Protein structure determination from low-resolution experimental data

从低分辨率实验数据确定蛋白质结构

• 批准号: 9287589
• 负责人: Frank P DiMaio
• 金额: $ 28.02万
• 依托单位: UNIVERSITY OF WASHINGTON
• 依托单位国家: 美国
• 财政年份: 2017
• 资助国家: 美国
• 起止时间: 2017-08-01 至 2022-07-31
• 项目状态: 已结题
• 来源: https://reporter.nih.gov/project-details/9287589
• 关键词: Address; Adopted; Biological; Biology; Complex; Computing Methodologies; Cryoelectron Microscopy; Data; Data Set; Development; Drug Design; Drug Targeting; Goals; Homologous Gene; Machine Learning; Maps; Methods; Modeling; Molecular Conformation; Molecular Machines; Mutation; Phase; Positioning Attribute; Proteins; Refit; Research; Resolution; Roentgen Rays; Sampling; Source; Structure; System; Testing; Torsion; Uncertainty; Validation; Work; X ray diffraction analysis; X-Ray Crystallography; X-Ray Diffraction; atomic data; atomic interactions; computerized tools; exhaustion; flexibility; human disease; improved; insight; method development; model building; next generation; novel; protein complex; protein structure; reconstruction; three dimensional structure; tool

Project Abstract Determination of a protein’s three-dimensional structure is of critical importance in biology, providing insights to biological mechanisms and important targets for drug design. While high- resolution X-ray diffraction data provides an atomic view of cellular components, for many interesting and biologically relevant complexes, it may only be possible to obtain low-resolution structural information. Both cryo-electron microscopy and X-ray crystallography, when applied to large, flexible molecular machines, often produce data of 3-6 Å resolution. Extracting detailed atomic information from this data, critical in understanding function, the effects of mutation, or in designing drugs is impossible due to the low number of observations and the large conformational space proteins may adopt. I propose to develop computational methods for extracting high-resolution atomic models from this low-resolution data, bridging the “resolution gap” with computational methods. My proposed research develops and extends our labs’ methods for automatically inferring atomic accuracy models, from these “near-atomic” resolution sources of experimental data. We develop novel conformational sampling methods, guided by experimental data, to infer atomic information both in cases where homologous high-resolution data is available, and where it is not. Additionally, we propose development of methods for estimating model uncertainty; these are critical in understanding to what degree structural conclusions may be made from a particular dataset. Finally, in pushing the resolution limit further, we develop general tools for biomolecular forcefield optimization. These machine-learning tools will allow development of a next-generation forcefield, critical in extending the resolution limit of data from which we can infer atomic details. The overall goal of the proposed research is robust and accessible methods to determine protein structures to atomic accuracy from only sparse experimental data. Combined, the three aims in this proposal will lead to dramatic improvements in our ability to infer atomic interactions from sparse experimental data. This will lead to determination of structures that will reveal key insights into how biomedically important protein complexes perform their function and what goes wrong in human disease.

项目摘要 确定蛋白质的三维结构在生物学中至关重要， 为药物设计提供生物学机制和重要靶点的见解。虽然高- 分辨率X射线衍射数据提供了细胞成分的原子视图，对于许多 有趣的和生物相关的复合物，它可能只可能获得低分辨率 结构信息。冷冻电子显微镜和X射线晶体学，当应用时 到大型、灵活的分子机器，通常产生3-6 μ m分辨率的数据。提取详细 这些数据中的原子信息，对于理解功能，突变的影响或 设计药物是不可能的，因为观察数量少， 构象空间蛋白质可以采用。我建议开发计算方法， 从低分辨率数据中提取高分辨率原子模型，桥接“分辨率” gap”的计算方法。 我提出的研究开发和扩展了我们实验室的自动推断方法， 原子精度模型，从这些“近原子”的实验数据分辨率来源。我们 开发新的构象采样方法，以实验数据为指导，推断原子 在同源高分辨率数据可用的情况下，以及在 没有此外，我们提出了估计模型不确定性的方法的发展;这些 在理解从一个结构性的结论中可以得出什么程度上是至关重要的。 特定的数据集。最后，在进一步推动分辨率极限的过程中，我们开发了通用工具， 生物分子力场优化这些机器学习工具将允许开发一个 下一代力场，在扩展数据的分辨率极限方面至关重要， 推断原子细节。 拟议研究的总体目标是确定可靠和可访问的方法 蛋白质结构的原子精度从只有稀疏的实验数据。结合起来，这三个 这项提案的目标将大大提高我们推断原子相互作用的能力 从稀疏的实验数据。这将导致确定的结构，将揭示关键 深入了解生物医学上重要的蛋白质复合物如何发挥其功能， 在人类疾病中是错误的