Kim Tom Dongmin, Pretorius Daniella, Murray James W, Cardona Tanai
School of Biological and Behavioural Sciences, Queen Mary University of London, London, UK.
Department of Life Sciences, Imperial College London, London, UK.
Physiol Plant. 2025 May-Jun;177(3):e70284. doi: 10.1111/ppl.70284.
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 evolved from an ancestral form of G4 D1. This work demonstrates the potential of AlphaFold and Foldtree to study the molecular evolution of photosynthesis.
尽管我们对光系统II的了解已扩展到包括时间分辨的原子细节，但该酶实验结构的多样性仍然有限。利用AlphaFold进行蛋白质结构预测的最新进展为填补非模型系统结构多样性方面的这一空白提供了一种很有前景的方法。本研究使用AlphaFold预测了广泛光合生物中光系统II的核心亚基D1蛋白的结构。预测产生了高置信度的结构，结构比对分析突出了不同D1组中的保守区域，这些区域与高pLDDT评分区域一致。相比之下，DE环和末端区域中变化的pLDDT似乎与不同程度的结构灵活性或无序性相关。随后使用Foldtree进行的结构系统发育分析提供了一棵与先前基于序列的研究高度一致的树。此外，系统发育支持一种简约的情况，即远红D1和D1从G4 D1的祖先形式进化而来。这项工作证明了AlphaFold和Foldtree在研究光合作用分子进化方面的潜力。
