Photos of the XFEL device during laser alignment. Three metal-covered fibers (the chain-like tube in the upper right corner) illuminate the protein sample and circulate them through part of the photosynthesis reaction. The green dot in the middle is the interaction point where XFEL will hit the sample. (Source: Hiroki Makita/Berkeley Lab)
Scientists at Berkeley Lab specialize in basic scientific questions. Once these questions are answered, they may lead to world advances in technology, medicine, or energy.
One of these big questions is how photosynthesis happens. The enzyme-based process that uses water and sunlight to convert carbon dioxide into food is actually the basis of life on earth-understanding this reaction at the atomic level may lead to the mass production of renewable fuels, which are made of greenhouse gases sucked from the earth production. Air. Indeed, the world is changing.
For years, a team in the Molecular Biophysics and Integrated Bioimaging (MBIB) Department of Berkeley Lab has been revealing the precise, step-by-step details of photosynthesis. They just revealed another aspect published in Nature Communications earlier this month. Their current work focuses on Photosystem II (PS II), an enzyme that splits water into oxygen, hydrogen ions, and free electrons that power the rest of the process, ultimately producing sugar molecules.
We spoke with two members, co-first author and senior scientist Vittal Yachandra, and co-first author and postdoctoral researcher Philipp Simon to discuss their latest milestones, shooting things with lasers, and why they chose this field.
Q: What did you find in the latest paper?
Vittal Yachandra-Physical Biological Science Portrait.
Yachandra: The protein PS II found in all plants uses sunlight to split water
Embedded in a membrane called the thylakoid membrane in the chloroplast, it produces all the oxygen we breathe. Interestingly, water is the ubiquitous "solvent" in all biological processes and the "substrate" of the reaction, which means that it is one of the reactants of the enzyme. This raises a question as to how water flows into the active site (enzyme area where the action takes place) of PS II, which contains metallic manganese-calcium complex (Mn4Ca).
This may be an important aspect of the active site to prevent water from interacting with it prematurely, leading to the formation of unwanted and harmful intermediates, such as peroxides, which can damage proteins.
We also found that the [known] proton channel of PS II actually contains a "proton gate". Protons produced during water decomposition
Remember this picture from the biology class?
To react, they need to be removed from the catalytic site. This gate basically prevents protons from returning to the catalyst and makes it a one-way street.
These two findings show how important the entire protein, not just the metal sites, is for the catalytic reaction. Figuring out how PS II performs the water splitting reaction is an important part of our research and one of the major scientific challenges facing the Department of Energy.
Question: What is an X-ray-free electron laser? Why use it?
Yachandra: X-ray free electron laser (XFEL) is a tool developed to generate very strong ultra-short X-ray pulses. These X-ray laser pulses enable us to understand the properties of matter on the scale of atoms and molecules and on the time scale of atomic motion and chemical reactions. The XFEL system directs a super-focused photon beam (atomic-sized wavelength) at a molecular sample and takes a snapshot of how photons are diffracted from the molecule. The entire process from pulse to image is completed in tens of trillions of a second.
Simon: I would like to mention two main advantages: First, it uses ultra-short X-ray pulses to acquire images, and then interprets it as a mapping structure. As used in traditional crystallography, intense X-rays can damage and eventually destroy proteins, especially metal catalytic centers. But XFEL allows us to detect our structure faster than it can cause damage, so it can "surpass it." Another advantage is that our structure is determined under well-controlled lighting conditions and room temperature. Imagine you want to study the flow of water, but this is a cold (non-California) winter, and everything is frozen; not the same, right? The same is true for proteins, especially in this work that focuses on hydrodynamics and amino acid functions. We hope that they can move and react as they do in nature. Only at room temperature can we understand how proteins coordinate and catalyze reactions.
Philipp Simone (right) and Roberto Alonso-Mori, another author of the new study, set up equipment on the macromolecular femtosecond crystallography instrument of the linear accelerator coherent light source at the SLAC National Accelerator Laboratory. (Source: Hiroki Makita/Berkeley Lab)
Q: It sounds like XFEL has many advantages. Do they have challenges?
Simon: The structure data recorded by the X-ray free electron laser is very complicated. Only by cooperating with so many experts can we get the final structure we show here. In addition, my colleague Rana Hussein [the co-first author of Humboldt University] did an excellent job of carefully examining all the water locations in the real large channels that are present in the protein. But even so, the individual puzzles were really confusing at first, and we spent a lot of time scanning them from all directions until the final picture appeared.
Q: Are there any surprises during the research process?
Simon: In science, it is definitely the first time we saw the proton door open. However, the best moment is when we successfully complete an X-ray beam time meeting—in the pre-pandemic period, when there were more than 20 people around us—all the faces were smiling...and then pure Ko [co-lead author Junko Yano] ice cream surprises us.
Yachandra: The active site is not easily exposed to water, so it is obvious that the enzyme may not directly use water from the outside of the membrane where PS II is located. Although there are many potential channels in PS II, this study shows that by determining the movement of water in the channel during the reaction in real time, a specific channel is involved in the process of transporting water from the outside.
Q: Philipp, why are you attracted to the Institute of Photosynthesis?
Simon: I am a well-trained physicist, specializing in optics and solid-state physics. After completing my studies, I am looking for more applied research, in which my research results can be directly embedded in a wider context. When I first read about the opportunity to study the function of photosynthetic proteins, I knew this was the job I wanted. It combines my love of nature and the technology I learned during my studies, and the result provides an understanding of our surroundings, and it also inspired bionic technology to collect solar energy.
Q. Vittal, what motivates you?
Yachandra: I have been involved in photosynthesis research for a long time. Our research aims to understand how plants use light to split water in such an easy way, and it is very difficult to simulate this reaction in an artificial system. Collaborate with our team members It is very interesting to work together, especially Junko Yano and Jan Kern, the co-leaders of this paper and my long-term colleagues at MBIB, as well as Paul Adams and Nick Sauter from our department.
This photo was taken in 2018 and shows the many contributors to the paper. From left to right: Vittal Yachandra, Iris Young, Nicholas Sauter, Sheraz Gul, Jan Kern, Ruchira Chatterjee, Aaron Brewster, Junko Yano and Nigel Moriarty, all at MBIB, in the biological sciences area of Berkeley Lab. (Source: Marilyn Sargent/Berkeley Lab)
The research included scientists from Berkeley Lab, Uppsala University, Humboldt University, SLAC and the University of Wisconsin-Madison.
Lawrence Berkeley National Laboratory was established in 1931. It firmly believes that the biggest scientific challenge is best solved by the team. Lawrence Berkeley National Laboratory and its scientists have won 14 Nobel Prizes. Today, Berkeley Lab researchers develop sustainable energy and environmental solutions, create useful new materials, advance the frontiers of computing, and explore the mysteries of life, matter, and the universe. Scientists from all over the world rely on laboratory facilities to carry out their own discovery science. The Berkeley Laboratory is a multi-project national laboratory managed by the University of California for the Office of Science of the Department of Energy.
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