Photobiology of Vision & Photosynthesis

光合作用是地球生物圈中几乎所有生命的主要能量来源。在许多生物体中，光能通过光合作用细胞器有效地获得。在紫色细菌中，光合作用细胞器是质膜上的球状凹痕，称为色团。紫色细菌是此类生物中最简单、时间最长的例子之一。以前的研究工作是在单个蛋白质的水平上研究光合作用过程，但很少在整个系统的规模上进行研究。这个项目将研究蛋白质和膜对生色团的结构和自组织的贡献，以及它们在作为光合器官的功能中的潜在作用。这个项目将探索光合作用蛋白质在色团中的组织，以及它们的位置与整体细胞器结构和光合作用效率的相关性。全原子和粗粒度的分子动力学模拟都将被用来确定不同的蛋白质如何单独地和通过集体堆积来创造许多物种的色团所共有的泡状形状。模拟的蛋白质系统将包括捕光复合体1和2、反应中心、Bc1-复合体和PufX。光合作用所必需的过程是如何发生的，例如尽管生色团明显拥挤，但苯二酚在反应中心和Bc1-复合体之间的迁移，也将通过生色团的建模来解决。计算生物物理学的一个关键目标是从生理过程的基本原理出发，在系统水平上进行模拟。随着光合作用蛋白质晶体结构的日益丰富和NSF计算中心计算能力的提高，从系统的角度研究光合作用正变得可行。将来自多个来源的数据结合在一起，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，将为基本细胞器如何组织自己和功能以及这两项任务如何相互影响提供独特的观点。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调查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他的团队向91,000多名用户分发的免费提供的领先分子图形软件VMD中。关于细菌发色团的案例研究将被开发出来，并作为电子教科书在该组织广受欢迎的网站上提供。该组织目前的研讨会计划将扩大到包括研讨会，以帮助高中教师将计算工具整合到他们的课程中。特别是，将开发一个基于VMD的光合作用教学模块，这是高中生物学中普遍存在的一个主题。该项目由生物科学局分子和细胞生物科学部的分子生物物理学计划和数学和物理科学局的物理司共同支持。

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.