This tool searches protein data bank (PDB) files for photosynthetic pigments (currently chlorophyll a, chlorophyll b, pheophytin a, bacteriochlorophyll a are supported), and uses a vacuum-phase transition electrostatic potential (TrESP) model [J. Phys. Chem. B 2006, 110, 17268] to calculate inter-site electronic couplings and the Qy absorption spectrum for the protein. The Charge Density Coupling (CDC) [Photosynth Res 95, 197 (2008)] and normal-coordinate structural decomposition (NSD) [J. Phys. Chem. B, 101, 1684-1699 (1997), Biophys. J., 93, 2240-2254 (2007)] models can also be used to predict pigment site energies based on local electrostatics and/or ring deformation. 

VERSION UPDATE: Update implemented Dec 17, 2021 reverses the sign on calculated CD spectra. (See "How does it work" documentation in main simulation window for details.) 

Coupling calculations are carried out as described in [Reppert et al. J. Phys. Chem. B 2010, 114, 36, 11884–11898]. Excitonic structure calculations are similar, but use a generic variable-width Gaussian profile for homogeneous broadening rather than a single-site absorption spectrum.

Molecular Dynamics force fields for chlorophyll pigments are adopted from the following sources:

• For Chlorophyll a: K. Karki and D. Roccatano, J. Chem. Theory Comput. 2011, 7, 4, 1131 [https://pubs.acs.org/doi/10.1021/ct1004627]
• For Bacteriochlorophyll a: M. Ceccarelli, P. Procacci, M. Marchi, J. Comput. Chem. 2002, 24, 129 [https://doi.org/10.1002/jcc.10198] We thank Yongbin Kim, Jack Lawrence, and Lyudmila Slipchenko for providing GROMACS topology files for this force field.

The TrESP protocol and vacuum transition charges are taken from the following publications: 

• Madjet et al. J. Phys. Chem. B, 110, 34, 17268–17281 [https://doi.org/10.1021/jp0615398] (Bacteriochlorophyll a & Chlorophyll a)
• Renger et al. J. Phys. Chem. B 2007, 111, 35, 10487–10501 [https://doi.org/10.1021/jp0717241] (Chlorophyll b, transition charges q₁₀)
• Renger, T. Biophysical Journal 2008, 95, 105-119, [https://doi.org/10.1529/biophysj.107.123935] (Pheophytin a)

Ground state (q₀₀) and excited state (q₁₁) partial charges for Chlorophyll b were kindly provided by T. Renger.

The CDC method is described here:

• Adolphs, J., Müh, F., Madjet, M.EA. Renger, T. Photosynth Res 95, 197 (2008). [https://doi.org/10.1007/s11120-007-9248-z]

Normal-coordinate structural decomposition (NSD) calculations based on the work of Jentzen et al. and Zucchelli et al:

• Jentzen, Walter; Song, Xing-Zhi; Shelnutt, John A.; J. Phys. Chem. B, 101, 1684-1699 (1997)
• Zucchelli, Giuseppe; Brogioli, Doriano; Casazza, Anna Paola; Garlaschi, Flavio M.; Jennings, Robert C. Biophys. J., 93, 2240-2254 (2007)

Phonon spectral density parameters use the log-normal fits reported by Kell et al [J. Phys. Chem. B 2013, 117, 24, 7317–7323] to experimental difference-fluorescence-line-narrowed (dFLN) data from the following papers:

• CLA-WSCP and CLB-WSCP: J. Pieper, M. Rätsep, I. Trostmann, H. Paulsen, G. Renger, and A. Freiberg. [J. Phys. Chem. B 2011, 115, 14, 4042–4052]
• CLA-CP29: M. Rätsep, J. Pieper, K.-D. Irrgang, and A. Freiberg [J. Phys. Chem. B 2008, 112, 1, 110–118]
• BCA-FMO: M. Rätsep and J. Freiberg [J. Luminescence 2007, 127, 1, 251-259]

Vibrational spectral densities (frequencies and Huang-Rhys factors) are taken from the same experimental dFLN papers from which the corresponding phonon densities are derived.

Researchers should cite this work as follows:

• Safa Ahad, Chientzu Lin, Michael Earl Reppert (2023), "Photosynthetic Protein Spectroscopy Lab," https://nanohub.org/resources/pigmenthunter. (DOI: 10.21981/744F-DE56).

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1. Electrical and Optical properties
2. fluorescence imaging
3. molecular spectroscopy
4. nano/bio
5. photosynthesis
6. photosynthetic proteins
7. PigmentHunter
8. proteins