Improved Algorithms for Macromolecular Structure Determination by cyro-EM

冷冻电镜大分子结构测定的改进算法

• 批准号: 8896811
• 负责人: Amit Singer
• 金额: $ 32.51万
• 依托单位: PRINCETON UNIVERSITY
• 依托单位国家: 美国
• 财政年份: 2009
• 资助国家: 美国
• 起止时间: 2009-08-01 至 2018-06-30
• 项目状态: 已结题
• 来源: https://reporter.nih.gov/project-details/8896811
• 关键词: Algorithms; Area; Biological; Biological Process; Classification; Complex; Computational algorithm; Computer software; Cryoelectron Microscopy; Crystallization; Data; Data Set; Detection; Development; Drug Design; Electron Microscope; Electron Microscopy; Electrons; Exhibits; Failure; Freezing; Goals; Health; Heterogeneity; Ice; Image; Individual; Investigation; Lead; Linear Algebra; Liquid substance; Macromolecular Complexes; Methods; Molecular; Molecular Conformation; Molecular Structure; Motion; Names; Nitrogen; Noise; Output; Particle Size; Performance; Population; Positioning Attribute; Preparation; Proteins; Research; Resolution; Resort; Rotation; Sampling; Signal Transduction; Specimen; Staining method; Stains; Structure; Techniques; Temperature; Universities; Validation; Variant; X-Ray Crystallography; base; computer framework; cost; heuristics; image processing; improved; insight; interest; macromolecule; novel; novel strategies; open source; particle; polypeptide; programs; protein structure; reconstruction; signal processing; structural biology; success; theories; three dimensional structure

DESCRIPTION (provided by applicant): Single-particle electron cryomicroscopy (cryo-EM) is a method for observing the three- dimensional structures of large macromolecules. In cryo-EM the experimental data consist of noisy, random projection images of macromolecular "particles", and the problem is finding the 3D structure which is consistent with these images. The proposal aims to develop and apply to experimental data novel algorithms for solving two difficult mathematical problems posed by this technique of structural biology. First, classical cryo-EM reconstruction techniques assume that the particles are identical. However, in many datasets this assumption does not hold. Some molecules of interest have more than one conformational state. These structural variations are of great interest to biologists, as they provide insight int the functioning of the molecule. The first area of investigation in this project is the development of algorithmic and mathematical framework for determining structures associated with heterogeneous particle populations. The proposed algorithm is not only faster than existing techniques but is also mathematically provable to reveal the different conformations if the number of images is sufficiently large. Second, a major limiting factor for present cryo-EM studies is the particle size. Images of small particles are often too noisy for existing methods to provide valid three-dimensional reconstructions; although the images contain structural information, the assignment of orientations to the individual particles is unreliable. The second area of investigation focuses on developing a radical new approach for reconstruction of small particles without the need for determining particle orientations.

描述(申请人提供)：单粒子电子冷冻显微镜(Cryo-EM)是一种观察大分子三维结构的方法。在低温电子显微镜中，实验数据由噪声的、随机的大分子“粒子”投影图像组成，问题是找到与这些图像一致的3D结构。该提案旨在开发新的算法并将其应用于实验数据，以解决由这种结构生物学技术提出的两个困难的数学问题。首先，经典的低温电磁重建技术假定粒子是相同的。然而，在许多数据集中，这一假设并不成立。一些感兴趣的分子有不止一个构象状态。生物学家对这些结构变化非常感兴趣，因为它们提供了对分子功能的洞察。这个项目的第一个调查领域是发展 用于确定与异质颗粒种群相关的结构的算法和数学框架。该算法不仅比现有技术速度快，而且在图像数量足够大的情况下，还可以从数学上证明不同的构象。其次，目前低温电磁研究的一个主要限制因素是颗粒大小。小颗粒的图像通常太过嘈杂，现有的方法无法 提供有效的三维重建；尽管图像包含结构信息，但对单个粒子的定向分配是不可靠的。第二个研究领域的重点是开发一种激进的新方法来重建小粒子，而不需要确定粒子的取向。