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.
Human civilization runs on a staggering 15 billion kW of energy. The welfare of future generations depends on abundant availability of clean and renewable energy sources. Fortunately, the sun provides our planet with almost 10,000 times our current energy needs. Nature has evolved complex quantum devices to harvest and convert solar energy in the form of photosynthesis. Researchers at the University of Illinois at Urbana-Champaign have determined for the first time the organization and function of an entire photosynthetic machine, the chromatophore, converting solar energy to ATP, life's universal energy currency. The photosynthetic apparatus of the chromatophore displays an integration of hundreds of cooperating proteins, comprising millions of atoms. Efficient conversion and storage of solar energy is a daunting challenge. Photosynthetic systems found in nature feature solutions that our technology has yet to match such as self-assembly, adaptation and optimization to environmental conditions, self-repair, and great efficiency from light capture to energy storage and transfer. Understanding how nature implements these solutions will permit the development of better solar energy harvesters, artificial or biological. The Theoretical and Computational Biophysics Group at the University of Illinois at Urbana-Champaign has studied photosynthesis for over 20 years. The NSF funded research began with the elucidation of single protein structures containing a few pigments and determination of the basic quantum mechanical processes associated with light harvesting. Today, researchers determine how entire photosynthetic systems - essentially, quantum devices made of hundreds of proteins and thousands of pigments - are organized and function with remarkable efficiency. This research utilizes molecular simulation and visualization software packages, NAMD and VMD, developed at the University of Illinois, made freely available nationwide and adopted by over a hundred thousand users across the world.
