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Seeing the Big Picture in Photosynthetic Light Harvesting

Berkeley Lab Researchers Create First Computational Model to Simulate Multiple Antenna Proteins

January 19, 2016

Contact: Lynn Yarris, [email protected]

Graham Fleming image 1

First computational model to simulate multiple antenna proteins. The photosystem II (PSII) complexes are shown in teals, the light harvesting complexes (LHC II) are shown in green.

To understand what goes on inside a beehive, you can’t just study the activity of a single bee. Likewise, to understand the photosynthetic light harvesting that takes place inside the chloroplast of a leaf, you can’t just study the activity of a single antenna protein. So researchers with Lawrence Berkeley National Laboratory and the University of California (UC) Berkeley created the first computational model that simulates the light-harvesting activity of the thousands of antenna proteins that would be interacting in the chloroplast of an actual leaf.

The results from this model, published January 18 in the Proceedings of the National Academy of Sciences, point the way to improving the yields of food and fuel crops and developing artificial photosynthesis technologies for next generation solar energy systems. Computational work for this research was carried out at NERSC.

The new model simulates light-harvesting across several hundred nanometers of a thylakoid membrane, which is the membrane within a chloroplast that harbors photosystem II (PSII), a complex of antennae made up of mostly of chlorophyll-containing proteins. The antennae in PSII gain “excitation” energy when they absorb sunlight and, through quantum mechanical effects, almost instantaneously transport this extra energy to reaction centers for conversion into chemical energy. Previous models of PSII simulated energy transport within a single antenna protein.

“Our model, which looked at some 10,000 proteins containing about 100,000 chlorophyll molecules, is the first to simulate a region of the PSII membrane large enough to represent behavior in a chloroplast while respecting and using both the quantum dynamics and the spatial structure of the membrane’s components,” said chemist Graham Fleming, who oversaw the development of this model and is a world authority on the quantum dynamics of photosynthesis. He holds appointments with Berkeley Lab, UC Berkeley and the Kavli Energy NanoScience Institute at Berkeley. “We use insights from structural biology, advanced spectroscopy and theory to reproduce observed phenomena spanning from one nanometer to hundreds of nanometers, and from ten femtoseconds to one nanosecond. This enables us to explain the mechanisms underlying the high quantum efficiency of PSII light harvesting in ideal conditions for the first time.”

Energy-Dependent Quenching

The ability of green plants to thrive in sunlight stems in part from the flexibility that PSII displays in harvesting solar energy. At low levels of light, through quantum processes that have been modeled by Fleming and coworkers, a photon of sunlight can be utilized for creation of chemical energy with more than 90-percent probability. Thanks to a protective mechanism known as “energy-dependent quenching,” PSII is able to ensure that a plant absorbs only the amount of solar energy it needs while excess energy that might damage the plant is safely dissipated.

Earlier work by Fleming and his research group revealed a molecular mechanism by which PSII is able to act as a sort of photosynthetic “dimmer switch” to regulate the amount of solar energy transported to the reaction center. However, this work was done for a single PSII antenna and did not reflect how these mechanisms might affect the transport of energy across assemblies of antennae, which in turn would affect the photochemical yield in the reaction centers of a functional thylakoid membrane.

“Our new model shows that excitation energy moves diffusively through the antennae with a diffusion length of 50 nanometers until it reaches a reaction center,” Fleming said. “The diffusion length of this excitation energy determines PSII’s high quantum efficiency in ideal conditions, and how that efficiency is altered by the membrane morphology and the closure of reaction centers. Ultimately, this means that the diffusion length of this excitation energy determines the photosynthetic efficiency of the host plant.”

Given that the ability of PSII to regulate the amount of solar energy being converted to chemical energy is essential for optimal plant fitness in natural sunlight, understanding this ability and learning to manipulate it is a prerequisite for systematically engineering the light-harvesting apparatus in crops. It should also be highly useful for designing artificial materials with the same flexible properties.

“Our next step is to learn now to model a system of PSII’s complexity over timescales ranging from femtoseconds to minutes, and lengthscales ranging from nanometers to micrometers,” Fleming said.


About Computing Sciences at Berkeley Lab

High performance computing plays a critical role in scientific discovery, and researchers increasingly rely on advances in computer science, mathematics, computational science, data science, and large-scale computing and networking to increase our understanding of ourselves, our planet, and our universe. Berkeley Lab’s Computing Sciences Area researches, develops, and deploys new foundations, tools, and technologies to meet these needs and to advance research across a broad range of scientific disciplines.

Founded in 1931 on the belief that the biggest scientific challenges are best addressed by teams, Lawrence Berkeley National Laboratory and its scientists have been recognized with 13 Nobel Prizes. Today, Berkeley Lab researchers develop sustainable energy and environmental solutions, create useful new materials, advance the frontiers of computing, and probe the mysteries of life, matter, and the universe. Scientists from around the world rely on the Lab’s facilities for their own discovery science. Berkeley Lab is a multiprogram national laboratory, managed by the University of California for the U.S. Department of Energy’s Office of Science.

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