From DOE’s Lawrence Berkeley National Laboratory (US) : “Chloro-phylling in the Answers to Big Questions”

From DOE’s Lawrence Berkeley National Laboratory (US)

November 30, 2021
Aliyah Kovner

A photo of the XFEL equipment during laser alignment. The three metal-covered fibers (the chainmail-like tubes in top right corner) illuminate the protein samples and cycle them through part of the photosynthetic reaction. The green point in the center is the interaction point where the XFEL will hit the samples. Credit: Hiroki Makita/Berkeley Lab.

Berkeley Lab scientists specialize in investigating fundamental scientific questions that, when answered, could lead to world-changing advances in technology, medicine, or energy.

One of these big questions is how, exactly, photosynthesis occurs. The enzyme-based process of converting carbon dioxide into food, using water and sunlight, is literally the foundation of life on Earth – and understanding the reaction at an atomic level could lead to vast production of renewable fuels made from greenhouse gases sucked out of the air. Pretty world changing, indeed.

A team from Berkeley Lab’s Molecular Biophysics and Integrated Bioimaging (MBIB) Division has been uncovering precise, step-by-step details of photosynthesis for years. They have just revealed another aspect, which was published earlier this month in Nature Communications. Their current work focuses on photosystem II (PS II), the enzyme that splits water into oxygen gas, hydrogen ions, and the free electrons that power the rest of the process, ultimately creating sugar molecules.

We spoke to two members, co-lead author and senior scientist Vittal Yachandra and co-first author and postdoctoral researcher Philipp Simon, about their latest milestones, shooting stuff with lasers, and why they chose this field.

Q. What did you discover in your latest paper?

Yachandra: The splitting of water using sunlight by the protein PS II, which is present in all plants

embedded in a membrane within chloroplasts called the thylakoid membrane, generates all the oxygen that we breathe. Interestingly, water, which is a ubiquitous “solvent” for all biological processes, is also a “substrate” for this reaction, meaning it is one of the reactants for this enzyme. That raises the question of how water is funneled into the active site – the area of the enzyme where the action happens – of PS II, which contains a metallic manganese-calcium complex (Mn4Ca).

This may be an important aspect of the active site, to prevent water from interacting with it prematurely, resulting in unwanted and deleterious intermediates such as peroxide from forming, which can cause damage to the protein.

We also found that PS II’s [known] proton channel actually also contains a “proton gate.” Protons are generated during the water-splitting reaction, and they need to be removed from the catalytic site. This gate essentially prevents the proton from coming back to the catalyst and makes it a one-way street.

These two discoveries show how important the whole protein, not just the metal site, is for carrying out the catalytic reaction. And figuring out how PS II carries out the water-splitting reaction is an important part of our research and one of the grand science challenges to the Department of Energy.

Remember this diagram from biology class?

Q. What is an X-ray free electron laser and why did you use it?

Yachandra: X-ray free electron laser (XFEL) is a tool developed for generating very intense, ultra-short pulses of X-rays. These X-ray laser pulses allow us to understand the properties of matter at the scale of atoms and molecules, and in the time scale of atomic motions and chemical reactions. XFEL systems point a super-focused photon beam (with a wavelength the size of an atom) at a sample of molecules and takes snapshots of how the photons diffract off the molecule. The entire process, from pulse to image, is completed in a few quadrillionths of a second.

Simon: There are two main advantages I’d like to mention: the first is that it uses an ultra-short X-ray pulse to get images that are then interpreted to map structures. Intense X-rays, like those used in traditional crystallography, damage and ultimately destroy proteins, especially the metallic catalytic centers. But XFELs allow us to probe our structures faster than the damage is caused, so it can “outrun it.” The other advantage is our structures are determined under very well-controlled illumination conditions and at room temperature. Imagine you want to study the flow of water, but it’s a cold (non-Californian) winter and all is frozen; it’s different, right? The same holds true for proteins, especially in this work focusing on water dynamics and the functions of amino acids. We want them to be able to move and react as they would in nature, only at room temperature we can understand how the protein orchestrates the catalytic reaction.

Philipp Simone, right, and Roberto Alonso-Mori, another author on the new study, set up equipment at the Macromolecular Femtosecond Crystallography instrument of the Linac Coherent Light Source, DOE’s SLAC National Accelerator Laboratory. Credit: Hiroki Makita/Berkeley Lab.


