Exploring the structural diversity and evolution of the D1 subunit of photosystem II using AlphaFold and Foldtree
File(s)
Author(s)
Kim, Tom Dongmin
Pretorius, Daniella
Murray, James W
Cardona, Tanai
Type
preprint
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 oNer 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 diNerent 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 diNerent degrees of structural flexibility or disorder. Subsequent structural phylogenetic analysis provided a phylogeny that is in good agreement with previous sequencebased 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.
Date Issued
2025-03-07
Citation
Cold Spring Harbor Laboratory, 2025
Journal / Book Title
Cold Spring Harbor Laboratory
Copyright Statement
Copyright © 2025 The Author(s). The copyright holder for this preprint is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. All rights reserved. No reuse allowed without permission.