Computing the relative affinity of chlorophylls 𝘢 and 𝘣 to light-harvesting complex II

In plants and algae, the primary antenna protein bound to photosystem II is light harvesting complex II (LHCII), a pigment-protein complex that binds both chlorophyll (Chl) 𝘢 and Chl 𝘣 molecules. Chl 𝘢 and Chl 𝘣 have similar structures but differ in the chemical composition of their side chains. Chl 𝘢 has a methyl group (-CH₃) on one of its pyrrole rings, while Chl 𝘣 has a formyl group (-CHO) in the same position. There are 14 Chl binding sites but it is not known how the protein selectively binds the right chlorophyll type in each site. Knowing the selection criteria would allow the design of light harvesting complexes which bind different Chl types allowing an organism to utilize light of different wavelengths. The difference in the binding affinity of Chl 𝘢 and Chl 𝘣 in pea and spinach LHCII was calculated using Multiconformation Continuum Electrostatics and Free Energy Perturbation. Both methods identify some Chl sites where the Chl type (𝘢 or 𝘣) bound has significantly higher affinity, especially when the protein provides a hydrogen bond for the Chl 𝘣 formyl group. However, the Chl 𝘢 sites often have little calculated preference for one Chl type, so they are predicted to bind a mixture of Chl 𝘢 and 𝘣. Therefore, the electron density of the spinach LHCII was reanalyzed, confirming there is negligible Chl 𝘣 in the Chl 𝘢 binding sites. It is suggested that the protein chooses the correct Chl type during folding, segregating the preferred Chl to the correct binding site.