Figure 6.

Light-Harvesting Protein Complex II. (Left & Center) Secondary structure of light-harvesting protein complex II (PDB code 1NKZ [67]). The purple coils are helices (12–37, 40–46); the 3₁₀-helices are blue (6–8). The green coils are other structures. (Left) Asymmetric unit (A₃B₃); (Center) Heterodimer (AB). (Right) Predicted CD Using CDCALC. The 1NKZ AB dimer is minimized with 5000 conjugate gradient steps using NAMD/CHARMM22. Calculated spectra ignore all CH₃ group hydrogens. The 6000 and 4000 refer to bandwidths in cm⁻¹. Calculated spectrum show the smallest RMSD 6000 OL ($\times$), the largest RMSD 4000Jy (o), and an example helical parameter result, 4000 Hy ($+$). The blue dots ($•$) are the experimental SRCD (CD0000114000) [44,59]. The CATH fold classification [53] is a combination of few secondary structures/irregular for chain A and mainly alpha/up-down bundle for chain B. Note: the complete hexameric asymmetric unit of the protein was not treated and neither were the any of the ligands (bacteriochlorophyll A, benzamidine, β-octylgucoside, rhodopin glucoside).