Rhodopsin, structural modeling

Teller, D. C., Okada, T., Behnke, C. A., Palczewski, K., and Stenkamp, R. E., Advances in determination of a high-resolution three-dimensional structure of rhodopsin, a model of G-protein-coupled receptors (GPCRs), Biochemistry, 40(26), 7761-7772, 2001. 

In Sections II and III, the crystal structure of rhodopsin is briefly reviewed and compared with the dynamic structure in micellar solutions and membranes as inferred from the biophysical methods mentioned above. A structural model of the cytoplasmic surface derived from solution NMR of peptides has been presented (Ifeagle et al., 1997 Katagadda et al., 2001), but this approach does not provide direct information on... 

Fig. 7. (A) Structural model of rhodopsin showing the location of cysteine substitution mutants in the C-terminal tail (325, 326, 328, 331, 332, 335-340). Mutants at 331 and 332 are not represented because these sites were not modeled in the crystal structure. Also shown are sites in C3 (dark spheres at 242, 245, 246, 249) and 65 in Cl discussed in the text. Dotted lines indicate sequences not modeled in the crystal structure. (B) Top row EPR spectra of 326R1 and 338R1, representing sites in the proximal and distal portions of the C-terminal tail, respectively center and bottom rows the two components of a and (3, respectively, resolved by spectral subtraction. In 338R1, the immobilized component is minor and is nearly invisible in the experimental spectrum.

Fig. 8. (A) Structural model of rhodopsin showing the location of cysteine substitution...

Fig. 10. (A) Structural model of rhodopsin showing the location of cysteine substitution mutants (136-155) in C2 and adjacent sequences in TM3 and TM4. (B) fsa values computed from the crystal structure for both A and B molecules (upper panel), and 5 1 (the inverse central linewidth) (bottom panel) for R1 at each site. The shaded vertical bars mark residues in TM3 and TM4.

Fig. 11. (A) Structural models of rhodopsin showing the location of cysteine substitution mutants in C3 and adjacent sequences in TM5 and TM6 (residues 225-256). The left panel is based on the crystal structure (1HZX, A chain), and the right panel on SDSL data for the solution structure. In each panel, both top (upper) and side (lower) views of the structure are shown. Individual residues in the sequence are represented by the Ca-Cp bonds in order to indicate the direction in which the side chains project. The bonds are coded according to local maxima (white), minima (black), or in-between (gray) values of II (O2). (B) /sa values computed from the crystal structure for both A and B molecules (upper panel), and n (O2) and II (NiEDDA) for R1 at each site (lower panel). The shaded vertical bars mark residues in TM5 and TM6, as indicated.

Fig. 17A (see color insert) shows a ribbon model of the rhodopsin structure indicating the residues assigned to the interface in each helix by a sphere centered on the corresponding of-carbon. Also shown is a sphere on the a-carbon of residue 314, which is located in the interface (see Section III,F). Clearly, these residues define a unique plane of intersection of the molecule with the membrane-aqueous interface. The shaded band in Fig. 17 represents a phospholipid bilayer with a phosphate-phosphate distance of 40 A, the expected thickness of the bilayer in the disk membrane (Saiz and Klein, 2001). The outer interface of the bilayer is positioned so that the polar head groups coincide with the intersection plane defined by the data in Fig. 16. This procedure then fixes the intersection plane of the molecule on the extracellular surface as well.

The position of rhodopsin in the membrane deduced from SDSL data is compatible with the topography of surface residues in the molecule. Figure 17B shows a space-filling model of the rhodopsin structure with residues color coded according to charge, polarity, and identity of tyrosines and tryptophans. It is clear that the demarcation between the charged and hydrophobic residues on the cytoplasmic surface defines... 

A structural model of the trimeric G protein and the receptor is presented in Fig. 5.19. In this model, the known structures of the ground state of rhodopsin and the structures of the transducin Gta- GDP (fly) complex have been modeled, taking into account the location of the lipid anchors and the known interaction sites between the receptor and the G protein ( Hamm, 2001). 

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