Q. It sounds like XFELs have a lot of advantages. Do they come with challenges?

Simon: The structural data recorded at X-ray free electron lasers is very complex, and only in collaboration with so many specialists one can obtain the final structure as we present it here. Also, my colleague Rana Hussein [co-first author from Humboldt University of Berlin [Humboldt-Universität zu Berlin](DE)] did a fabulous job in carefully checking all the water positions in the really large channels present in the protein. But even then, the single puzzle pieces were really confusing at first, and it took us many rounds of glancing at them from all sides until the final picture emerged.

Q. Were there any surprises during the research?

Simon: Scientifically, definitely the moment when we saw for the first time the opening of the proton gate. The best moments, however, are, when we finish a successful X-ray beamtime session – in pre-pandemic times we had more than 20 people around – and all the faces are smiling… and then Junko [co-lead author Junko Yano] surprises us with ice cream.

Yachandra: The active site is not easily accessible to water, so it was clear that the enzyme was probably not using water directly from the outside of the membrane where PS II is located. While there are many potential channels in PS II, this study showed that one specific channel is involved in ferrying water from the outside, by determining the motion of water in the channel during the reaction, in real time.

Q. Philipp, why were you drawn to photosynthesis research?

Simon: I am a trained physicist specializing in optics and solid-state physics. After finishing my studies, I was looking for more applied research, where the outcome of my research could be directly embedded in a broader context. When I first read about the opportunity to study the function of photosynthetic proteins, I knew that’s what I want to work on. It combines my love for nature, the techniques I learned during my studies, and the outcome provides understanding of our immediate environment while also inspiring biomimicking technologies to harvest solar energy.

Q. Vittal, what motivates you?

Yachandra: I have been involved with photosynthesis research for a very long time now, and our research is driven by our goal to understand how plants split water using light in such a facile manner, while it is so difficult to mimic this reaction in artificial systems. It has been a lot of fun, working with our group members and our collaborators, and especially, Junko Yano and Jan Kern, co-leads of this paper and my longtime colleagues in MBIB, and Paul Adams and Nick Sauter, also from our Division.

This study included scientists from Berkeley Lab, Uppsala University[Uppsala universitet](SE), Humboldt University of Berlin [Humboldt-Universität zu Berlin](DE), DOE’s SLAC National Accelerator Laboratory (US), and The University of Wisconsin–Madison(US).

See the full article here.

See also the new blog post from SLAC here.


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LBNL Molecular Foundry

Bringing Science Solutions to the World

In the world of science, Lawrence Berkeley National Laboratory (Berkeley Lab) (US) is synonymous with “excellence.” Thirteen Nobel prizes are associated with Berkeley Lab. Seventy Lab scientists are members of the The National Academy of Sciences (US), one of the highest honors for a scientist in the United States. Thirteen of our scientists have won the National Medal of Science, our nation’s highest award for lifetime achievement in fields of scientific research. Eighteen of our engineers have been elected to the The National Academy of Engineering (US), and three of our scientists have been elected into the Institute of Medicine. In addition, Berkeley Lab has trained thousands of university science and engineering students who are advancing technological innovations across the nation and around the world.

Berkeley Lab is a member of the national laboratory system supported by the U.S. Department of Energy through its Office of Science. It is managed by the University of California (US) and is charged with conducting unclassified research across a wide range of scientific disciplines. Located on a 202-acre site in the hills above the University of California- Berkeley campus that offers spectacular views of the San Francisco Bay, Berkeley Lab employs approximately 3,232 scientists, engineers and support staff. The Lab’s total costs for FY 2014 were $785 million. A recent study estimates the Laboratory’s overall economic impact through direct, indirect and induced spending on the nine counties that make up the San Francisco Bay Area to be nearly $700 million annually. The Lab was also responsible for creating 5,600 jobs locally and 12,000 nationally. The overall economic impact on the national economy is estimated at $1.6 billion a year. Technologies developed at Berkeley Lab have generated billions of dollars in revenues, and thousands of jobs. Savings as a result of Berkeley Lab developments in lighting and windows, and other energy-efficient technologies, have also been in the billions of dollars.

Berkeley Lab was founded in 1931 by Ernest Orlando Lawrence, a University of California-Berkeley (US) physicist who won the 1939 Nobel Prize in physics for his invention of the cyclotron, a circular particle accelerator that opened the door to high-energy physics. It was Lawrence’s belief that scientific research is best done through teams of individuals with different fields of expertise, working together. His teamwork concept is a Berkeley Lab legacy that continues today.



