Figure 1.
The tryptophan chromophores are shown in blue licorice.
Figure 2.
Calculated and experimental CD spectra of HCAII.
A. Near-UV: the experiment (black, continuous line); calculated using single crystal structure (blue, continuous line); averaged calculated spectrum using MD snapshots (red, continuous line); calculations using single crystal structure after scaling correction - red shifting by 6 nm (blue dotted line); averaged calculated spectrum using MD snapshots after scaling correction - red shifting by 6 nm (red dotted line); B. Far-UV: the experiment (in black); calculated with ab initio peptide chromophores using the crystal structure (in blue); with semi-empirical peptide chromophores and the crystal structure (in green); with ab initio chromophores based on MD snapshots (in red); with semi-empirical chromophores based on MD snapshots (in yellow).
Table 1.
Interactions between the aromatic chromophores in the near-UV CD of the wild type HCAII.
Table 2.
Interactions between chromophores in terms of distances and net interaction energies in the crystal structures and as averaged from the MD trajectory in the wild type HCAII.
Figure 3.
Calculated and experimental near-UV CD spectra of all tryptophan mutants of HCAII.
The experimental spectra are shown in black, the predicted spectra with the matrix method based on single structure are shown in blue; the predicted spectra with the matrix method based on the MD snapshots are shown in red; TDDFT calculations are shown in green.
Figure 4.
Comparison between the spectra calculated using Restricted Structural Model containing only the tryptophan and tyrosine chromophores (using TDDFT and the matrix method) and those calculated using the entire protein (using the matrix method).