TCBG Seminar

The effect of different structural characteristics of the retinal Schiff base on isomerization barriers and pKa of the chromophore

Doctor Emadeddin Tajkhorshid
Department of Molecular Biophysics
German Cancer Research Center
Heidelberg, Germany

Wednesday, September 9, 1998
1:00 pm (CT)
3269 Beckman Institute


The retinal Schiff base chromophore plays an important and central role in the function of retinal binding proteins, which demonstrate a wide range of biological activities. The photo-induced proton transfer in bacteriorhodopsin, and the process of vision are two of the most known and widely studied examples of these biological activities. With this regard, the isomerization barrier of different bonds and pKa of the chromophore are of essential importance. The role of different structural aspects of the retinal Schiff base molecule, including the number of double bonds and the methyl substitutions, as well as the potential effect of the ground state isomerization around different single and double bonds on the proton affinity of the molecule have been studied. The conjugated double bonds of the molecule provide a delocalized pi-electronic system, which is very sensitive to the electrostatic interaction of the chromophore with its environment. Furthermore, it influences the electron density on the Schiff base group (C=NH+), especially in the protonated form and, therefore, results in an increased pKa of the molecule, as compared to a non-conjugated Schiff base. The state of the protonation, in turn, influences the bond alternation and, consequently the isomerization barrier against rotation of different single or double bonds in the main chain. Because of the potentially significant steric interaction with the protein environment, modifying isomerization barriers may result in non-planar conformations of the chromophore, which are twisted at different single and/or double bonds. The extent and the location of the twist have significant effects on the pKa of the retinal Schiff base. The results demonstrate the importance of the consideration of the complete conjugated double bonds and, interestingly, methyl substitutions on the pKa and isomerization barrier of different bonds in the retinal Schiff base. The small machinery of the retinal Schiff base has been deliberately designed, and approximations in the structure of the model result in significant changes in calculated potential surfaces for the molecules.

Tea and coffee will be served in R3151 Beckman Institute at 2:15pm.

Main TCBG Seminars page