The laboratory was founded on August 26, 1931, by Ernest Lawrence, as the Radiation Laboratory of the University of California, Berkeley, associated with the Physics Department. It centered physics research around his new instrument, the cyclotron, a type of particle accelerator for which he was awarded the Nobel Prize in Physics in 1939.

LBNL 88 inch cyclotron.

LBNL 88 inch cyclotron.

Throughout the 1930s, Lawrence pushed to create larger and larger machines for physics research, courting private philanthropists for funding. He was the first to develop a large team to build big projects to make discoveries in basic research. Eventually these machines grew too large to be held on the university grounds, and in 1940 the lab moved to its current site atop the hill above campus. Part of the team put together during this period includes two other young scientists who went on to establish large laboratories; J. Robert Oppenheimer founded DOE’s Los Alamos Laboratory (US), and Robert Wilson founded Fermi National Accelerator Laboratory(US).


Leslie Groves visited Lawrence’s Radiation Laboratory in late 1942 as he was organizing the Manhattan Project, meeting J. Robert Oppenheimer for the first time. Oppenheimer was tasked with organizing the nuclear bomb development effort and founded today’s Los Alamos National Laboratory to help keep the work secret. At the RadLab, Lawrence and his colleagues developed the technique of electromagnetic enrichment of uranium using their experience with cyclotrons. The “calutrons” (named after the University) became the basic unit of the massive Y-12 facility in Oak Ridge, Tennessee. Lawrence’s lab helped contribute to what have been judged to be the three most valuable technology developments of the war (the atomic bomb, proximity fuse, and radar). The cyclotron, whose construction was stalled during the war, was finished in November 1946. The Manhattan Project shut down two months later.


After the war, the Radiation Laboratory became one of the first laboratories to be incorporated into the Atomic Energy Commission (AEC) (now Department of Energy (US). The most highly classified work remained at Los Alamos, but the RadLab remained involved. Edward Teller suggested setting up a second lab similar to Los Alamos to compete with their designs. This led to the creation of an offshoot of the RadLab (now the Lawrence Livermore National Laboratory (US)) in 1952. Some of the RadLab’s work was transferred to the new lab, but some classified research continued at Berkeley Lab until the 1970s, when it became a laboratory dedicated only to unclassified scientific research.

Shortly after the death of Lawrence in August 1958, the UC Radiation Laboratory (both branches) was renamed the Lawrence Radiation Laboratory. The Berkeley location became the Lawrence Berkeley Laboratory in 1971, although many continued to call it the RadLab. Gradually, another shortened form came into common usage, LBNL. Its formal name was amended to Ernest Orlando Lawrence Berkeley National Laboratory in 1995, when “National” was added to the names of all DOE labs. “Ernest Orlando” was later dropped to shorten the name. Today, the lab is commonly referred to as “Berkeley Lab”.

The Alvarez Physics Memos are a set of informal working papers of the large group of physicists, engineers, computer programmers, and technicians led by Luis W. Alvarez from the early 1950s until his death in 1988. Over 1700 memos are available on-line, hosted by the Laboratory.

The lab remains owned by the Department of Energy (US), with management from the University of California (US). Companies such as Intel were funding the lab’s research into computing chips.

Science mission

From the 1950s through the present, Berkeley Lab has maintained its status as a major international center for physics research, and has also diversified its research program into almost every realm of scientific investigation. Its mission is to solve the most pressing and profound scientific problems facing humanity, conduct basic research for a secure energy future, understand living systems to improve the environment, health, and energy supply, understand matter and energy in the universe, build and safely operate leading scientific facilities for the nation, and train the next generation of scientists and engineers.

The Laboratory’s 20 scientific divisions are organized within six areas of research: Computing Sciences; Physical Sciences; Earth and Environmental Sciences; Biosciences; Energy Sciences; and Energy Technologies. Berkeley Lab has six main science thrusts: advancing integrated fundamental energy science; integrative biological and environmental system science; advanced computing for science impact; discovering the fundamental properties of matter and energy; accelerators for the future; and developing energy technology innovations for a sustainable future. It was Lawrence’s belief that scientific research is best done through teams of individuals with different fields of expertise, working together. His teamwork concept is a Berkeley Lab tradition that continues today.

