Crystallography; alpha helix; beta pleated sheet; density; macromolecule; tool

This subproject is one of many research subprojects utilizing the resources provided by a Center grant funded by NIH/NCRR. The subproject and investigator (PI) may have received primary funding from another NIH source, and thus could be represented in other CRISP entries. The institution listed is for the Center, which is not necessarily the institution for the investigator. As cryo-EM pushes towards atomic resolution, more complete and accurate annotation of the density map becomes possible. At subnanometer resolutions, secondary structure elements become visible; alpha helices ap-pear as cylinders and beta sheets appear as thin, flat planes. These features can be represented as simple geometric objects, having no relationship to the primary sequence. Moving to slightly higher resolutions, con-nectivity between the secondary structure elements can be seen, from which simple cartoon structural models can be derived, as in the 6.8 ¿ resolution structure of RDV (Zhou et al., 2001). Once 4.5 ¿ resolution has been reached, the pitch of the alpha helices, as well as separation of the strands in beta sheets become visible. At this resolution (4.5-4.2 ¿), it has been possible to construct C-alpha backbone models for GroEL and epsilon15 phage (Jiang et al., 2008; Ludtke et al., 2008). In addition, some bulky amino acid sidechains can be seen, although their shapes generally remain ambiguous. Presently, Mat Baker and co-workers are developing a graphical tool, called Gorgon, which helps to automate and simplify these cryo-EM modeling steps. Current model generation is largely a manual process that can take weeks to months. Gorgon will allow for rapid and accurate model generation, which will be necessary as we move to other maps. This de novo cryo-EM modeling approach will help to bridge the gap between cryo-EM and X-ray crystallography.

这个子项目是许多研究子项目中的一个 由NIH/NCRR资助的中心赠款提供的资源。子项目和 研究者（PI）可能从另一个NIH来源获得了主要资金， 因此可以在其他CRISP条目中表示。所列机构为 研究中心，而研究中心不一定是研究者所在的机构。 随着冷冻EM向原子分辨率的推进，密度图的更完整和准确的注释成为可能。在亚纳米分辨率下，二级结构元素变得可见; α螺旋呈现为圆柱体，β片层呈现为薄而平坦的平面。这些特征可以表示为简单的几何对象，与主序列没有关系。移动到稍微更高的分辨率，可以看到二级结构元件之间的连接性，从中可以导出简单的卡通结构模型，如RDV的6.8 ½分辨率结构（Zhou等人，2001年）。一旦达到4.5 <$分辨率，α螺旋的螺距以及β折叠中链的分离变得可见。在该分辨率（4.5-4.2 μ m）下，已经可以构建GroEL和ε 15噬菌体的C-α骨架模型（Jiang等人，2008; Ludtke等人，2008年）。此外，可以看到一些庞大的氨基酸侧链，尽管它们的形状通常保持模糊。 目前，Mat Baker及其同事正在开发一种名为Gorgon的图形工具，该工具有助于自动化和简化这些冷冻EM建模步骤。目前的模型生成主要是一个手动过程，可能需要数周到数月的时间。Gorgon将允许快速和准确的模型生成，这将是必要的，因为我们转移到其他地图。这种从头cryo-EM建模方法将有助于弥合cryo-EM和X射线晶体学之间的差距。