Photobiology of Vision & Photosynthesis

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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.