Exploring the Structural Diversity and Evolution of the D1 Subunit of Photosystem II Using AlphaFold and Foldtree
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Abstract
Although our knowledge of photosystem II has expanded to include time‐resolved atomic details, the diversity of experimental structures of the enzyme remains limited. Recent advances in protein structure prediction with AlphaFold offer a promising approach to fill this gap in structural diversity in non‐model systems. This study used AlphaFold to predict the structures of the D1 protein, the core subunit of photosystem II, across a broad range of photosynthetic organisms. The prediction produced high‐confidence structures, and structural alignment analyses highlighted conserved regions across the different D1 groups, which were in line with high pLDDT scoring regions. In contrast, varying pLDDT in the DE loop and terminal regions appears to correlate with different degrees of structural flexibility or disorder. Subsequent structural phylogenetic analysis using Foldtree provided a tree that is in good agreement with previous sequence‐based studies. Moreover, the phylogeny supports a parsimonious scenario in which far‐red D1 and D1 INT evolved from an ancestral form of G4 D1. This work demonstrates the potential of AlphaFold and Foldtree to study the molecular evolution of photosynthesis.
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Cites
Highly accurate protein structure prediction with AlphaFold
Jumper, J., Evans, R., Pritzel, A., Green, T., Figurnov, M., Ronneberger, O., Tunyasuvunakool, K., Bates, R., Žídek, A., Potapenko, A., et al. (2021) · Nature · doi:10.1038/s41586-021-03819-2 · Cited by 43,764 · see citing works
Accurate structure prediction of biomolecular interactions with AlphaFold 3
Abramson, J., Adler, J., Dunger, J., Evans, R., Green, T., Pritzel, A., Ronneberger, O., Willmore, L., Ballard, A. J., Bambrick, J., et al. (2024) · Nature · doi:10.1038/s41586-024-07487-w · Cited by 15,861 · see citing works
Impact of protein conformational diversity on AlphaFold predictions
Saldaño, T., Escobedo, N., Marchetti, J., Zea, D. J., Mac Donagh, J., Velez Rueda, A. J., Gonik, E., Melani, A. G., Novomisky Nechcoff, J., Salas, M. N., et al. (2021) · doi:10.1101/2021.10.27.466189 · Cited by 196 · cited 1× · see citing works
“Several studies have found that the pLDDT score is a good indicator of the flexibility of the region, with lower values indicating more dynamicity (Guo et al. 2022; Saldano et al. 2022; Ma et al. 2023).”
Early Archean origin of Photosystem <scp>II</scp>
Cardona, T., Sánchez‐Baracaldo, P., Rutherford, A. W., & Larkum, A. W. (2019) · Geobiology · doi:10.1111/gbi.12322 · Cited by 144 · see citing works
Self-citationThe Evolution and Evolvability of Photosystem II
Oliver, T., Kim, T. D., Trinugroho, J. P., Cordón-Preciado, V., Wijayatilake, N., Bhatia, A., Rutherford, A. W., & Cardona, T. (2023) · Annual Review of Plant Biology · doi:10.1146/annurev-arplant-070522-062509 · Cited by 52 · see citing works
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- Authors
- Kim, T. D., Pretorius, D., Murray, J. W., & Cardona, T.
- Affiliations
- Queen Mary University of London (GB)
- Imperial College London (GB)
- Venue
- Physiologia Plantarum
- Publisher
- Wiley
- Published
- 2025-05
- Volume
- 177
- Issue
- 3
- Pages
- e70284-e70284
- ISSN
- 0031-9317 (ISSN-L)
- 1399-3054
- PMC
- PMC12096807
- OpenAlex
- W4410589506
- Cited by
- 4
- References
- 5
- Citations by year
- 2026: 3 · 2025: 1
- FWCI
- 1.20
- Type
- journal article
- Language
- en
- Open access
- hybrid
- doi.org
- Licence
- Locations
- Physiologia Plantarum (publishedVersion, cc-by)
- bioRxiv (Cold Spring Harbor Laboratory) (acceptedVersion)
- PubMed Central (publishedVersion, cc-by)
- PubMed (publishedVersion)
- Spiral (Imperial College London) (submittedVersion)
- Funders
- Engineering and Physical Sciences Research Council (EP/S022856/1)
- UK Research and Innovation (MR/T017546/1, MR/T017546/2, MR/Y011635/1)
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Photosynthetic Processes and Mechanisms
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Protein Structure and Dynamics
- Physical Sciences › Materials Science › Materials Chemistry › Enzyme Structure and Function
- Keywords
- photosystem II, protein structure prediction, structural diversity, DE loop, structural flexibility, intrinsically disordered regions, photosynthetic organisms
- MeSH terms
- Models, Molecular, Photosynthesis, Phylogeny, Evolution, Molecular, Photosystem II Protein Complex
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