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PreprintCited by 4Photosynthetic Processes and MechanismsProtein Structure and DynamicsEnzyme Structure and Function

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Exploring the structural diversity and evolution of the D1 subunit of photosystem II using AlphaFold and Foldtree

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Kim, Tom Dongmin, Pretorius, Daniella, Murray, James W., Cardona, Tanai·2025·Physiologia Plantarum
DOI 10.1101/2025.03.06.641835PMC PMC12096807

Preprint — published as 10.1111/ppl.70284 · Paper page

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Abstract

While our knowledge of photosystem II has expanded to 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 appear to correlate with different degrees of structural flexibility or disorder. Subsequent structural phylogenetic analysis provided a phylogeny 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 the ancestral form of G4 D1. This study demonstrates the potential of AlphaFold in studies on structural diversity and the evolution of photosynthesis.

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Metadata

Authors
Kim, T. D., Pretorius, D., Murray, J. W., & Cardona, T.
Affiliations
  • Queen Mary University of London (GB)
  • Imperial College London (GB)
ORCID
Venue
Physiologia Plantarum
Publisher
openRxiv
Published
2025-03-07
Volume
177
Issue
3
Pages
e70284-e70284
ISSN
0031-9317 (ISSN-L)
DOI
10.1101/2025.03.06.641835
PMC
PMC12096807
OpenAlex
W4410589506
Cited by
4
References
1
Citations by year
2026: 3 · 2025: 1
FWCI
1.20
Type
journal article
Language
en
Open access
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
  • UK Research and Innovation (MR/Y011635/1, MR/T017546/1, MR/T017546/2)
  • Engineering and Physical Sciences Research Council (EP/S022856/1)
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
  • Life Sciences › Biochemistry, Genetics and Molecular Biology › Structural Biology › 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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