Photobiology of Vision & Photosynthesis
视觉光生物学
基本信息
- 批准号:0744057
- 负责人:
- 金额:$ 68万
- 依托单位:
- 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:2008-03-01 至 2013-02-28
- 项目状态:已结题
- 来源:
- 关键词:
项目摘要
Photosynthesis is the principal source of energy for nearly all life in Earth's biosphere. Light energy is efficiently harvested in many organisms by photosynthetic organelles. In purple bacteria, which are among the simplest and longest studied examples of such organisms, the photosynthetic organelles are bulbous indentations of the plasma membrane, called chromatophores. Previous research efforts have studied the photosynthetic process at the level of individual proteins, but rarely on the scale of an entire system. This project will examine the protein and membrane contributions to the structure and self-organization of the chromatophore, and their potential role in its function as a photosynthetic organelle. This project will explore the organization of photosynthetic proteins in the chromatophore and the relevance of their placement to overall organelle structure and photosynthetic efficiency. Both all-atom and coarse-grained molecular dynamics simulations will be used to determine how different proteins, individually and through collective packing, create the vesicular shape common to many species' chromatophores. The protein systems simulated will include light harvesting complexes 1 and 2, reaction center, bc1-complex, and PufX. How processes necessary for photosynthesis occur, such as the migration of quinones between the reaction center and the bc1-complex, despite the apparent crowding in chromatophores, will also be addressed through modeling of the chromatophore. A key goal of computational biophysics is the simulation from first principles of physiological processes at the systems level. With the growing availability of crystal structures for photosynthetic proteins and the increasing computational power available from NSF computing centers, the study of photosynthesis in silico from a systems point of view is becoming feasible. The combination of data from multiple sources, including atomic force and electron microscopy, molecular dynamics simulations, and quantum mechanical calculations, will grant a unique view of how a rudimentary organelle organizes itself and functions, and how these two tasks affect one another. This project will create a basis for interdisciplinary cooperation between experimental biologists, theoretical physicists, theoretical chemists, and computer scientists. This provides an exceptional research training opportunity for graduate and undergraduate students as well as postdocs from any of these diverse backgrounds. The planned activities will extend the strong outreach programs already developed by the principal investigator. Advanced membrane building and analysis tools will be added to the freely available leading molecular graphics software VMD that is distributed by his group to over 91,000 users. A case study on the bacterial chromatophore will be developed and made available on the group's highly popular website as an electronic textbook. The group's current workshop program will be extended to include workshops to help high school teachers integrate computational tools into their curricula. In particular, a VMD-based teaching module on photosynthesis, a ubiquitous topic in high school biology, will be developed. This project is jointly supported by the Molecular Biophysics Program in the Division of Molecular and Cellular Biosciences in the Directorate for Biological Sciences and the Division of Physics in the Mathematical and Physical Sciences Directorate.
