About This Project
Photosynthesis sustains the biosphere, but it operates with low overall efficiency. By designing brand new proteins for high-efficiency photosynthesis, we hope to engineer plants and algae to increase production of food and renewable solar fuels. In this project, we will leverage recent breakthroughs in artificial intelligence to design proteins that assemble metal clusters to catalyze water oxidation, a critical step toward enhanced photosynthesis for food security and to fight climate change.
Ask the ScientistsJoin The Discussion
What is the context of this research?
We depend upon photosynthesis for food and our oxygen-rich atmosphere. However, photosynthesis is inefficient, partly due to the inability of oxygenic phototrophs to absorb infrared light; extending the upper wavelength limit of photosynthetically active radiation from 700 to 1000 nm would nearly double the number of solar photons available for photosynthesis. In addition, electron tunneling theory suggests photosynthetic reaction center proteins separate charge with efficiencies substantially below the theoretical maximum. These losses limit photosynthetic growth for food and biofuels. Traditional plant breeding strategies progressively improved crop yields in the 20th century but now provide diminishing returns; further gains will require direct manipulation of photosynthetic processes.
What is the significance of this project?
A central challenge in developing high-efficiency photosynthetic pathways is water oxidation to make O2 and reducing equivalents for fuel production. Photosystem II (PSII) is the only water-oxidizing protein, but its evolutionary legacy has made it complex and fragile with interdependent parts, impeding efforts to rewire PSII to improve efficiency. De novo design of water oxidases is a significant hurdle, but recent advances in computational protein design incorporating artificial intelligence (AI) have made protein design more powerful than ever. Early work shows de novo proteins can precisely position chlorophylls and other redox centers for light-driven electron transport. De novo water oxidases may lead to improved food production, renewable fuel generation, and carbon sequestration.
What are the goals of the project?
To develop new high-efficiency photosynthetic organisms for enhanced food and renewable fuel production, we will design proteins for photochemical water oxidation using Earth-abundant, bio-available components. Other water oxidation catalysts including synthetic Co4O4 clusters (which do not self-assemble in vivo) and the Mn4CaO5 cluster of PSII (which is difficult to reengineer) use transition metal oxide cubane structures for catalysis. Starting December 1, 2023, we will use new AI tools to design proteins that self-assemble Mn4O4 and Co4O4 complexes and test them for metal cluster assembly and photochemical O2 evolution activity. If successful, our de novo proteins will serve as bio-compatible water oxidation modules that can be coupled to new photosynthetic electron transport chains.
One of the largest expenses for this project will be $21,000 for eBlock Gene Fragments from Integrated DNA Technologies. This will cover ~300 eBlock genes (~1000 base pairs each) for expression of the designed metal cluster proteins that will be the focus of our experimental efforts in the last 20 months of the 2-year project. This budget is critical to the success of our larger research project that includes the photosystems being designed as part of our Advanced Research Projects Agency - Energy (ARPA-E) grant because it supports our efforts in a new direction, namely water oxidation, which will be an essential component of a new photosynthetic pathway. Wages for the 2 Ph.D. students and 1 research scientist are already partially supported by the ARPA-E grant until March 27, 2025, alleviating the salary burden on this Homeworld Garden grant. Consumables will include laboratory chemicals and common equipment such as pipettes, chromatography columns, Strep-Tactin® resin, etc.
Starting Dec. 1, 2023, we will carry out a 2-year project to design and characterize de novo proteins for photochemical water oxidation. In the first 4 months, we will design metal cluster-assembling proteins using the latest computational protein design tools built upon artificial intelligence. We will test our designed proteins using a battery of biochemical and biophysical experiments to determine their 3D structures, metal cluster properties, and water oxidation activities by Dec. 1, 2025.
Apr 01, 2024
Design 300 water oxidation proteins using computational methods. Designs should be predicted to fold correctly with high AlphaFold metrics.
Oct 01, 2024
Experimentally identify designed metalloproteins with intended 3D shapes and secondary structure content.
Apr 01, 2025
Assemble intended metal-oxo cubane structures using de novo proteins.
Dec 01, 2025
Characterize oxygen evolution activity of designed metal-oxo cubane proteins.
Dec 01, 2025
Solve X-ray crystal structures of metal cluster proteins.
Meet the Team
Nathan Ennist, Avi Swartz and Peik Lund-Andersen make up the de novo photosystem team at the Institute for Protein Design. Nate brings 12 years of experience in bioenergetics and protein design, Avi contributes a deep background in computer science, and Peik is cultivating his expertise in inorganic chemistry and potentiometry. The team came together in 2022 to work on their grand vision of developing new proteins for high-efficiency photosynthesis for enhanced production of food and biofuels.
Nathan Ennist, Ph.D. is an Acting Instructor doing research in the Department of Biochemistry at the University of Washington. As part of David Baker’s group at the Institute for Protein Design (IPD), Nate mentors Ph.D. students Avi Swartz and Peik Lund-Andersen, and together they work to design new proteins for high-efficiency photosynthesis. Nate first joined the Baker group as a postdoc in 2017, when he started working on chlorophyll binding proteins for light harvesting and charge separation. Nate employs cutting edge computational protein design methods to create multi-cofactor proteins for energy transfer and electron transfer. Nate wrote a grant proposal on behalf of the Baker group for an Advanced Research Projects Agency-Energy (ARPA-E) award for a project titled, “Harvesting Infrared Light to Improve Photosynthetic Biomass Production” which was funded for $1,347,122 over 3 years starting March 28, 2022. Nate has published on the de novo design of photochemical reaction center proteins and chlorophyll dimer proteins that precisely mimic the structures of native chlorophyll special pairs found in photosynthetic reaction centers (preprint).
Nate completed his Ph.D. in 2017 at the University of Pennsylvania in the lab of Prof. P. Leslie Dutton, where he designed and characterized photochemical reaction centers and oxygen transport proteins. In the Dutton group, Nate developed expertise in protein redox chemistry, anaerobic techniques, metalloprotein design, X-ray crystallography, transient absorption spectroscopy, and other spectroscopic methods.
Nate’s long-term career goal is to become a professor to continue mentoring students and working to build more efficient photosynthetic pathways for enhanced production of food and renewable fuels.
Peik Lund-Andersen obtained a B.S in Molecular Biology from the University of Idaho, where he conducted research using molecular modeling and molecular dynamics simulations to probe protein-protein and protein-small molecule interactions. While there he won the prestigious Goldwater Scholarship for his work identifying possible animal reservoirs of COVID-19. Peik is now a second year Molecular Engineering graduate student working under David Baker at the University of Washington’s Institute for Protein Design. His current work involves designing redox active proteins to assemble photochemical reaction centers. During his PhD he aims to gain an in-depth understanding of biological electron transport and bioinorganic chemistry. His long term goal is to engineer proteins for the sustainable production of fuels and other valuable chemicals.
Avi Swartz’s experience is primarily in computational techniques and structural biology: his undergraduate degree was in computer science at Harvard University, and while there he performed term time research in developing machine learning architecture to disentangle protein evolution and structural information from metagenomic multiple sequence alignments.
Avi is now a third year graduate student in Molecular and Cell Biology, working under David Baker in the Institute of Protein Design at the University of Washington. In his Ph.D., Avi aims to continue developing his computational skills while also learning the experimental biochemistry as well as the physics and chemistry necessary to test his computational designs. After earning his Ph.D., Avi plans to continue in the academic track with a focus on using these computational protein design skills on meaningful biological problems.
- $0Total Donations
- $0Average Donation