Berkeley Lab operates five major National User Facilities for the DOE Office of Science (US):

The Advanced Light Source (ALS) is a synchrotron light source with 41 beam lines providing ultraviolet, soft x-ray, and hard x-ray light to scientific experiments.


The ALS is one of the world’s brightest sources of soft x-rays, which are used to characterize the electronic structure of matter and to reveal microscopic structures with elemental and chemical specificity. About 2,500 scientist-users carry out research at ALS every year. Berkeley Lab is proposing an upgrade of ALS which would increase the coherent flux of soft x-rays by two-three orders of magnitude.

The DOE Joint Genome Institute (US) supports genomic research in support of the DOE missions in alternative energy, global carbon cycling, and environmental management. The JGI’s partner laboratories are Berkeley Lab, DOE’s Lawrence Livermore National Laboratory (US), DOE’s Oak Ridge National Laboratory (US)(ORNL), DOE’s Pacific Northwest National Laboratory (US) (PNNL), and the HudsonAlpha Institute for Biotechnology (US). The JGI’s central role is the development of a diversity of large-scale experimental and computational capabilities to link sequence to biological insights relevant to energy and environmental research. Approximately 1,200 scientist-users take advantage of JGI’s capabilities for their research every year.

The LBNL Molecular Foundry (US) [above] is a multidisciplinary nanoscience research facility. Its seven research facilities focus on Imaging and Manipulation of Nanostructures; Nanofabrication; Theory of Nanostructured Materials; Inorganic Nanostructures; Biological Nanostructures; Organic and Macromolecular Synthesis; and Electron Microscopy. Approximately 700 scientist-users make use of these facilities in their research every year.

The DOE’s NERSC National Energy Research Scientific Computing Center (US) is the scientific computing facility that provides large-scale computing for the DOE’s unclassified research programs. Its current systems provide over 3 billion computational hours annually. NERSC supports 6,000 scientific users from universities, national laboratories, and industry.

DOE’s NERSC National Energy Research Scientific Computing Center(US) at Lawrence Berkeley National Laboratory

Cray Cori II supercomputer at National Energy Research Scientific Computing Center(US) at DOE’s Lawrence Berkeley National Laboratory(US), named after Gerty Cori, the first American woman to win a Nobel Prize in science.

NERSC Hopper Cray XE6 supercomputer.

NERSC Cray XC30 Edison supercomputer

NERSC GPFS for Life Sciences.

The Genepool system is a cluster dedicated to the DOE Joint Genome Institute’s computing needs. Denovo is a smaller test system for Genepool that is primarily used by NERSC staff to test new system configurations and software.

NERSC PDSF computer cluster in 2003.

PDSF is a networked distributed computing cluster designed primarily to meet the detector simulation and data analysis requirements of physics, astrophysics and nuclear science collaborations.

Cray Shasta Perlmutter SC18 AMD Epyc Nvidia pre-exascale supercomputer.

NERSC is a DOE Office of Science User Facility.

The DOE’s Energy Science Network (US) is a high-speed network infrastructure optimized for very large scientific data flows. ESNet provides connectivity for all major DOE sites and facilities, and the network transports roughly 35 petabytes of traffic each month.

Berkeley Lab is the lead partner in the DOE’s Joint Bioenergy Institute (US) (JBEI), located in Emeryville, California. Other partners are the DOE’s Sandia National Laboratory (US), the University of California (UC) campuses of Berkeley and Davis, the Carnegie Institution for Science (US), and DOE’s Lawrence Livermore National Laboratory (US) (LLNL). JBEI’s primary scientific mission is to advance the development of the next generation of biofuels – liquid fuels derived from the solar energy stored in plant biomass. JBEI is one of three new U.S. Department of Energy (DOE) Bioenergy Research Centers (BRCs).

Berkeley Lab has a major role in two DOE Energy Innovation Hubs. The mission of the Joint Center for Artificial Photosynthesis (JCAP) is to find a cost-effective method to produce fuels using only sunlight, water, and carbon dioxide. The lead institution for JCAP is the California Institute of Technology (US) and Berkeley Lab is the second institutional center. The mission of the Joint Center for Energy Storage Research (JCESR) is to create next-generation battery technologies that will transform transportation and the electricity grid. DOE’s Argonne National Laboratory (US) leads JCESR and Berkeley Lab is a major partner.