Exploring the Structural Diversity and Evolution of the D1 Subunit of Photosystem II Using AlphaFold and Foldtree

Area of Science:

• Biochemistry
• Structural Biology
• Molecular Evolution

Background:

• Experimental structures of photosystem II (PSII) are limited, hindering a full understanding of its diversity.
• Protein structure prediction tools like AlphaFold offer a way to explore structural diversity in non-model organisms.

Purpose of the Study:

• To predict the structures of the D1 protein, a core subunit of PSII, across various photosynthetic organisms using AlphaFold.
• To analyze the structural diversity, conserved regions, and evolutionary relationships of D1 proteins.

Main Methods:

• Utilized AlphaFold for high-confidence prediction of D1 protein structures.
• Performed structural alignment analyses to identify conserved regions.
• Conducted structural phylogenetic analysis using Foldtree.

Main Results:

• Generated high-confidence D1 protein structures with conserved regions identified.
• Observed varying pLDDT scores correlating with structural flexibility in specific regions (DE loop, termini).
• Developed a phylogenetic tree consistent with sequence-based studies, suggesting evolutionary pathways for D1 variants.

Conclusions:

• AlphaFold and Foldtree are powerful tools for studying the molecular evolution of photosynthesis.
• The predicted structures provide insights into D1 protein diversity and evolutionary history.
• This approach can fill structural gaps in non-model photosynthetic systems.