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Georgia State University

Calculated Vibrational Properties of Pigments in Protein Binding Sites

Tuesday January 17, 2012

1:30pm PHYS 242

Coffee and doughnuts served at 1:15pm in the same room.

http://www.phy-astr.gsu.edu/hastings/index.html

Detailed computational studies of the vibrational properties of quinones involved in solar energy conversion processes in photosynthetic reaction centers have been undertaken. The primary focus of these studies has been the calculation of the vibrational properties of the ubiquinone molecule that occupies the QA binding site in purple bacterial photosynthetic reaction centers. The applicability of the calculations is demonstrated via simulation of available experimental (isotope edited) FTIR difference spectra. The experimental FTIR spectra for neutral ubiquinone in solution are very different from the spectra associated with ubiquinone in the QA binding site. For this reason a QM/MM method (ONIOM method) was used in which the pigment was treated using density functional theory based methods while the protein was treated using molecular mechanics. The ONIOM calculated FTIR difference spectra accurately model the experimental spectra, and help resolve long standing and controversial issues related to how the ubiquinone in the QA binding site is hydrogen bonded. To further validate the usefulness of the ONIOM approach experimental isotope edited FTIR spectra obtained using purple bacterial reaction centers with a range of chainless symmetrical quinones incorporated were modeled. The agreement between the calculated and experimental spectra is outstanding. This work demonstrates that a computational-based interpretation of FTIR difference spectra associated with protein-bound cofactors is now possible. This approach will be applicable to FTIR studies of many pigment-containing proteins. Reference: Lamichhane and Hastings (2011) Calculated vibrational properties of pigments in protein binding sites, PNAS 108, 10526-10531.