Fig. 6: Doorway state analysis of amide I modes resolves the frequency-structure relation of the F-actin.
From: Crowding alters F-actin secondary structure and hydration
a Experimental lineshape (brown solid line) overlaid with calculated IR modes (black sticks) of amide I stretch. The stick spectrum in black is generated by taking the square of the dot product of the eigenvectors of the one-exciton amide I Hamiltonian and the local amide I mode transition dipole moments, convoluted with Lorentzian lineshapes with a width of 0.01 cm−1. The shaded areas indicate six frequency regions for doorway state analysis, as listed in Table 1. b Visualization of monomer secondary structures and doorway state calculations for regions R1, R3, and R5 as indicated in the panel above. Amino acid residues are color-mapped to encode the amplitude and phase of each local amide I site within a given delocalized doorway state. Red and blue represent the positive and negative phases, respectively, where the intensity of the color encodes the amplitude of the amide I stretch. Sites that contribute little or none to a given state appear in white.
