Paper Citing NAMD - Abstract
Chen, Min-Hsuan; Sandberg, Daniel J.; Babu, Kunnel R.; Bubis, Jose; Surya, Arjun; Ramos, Lavoisier S.; Zapata, Heidi J.; Galan, Jhenny F.; Sandberg, Megan N.; Birge, Robert R.; Knox, Barry E.
Conserved Residues in the Extracellular Loops of Short-Wavelength Cone Visual Pigments
BIOCHEMISTRY, 50:6763-6773, AUG 16 2011
The role of the extracellular loop region of a short-wavelength sensitive pigment, Xen opus violet cone opsin, is investigated via computational modeling, mutagenesis, and spectroscopy. The computational models predict a complex H-bonding network that stabilizes and connects the EC2-EC3 loop and the N-terminus. Mutations that are predicted to disrupt the H-bonding network are shown to produce visual pigments that do not stably bind chromophore and exhibit properties of a misfolded protein. The potential role of a disulfide bond between two conserved Cys residues, Cys(105) in TM3 and Cys(182) in EC2, is necessary for proper folding and trafficking in VCOP. Lastly, certain residues in the EC2 loop are predicted to stabilize the formation of two antiparallel beta-strands joined by a hairpin turn, which interact with the chromophore via H-bonding or van der Waals interactions. Mutations of conserved residues result in a decrease in the level of chromophore binding. These results demonstrate that the extracellular loops are crucial for the formation of this cone visual pigment. Moreover, there are significant differences in the structure and function VCOP compared to that in rhodopsin. of this region in
