Fig. 5.

Critical folding residues in rhodopsin. (A) first and GNM core residues. Both methods select the cysteine residues forming the critical disulfide bond, shown by space-filling yellow spheres. The other seven residues found in common by these methods are shown in cyan. The remaining seven GNM fast mode peak residues are shown in green, and the remaining first core residues from line C in Fig. 2 are shown in red. The two next largest rigid clusters, from first analysis, are shown in violet and pink to lie at the CP end of the TM region. (B) Local neighborhood of the most stable residues. The nine residues in common between first and GNM fast mode peaks (cyan and yellow in A) are shown by thick, colored sticks. At the center of this cluster are the cysteine residues (C110 and C187 in yellow) that form the critical disulfide bond. F103 (green), five of the common residues (E113, G114, P180, C185, and S186 in red), and the RET chromophore (Retinal, cyan) are located within 4 Å of this disulfide bond and span the TM-EC interface (suggested by the thick blue curve). The other residue in common between these methods, R177 (blue), demonstrates how this local stability is propagated across side-chain interactions. Side chains for a few of the 45 first folding core residues are shown by thin sticks to orient the reader.