光合作用是地球生物圈中几乎所有生命的主要能量来源。许多生物体通过光合作用细胞器有效地收集光能。紫色细菌是这类生物中最简单、研究时间最长的例子之一。在紫色细菌中,光合作用细胞器是质膜上的球状凹痕,称为色素体。以前的研究工作已经在单个蛋白质的水平上研究了光合作用过程,但很少在整个系统的规模上。该项目将研究蛋白质和膜对染色质结构和自组织的贡献,以及它们在其作为光合细胞器功能中的潜在作用。该项目将探索染色质中光合蛋白的组织及其与整体细胞器结构和光合效率的相关性。全原子和粗粒度分子动力学模拟将用于确定不同的蛋白质是如何单独和通过集体包装形成许多物种的染色质共同的囊泡形状的。模拟的蛋白质系统将包括光收集复合物1和2、反应中心、bc1-复合物和PufX。光合作用的必要过程是如何发生的,如醌在反应中心和bc1复合物之间的迁移,尽管在染色质中明显拥挤,也将通过染色质的建模来解决。计算生物物理学的一个关键目标是在系统水平上从生理过程的第一原理进行模拟。随着光合作用蛋白晶体结构的日益可用性和NSF计算中心可用的计算能力的增加,从系统的角度研究硅光合作用变得可行。来自多个来源的数据,包括原子力和电子显微镜、分子动力学模拟和量子力学计算,将提供一个独特的视角来研究一个基本的细胞器是如何组织自身和功能的,以及这两个任务是如何相互影响的。该项目将为实验生物学家、理论物理学家、理论化学家和计算机科学家之间的跨学科合作奠定基础。这为研究生和本科生以及来自这些不同背景的博士后提供了一个特殊的研究培训机会。计划中的活动将扩展首席研究员已经制定的强有力的外展计划。先进的膜构建和分析工具将被添加到免费提供的领先分子图形软件VMD中,该软件由他的团队分发给超过91,000名用户。一个关于细菌染色质的案例研究将被开发出来,并作为电子教科书发布在该组织广受欢迎的网站上。该组织目前的研讨会计划将扩展到包括帮助高中教师将计算工具整合到他们的课程中的研讨会。特别是,将开发一个基于vmd的光合作用教学模块,这是一个在高中生物中普遍存在的话题。该项目由生物科学理事会分子和细胞生物科学部的分子生物物理学项目和数学与物理科学理事会的物理部共同支持。
项目成果
期刊论文数量(0)
专著数量(0)
科研奖励数量(0)
会议论文数量(0)
专利数量(0)
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Klaus Schulten其他文献
Molecular biomimetics: nanotechnology through biology
分子仿生学:通过生物学的纳米技术
- DOI:
10.1038/nmat964 - 发表时间:
2003-09-01 - 期刊:
- 影响因子:38.500
- 作者:
Mehmet Sarikaya;Candan Tamerler;Alex K. -Y. Jen;Klaus Schulten;François Baneyx - 通讯作者:
François Baneyx
Observation and simulation to study mechanical properties of proteins
- DOI:
10.1016/s1093-3263(00)80129-1 - 发表时间:
2000-01-01 - 期刊:
- 影响因子:
- 作者:
Klaus Schulten - 通讯作者:
Klaus Schulten
The Conformational Transition of Kv1.2 Voltage Sensor Domain from Molecular Dynamics Simulations
- DOI:
10.1016/j.bpj.2010.12.1760 - 发表时间:
2011-02-02 - 期刊:
- 影响因子:
- 作者:
Luca Maragliano;Fatemeh Khalili-Araghi;Emad Tajkhorshid;Klaus Schulten;Benoit Roux - 通讯作者:
Benoit Roux
Electrically Induced Conformational Change of Peptides on Metallic
金属上肽的电致构象变化
- DOI:
- 发表时间:
2012 - 期刊:
- 影响因子:0
- 作者:
Nanosurfaces Chen;Eduardo R. Cruz;Jaie C. Woodard;M. Gartia;Klaus Schulten;Logan Liu - 通讯作者:
Logan Liu
NIH Resource for Macromolecular Modeling and Bioinformatics
NIH 大分子建模和生物信息学资源
- DOI:
10.1007/s00418-007-0297-3 - 发表时间:
2002 - 期刊:
- 影响因子:2.3
- 作者:
Klaus Schulten;Principal Investigator - 通讯作者:
Principal Investigator
Klaus Schulten的其他文献
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{{ truncateString('Klaus Schulten', 18)}}的其他基金
Collaborative Research: Advanced Methodology for Calculation of Pairwise Interactions
合作研究:计算成对相互作用的先进方法
- 批准号:
0957273 - 财政年份:2010
- 资助金额:
$ 68万 - 项目类别:
Standard Grant
Photobiology of Vision and Photosynthesis
视觉和光合作用的光生物学
- 批准号:
0234938 - 财政年份:2003
- 资助金额:
$ 68万 - 项目类别:
Continuing Grant
Simulation of the Functional Dynamics of Bacteriohodopsin in the Integral Purple Membrane
整体紫膜中细菌视紫红质功能动力学的模拟
- 批准号:
9982629 - 财政年份:2000
- 资助金额:
$ 68万 - 项目类别:
Continuing Grant
A Workstation Cluster for High Performance Computing in Structural Biology
用于结构生物学高性能计算的工作站集群
- 批准号:
9423827 - 财政年份:1995
- 资助金额:
$ 68万 - 项目类别:
Standard Grant
Advanced Computational Approaches to Biomolecular Modelling and Structure Determination
生物分子建模和结构测定的高级计算方法
- 批准号:
9318159 - 财政年份:1993
- 资助金额:
$ 68万 - 项目类别:
Continuing Grant
Development and Function of Brain Maps in the Visual System
视觉系统中脑图的发展和功能
- 批准号:
9122522 - 财政年份:1991
- 资助金额:
$ 68万 - 项目类别:
Standard Grant
Computational Neural Science on the Connection Machine: Adaptative Map Algorithms for Real World Problems
连接机上的计算神经科学:现实世界问题的自适应地图算法
- 批准号:
9015561 - 财政年份:1990
- 资助金额:
$ 68万 - 项目类别:
Standard Grant
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