At the origin of the selectivity of the chlorophyll-binding sites in Light Harvesting Complex II (LHCII)

Computing the Relative Affinity of Chlorophylls a and b to Light-Harvesting Complex II

“…The ΔΔ G a → b for spinach LHCII was previously calculated by Elias et al using MMPBSA. The numerical values are significantly different from those found with MCCE and FEP, yet the overall conclusion is similar.…”

“…MCCE, FEP, and MMPBSA are calculations based on classical force fields, so they do not capture the differences in the bonded interactions between the metal center and the axial ligand. However, recent DFT studies have shown that the strength of the Chl b formyl hydrogen bonds are not strongly affected by the nature of the axial ligand to the Mg …”

“… a The carotenoid type only affected the relative binding affinity for Chl a -611 and Chl b -601. MMPBSA and MCCE calculations for spinach chain A calculations are reported in Table S3. …”

“…The arms of the U have five Chls a (Figure 1B). 23 computational studies of spinach LHCII binding show that some sites have a clear affinity for the Chl variant that is bound, but others do not. Thus, the MMPBSA did not reliably assign the occupant of each binding site.…”

“…The new calculations show that sites with a hydrogen bond donor placed to associate with the Chl b formyl group do bind that Chl type with significant affinity. However, the sites that contain Chl a in the experimental structures often have little preference for one type of Chl in the calculations and therefore are expected to bind a mixture of Chl a and b. MCCE and FEP calculations yield similar conclusions and are in general agreement with earlier MMPBSA 23 calculations. However, a reanalysis of the pea electron density confirms that the binding sites do contain a single Chl type.…”