Rhodopsin secondary structure

FIGURE 125.1 Structure of bovine rhodopsin. Secondary structure of rhodopsin is shown in (a). The three-dimensional structure of rhodopsin is shown in (b). The coordinate (IF88) was retrieved from the Protein Data Bank. 

Figure 5.1.1-1 Predicted secondary structure of salamander red rod rhodopsin. 6...

Monomolecular films of the membrane protein rhodopsin have been investigated in situ at the air-water interface by PM-IRRAS and X-ray reflectivity in order to find conditions that retain the protein secondary structure [104]. The spreading of rhodopsin at 0 or 5 mN/m followed by a 30 min incubation time at 21 °C resulted in the unfolding of rhodopsin. In contrast, when spreading is performed at 5 or 10 mN/m followed by an immediate compression at, respectively, 4 or 21 °C, the secondary structure of the protein is retained. 

Bohr, H., Bohr, J., Brunak, S., Cotterill, R. M., Lautrup, B., Norskov, L., Olsen, O. H. Petersen, S. B. (1988). Protein secondary structure and homology by neural networks. The alpha-helices in rhodopsin. FEBS Lett 241,223-8. 

It has been shown that n (O2) for R1 is in fact proportional to the fractional solvent accessibility ( Jsa) of the native side chain at the same site computed from the corresponding crystal structure (Isas et al., 2002). The sequence dependence of the solvent accessibility, measured by either fsa or n (O2), is a fingerprint for a protein fold. For example, solvent accessibility is periodic through regular secondary structure, and the period and phase of the function identify the type of secondary structure and its orientation in the protein, respectively. In nonregular secondary structure encountered in loops, the solvent accessibility is not necessarily periodic, but the functional dependence on sequence remains characteristic of the fold. Thus, comparison of a computed from a crystal structure and n (O2) determined experimentally for the protein in solution is a convenient and efficient way of comparing the solution and crystal structures. This will be the method used below for rhodopsin. 

AMI and PM3 for the description of the secondary structure in peptides and proteins has been performed recently [116], and it was shown that the description of the peptide conformers is considerably improved by OM1 and OM2 compared with AMI and PM3, although in some cases, there still were discrepancies with available ab initio data. MNDO-PSDCI molecular orbital theory has recently been used to calculate the spectroscopic properties of sensory rhodopsin from Natronobacterium pharaonis [117], demonstrating that MNDO is also a reliable tool for the calculation of optical spectra. 

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