Molecular Modeling of Bioenergetic Systems

生物能系统的分子建模

• 批准号: 1616590
• 负责人: Zaida Luthey-Schulten
• 金额: $ 112.09万
• 依托单位: University of Illinois at Urbana-Champaign
• 依托单位国家: 美国
• 项目类别: Continuing Grant
• 财政年份: 2016
• 资助国家: 美国
• 起止时间: 2016-08-01 至 2022-07-31
• 项目状态: 已结题
• 来源: https://www.nsf.gov/awardsearch/showAward?AWD_ID=1616590&HistoricalAwards=false
• 关键词: Molecular; Modeling; Bioenergetic; Systems

The project, building on very recent experimental and computational methodologies, investigates at atomic level detail the key macromolecular apparatus that generates energy from sun light or food in higher life forms. Outcomes of the research are new solutions for solar energy conversion and agriculture as well as health benefits. The research extends the size scale of macromolecular systems within cells that can be studied and advances the technological frontier of computational technologies employed in the life sciences. The project provides an exceptional interdisciplinary training opportunity for young researchers from the fields of biology, chemistry, physics, and computer science. Planned activities also include development of advanced visualization and analysis tools, dissemination of teaching material on photosynthesis and respiration, and the production of a movie "Birth of Planet Earth" showcasing the early evolution of photosynthesis establishing life on Earth.Two ubiquitous biological energy conversion systems are investigated: the thylakoid systems of plant chloroplasts and the respiratory complex of mitochondria. The two macromolecular systems involve large protein complexes and share physical processes as well as constituent proteins. The project combines molecular electronics, stochastic quantum mechanics, and molecular dynamics methods to answer critical questions in bioenergetics: how do the many participating processes coordinate themselves and, in some cases, how do they achieve actually their conversion function? The research strategy for the two systems is anchored in the PI's four decades of work, including work on the photosynthetic apparatus of purple bacteria. In case of the first system, the supramolecular organization of the thylakoid membrane will be determined along with its energy transfer and conversion processes. In case of the second system, the ability of the respiratory complexes of mitochondria to harness energy will be determined on the basis of published structures. For both systems a detailed computational description of energy storage and transduction will be provided that extends understanding of these systems beyond what is provided by experiment alone. The findings are expected to resolve apparent discrepancies between structural and functional characteristics of the systems. The research links atomic level supramolecular structure to energy and charge transfer processes through dissipative quantum mechanics and molecular dynamics descriptions.This project is jointly funded by the Molecular Biophysics Cluster in the Division of Molecular and Cellular Biosciences and the Physics of Living Systems Program in the Division of Physics.

该项目以最新的实验和计算方法为基础，在原子水平上详细研究了在高等生命形式中从阳光或食物中产生能量的关键大分子装置。 研究成果是太阳能转换和农业以及健康效益的新解决方案。这项研究扩展了可以研究的细胞内大分子系统的规模，并推进了生命科学中使用的计算技术的技术前沿。该项目为来自生物学，化学，物理学和计算机科学领域的年轻研究人员提供了一个特殊的跨学科培训机会。计划的活动还包括开发先进的可视化和分析工具，散发关于光合作用和呼吸作用的教材，制作电影“行星地球的诞生”，展示光合作用在地球上建立生命的早期演变，研究两个普遍存在的生物能量转换系统：植物叶绿体的类囊体系统和线粒体的呼吸复合体。这两个大分子系统涉及大的蛋白质复合物，并共享物理过程以及组成蛋白质。该项目结合了分子电子学，随机量子力学和分子动力学方法来回答生物能量学中的关键问题：许多参与过程如何协调自己，以及在某些情况下，它们如何实现转换功能？这两个系统的研究策略是基于PI四十年的工作，包括对紫色细菌光合装置的研究。在第一个系统的情况下，类囊体膜的超分子结构将与其能量传递和转换过程一起被确定沿着。在第二种系统的情况下，线粒体的呼吸复合物利用能量的能力将基于公开的结构来确定。对于这两个系统的能量存储和转换的详细计算描述将提供扩展这些系统的理解超出了什么是由实验单独提供。预计调查结果将解决系统结构和功能特征之间的明显差异。该研究通过耗散量子力学和分子动力学描述将原子水平的超分子结构与能量和电荷转移过程联系起来。该项目由分子和细胞生物科学部的分子生物物理学集群和物理学部的生命系统物理学计划共同资助。

项目成果

Multiscale modeling and cinematic visualization of photosynthetic energy conversion processes from electronic to cell scales

• DOI: 10.1016/j.parco.2020.102698
• 发表时间: 2021-02-09
• 期刊: PARALLEL COMPUTING
• 影响因子: 1.4
• 作者: Sener, Melih;Levy, Stuart;Cox, Donna
• 通讯作者: Cox, Donna

Generalized correlation-based dynamical network analysis: a new high-performance approach for identifying allosteric communications in molecular dynamics trajectories

• DOI: 10.1063/5.0018980
• 发表时间: 2020-10-07
• 期刊: JOURNAL OF CHEMICAL PHYSICS
• 影响因子: 4.4
• 作者: Melo, Marcelo C. R.;Bernardi, Rafael C.;Luthey-Schulten, Zaida
• 通讯作者: Luthey-Schulten, Zaida