1. Conformational Homogeneity and Excited-State Isomerization Dynamics of the Bilin Chromophore in Phytochrome Cph1 from Resonance Raman Intensities 
Katelyn M. Spillane, Jyotishman Dasgupta, Richard A. Mathies 
Biophysical Journal 
Volume 102, Issue 3, Pages (February 2012)
DOI: /j.bpj
Copyright © 2012 Biophysical Society Terms and Conditions

2. Figure 1
Structural changes of the bilin chromophore during the Pr-to-Pfr photocycle in phytochrome. The ground-state Pr chromophore structure is depicted as ZZZssa at the AB, BC, and CD rings, respectively. Photoexcitation results in isomerization of the C15=C16 methine bridge between the C- and D-rings, yielding the red-shifted ZZEssa product Pfr. The D-ring in Pfr is twisted out of the plane by ∼20° due to the methyl-methyl steric interaction.
Biophysical Journal  , DOI: ( /j.bpj )
Copyright © 2012 Biophysical Society Terms and Conditions

3. Figure 2
Absorption spectra of the Pr and Pfr forms of phytochrome Cph1 in TES-glycerol buffer at 295 K. The Pr form absorbs light maximally at 660 nm whereas the Pfr form absorbs maximally at 700 nm. The two forms are photoconvertible at room temperature.
Biophysical Journal  , DOI: ( /j.bpj )
Copyright © 2012 Biophysical Society Terms and Conditions

4. Figure 3
Absorption spectrum of the Pr form of phytochrome Cph1 at (a) 295 K in TES-glycerol buffer (pH 8.0) and (b) 100 K in TES-glycerol buffer mixed with glycerol at a v/v ratio of 35:65. The calculated curves are shown (dashed lines) superimposed on the individual spectra and were determined using the parameters listed in Table 1.
Biophysical Journal  , DOI: ( /j.bpj )
Copyright © 2012 Biophysical Society Terms and Conditions

5. Figure 4
Absorption spectrum of the Pfr form of phytochrome Cph1 at (a) 295 K in TES-glycerol buffer (pH 8.0) and (b) 100 K in TES-glycerol buffer mixed with glycerol at a v/v ratio of 35:65. The calculated curves are shown (dashed lines) superimposed on the individual spectra and were determined using the parameters listed in Table 2.
Biophysical Journal  , DOI: ( /j.bpj )
Copyright © 2012 Biophysical Society Terms and Conditions

6. Figure 5
Stimulated Raman spectra (solid lines) of (a) 1.25 × 10−4 M Cph1 Pr and (b) 8.75 × 10−5 M Cph1 Pfr phytochrome obtained with a 3 μJ Raman pump pulse centered at 790.4 nm. Integrated areas of peak fits were used to determine the absolute Raman cross sections presented in Tables 1 and 2 using the 1049 cm−1 symmetric stretch of NO3− as an external standard. Peaks at 1049 cm−1 (indicated by ∗) are due to the glycerol internal standard, and the features at 650 and 760 cm−1 (indicated by a †) are detector artifacts.
Biophysical Journal  , DOI: ( /j.bpj )
Copyright © 2012 Biophysical Society Terms and Conditions

7. Figure 6
Representation of the initial geometric changes about the C- and D-rings of the excited Pfr form of phytochrome Cph1. (Arrows) Geometry change along the torsional and C15–H HOOP coordinates on a linear excited-state surface 20 fs after excitation. The phase of the torsion is chosen to swing the D-ring C17–CH3 group away from the steric clash with the C-ring. The phase of the C15–H HOOP is chosen to be consistent with the increase in the C14–C15 bond order upon π → π∗ excitation; this motion also keeps the C15 hydrogen on the same side of the C15=C16 bond during the isomerization.
Biophysical Journal  , DOI: ( /j.bpj )
Copyright © 2012 Biophysical Society Terms and Conditions