CAREER: Cryo-EM Guided de novo Protein Fold Elucidation

职业：冷冻电镜引导从头阐明蛋白质折叠

• 批准号: 0742762
• 负责人: Jens Meiler
• 金额: $ 73.86万
• 依托单位: Vanderbilt University
• 依托单位国家: 美国
• 项目类别: Continuing Grant
• 财政年份: 2008
• 资助国家: 美国
• 起止时间: 2008-08-01 至 2013-07-31
• 项目状态: 已结题
• 来源: https://www.nsf.gov/awardsearch/showAward?AWD_ID=0742762&HistoricalAwards=false
• 关键词: CAREER; Cryo; EM; Guided; de

The primary goal of this CAREER project is to integrate education and research to develop a novel protein structure prediction algorithm"EM-Fold" that advances resolution in protein structure elucidation from cryo-electron microscopy (EM) data. The concept of EM-Fold is developed with the ultimate goal of solving the structure of Ad protein IIIa. An increasing number of structural studies of large macromolecular protein complexes by cryo-electron microscopy have resulted in intermediate-resolution (5-10A) density maps. Currently no integrated approach is available to de novo build protein structures into sub-nanometer EM density maps. In aim I of the project EM-Fold is developed by deriving a protocol for consensus prediction of secondary structure elements, the development of knowledge-based scoring functions, and the implementation of the Monte Carlo assembly and refinement algorithms. Aim II focuses on testing of EM-Fold during the Critical Assessment for Techniques of protein Structure Prediction (CASP) experiment, the derivation of a rapid geometric hashing algorithm to fit structural models into cryo-EM densities, and the set up of a medium-scale experimental benchmark with simulated cryo-EM data sets. In aim III a resolution-increased cryo-EM data set for adenovirus will be recorded, the structure of adenovirus protein IIIa will be predicted, and a detailed confidence level will be assigned to the protein IIIa structure.The research carried out in this project is but one example for an increasing number of computational structural biology projects that pose interdisciplinary requirements on student education. To address this need a novel, integrated educational concept called "Research in Education RidE" is designed as a step-wise journey recruiting students through outreach activities and classroom education into their first research experiences. The outreach component consists of an annual molecular biophysics open house that brings over 100 undergraduate students to Vanderbilt University, primarily from groups underrepresented in science. The open house is complemented by a dedicated lecture series, "Protein Folding @ Home," presented at other undergraduate institutions and events. As a second educational module, the course "Protein Structure Prediction" lays the theoretical foundation for research. Course materials and workshop tutorials are made available online for usage by other teachers and students. In the third module research projects for undergraduate and high school students are aligned with tasks in the development of EM-Fold at appropriate levels of complexity.

这个职业项目的主要目标是将教育和研究相结合，开发一种新的蛋白质结构预测算法“EM-Fold”，该算法可以提高从低温电子显微镜(EM)数据进行蛋白质结构解析的分辨率。EM-折叠的概念是为了解决Ad蛋白质IIIa的结构而发展起来的。越来越多的大分子蛋白质复合体的冷冻电子显微镜结构研究已经产生了中分辨率(5-10A)密度图。目前，还没有一种综合的方法可以从头开始将蛋白质结构构建成亚纳米EM密度图。在项目目标I中，EM-Fold是通过推导二级结构元素的共识预测协议、开发基于知识的评分函数以及实施蒙特卡罗汇编和改进算法来开发的。目的II着重于蛋白质结构预测技术关键评估(CASP)实验中EM-折叠的测试，推导出将结构模型与低温EM密度相匹配的快速几何散列算法，并利用模拟的低温EM数据集建立中等规模的实验基准。在AIM III中，将记录腺病毒的分辨率增加的冷冻-EM数据集，预测腺病毒蛋白IIIa的结构，并将详细的置信度分配给蛋白质IIIa结构。本项目所进行的研究只是越来越多的计算结构生物学项目对学生教育提出跨学科要求的一个例子。为了满足这一需求，一种名为“教育研究”的新颖的综合教育概念被设计为一种循序渐进的旅程，通过外展活动和课堂教育招募学生进入他们的第一次研究经历。外展部分包括一年一度的分子生物物理学开放日，将100多名本科生带到范德比尔特大学，主要来自科学界代表性不足的群体。开放参观活动的补充是在其他本科生机构和活动中推出的专门的讲座系列，名为“蛋白质折叠@家”。作为第二个教育模块，《蛋白质结构预测》课程为研究奠定了理论基础。课程材料和工作坊教程在网上提供，供其他教师和学生使用。在第三个单元中，本科生和高中生的研究项目与EM-Fold开发中的任务相一致，复杂程度适当。