The origin of pigment-binding differences in CP29 and LHCII: the role of protein structure and dynamics

The first step of photosynthesis in plants is performed by the light-harvesting complexes (LHC), a large family of pigment-binding proteins embedded in the photosynthetic membranes. These complexes are conserved across species, suggesting that each has a distinct role. However, they display a high degree of sequence homology and their static structures are almost identical. What are then the structural features that determine their different properties? In this work, we compared the two best-characterized LHCs of plants: LHCII and CP29. Using molecular dynamics simulations, we could rationalize the difference between them in terms of pigment-binding properties. The data also show that while the loops between the helices are very flexible, the structure of the transmembrane regions remains very similar in the crystal and the membranes. However, the small structural differences significantly affect the excitonic coupling between some pigment pairs. Finally, we analyzed in detail the structure of the long N-terminus of CP29, showing that it is structurally stable and it remains on top of the membrane even in the absence of other proteins. Although the structural changes upon phosphorylation are minor, they can explain the differences in the absorption properties of the pigments observed experimentally.

Automated summary

The first step of photosynthesis in plants is performed by a family of pigment-binding proteins called light-harvesting complexes (LHC), which are embedded in the photosynthetic membranes. Despite their high degree of sequence homology and almost identical static structures, different LHCs have distinct roles and properties. In this study, we compared two well-studied LHCs in plants, LHCII and CP29, and used molecular dynamics simulations to explain their differences in pigment-binding properties. Our analysis revealed that while the loops between helices are flexible, the transmembrane regions have a consistent structure. However, small structural differences significantly affect excitonic coupling between pigments. Additionally, we investigated the structure of CP29's long N-terminus and found it to be structurally stable and present on the membrane even without other proteins. Minor structural changes upon phosphorylation can explain the observed differences in pigment absorption properties.