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H. Guo; Computational Studies on RPE65. Invest. Ophthalmol. Vis. Sci. 2007;48(13):2958.
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To obtain structural models for both forms of RPE65 and to determine the interactions between the proteins and their ligands by computational methods.Materials and
The homology comparative method and molecular mechanics method have been used to predict the structure of RPE65. A preliminary model of sRPE65 has been obtained from the 3D-PSSM server and the Scwrl program. The final model for sRPE65 is obtained by optimizing its preliminary structure through five molecular mechanics programs and two widely used force fields in Jackal and Tinker software package. The model for mRPE65 is built up through the autodock program and VMD program based on the model for sRPE65 because these two proteins have the same amino acid sequence and only differ in their post translation modifications (i.e., palmitoylation status). The interactions between the protein and their ligands have also been studied by the autodock program and ligplot program. Finally, by using an iterative method, the locations of binding sites in sRPE65 and mRPE65 for their substrate are identified.
The tertiary structure consists of three domains and each of them contains a right handed twisted beta barrel. Three palmitic acids covalently bind with mRPE65 at Cys231, Cys329, and Cys330. The binding site of RPE65 is located in the beta barrel of domain two and close to Leu450. Tyr368His and Leu450Met mutations have been reported to cause dysfunction of mRPE65 and the calculated docking energies for the mutants support this observation.
The RPE65 protein is located in RPE cells and plays a very important role in the visual cycle. The protein exists in two forms: sRPE65 and mRPE65 and the conversion between these two forms regulates the visual cycle. Dysfunction of RPE65 leads to numerous diseases such as childhood-onset retinal degeneration. The model for sRPE65 and mRPE65 suggests that RPE65 is cytosolic but mRPE65 is membrane associated due to the palmitoylation of mRPE65 which anchor the protein to the membrane. The locations of the binding sites are consistent with known mutations of RPE65 that cause its dysfunction. The preference of sRPE65 for the all trans retinol and the preference of mRPE65 for all trans retinyl ester are also consistent with these models.
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