We propose a dual-scale approach to predict the native structures of retinal proteins (RPs) by combining coarse-grained (CG) Monte-Carlo simulations and all-atom (AA) molecular dynamics simulations to pack their transmembrane helices correctly. This approach has been applied to obtain the structures of five RPs, including bacteriorhodopsin (BR), halorhodopsin (HR), sensory rhodopsin I (SRI), sensory rhodopsin II (SRII), and (bovine) rhodopsin. The proposed CG model predicts a reasonably good structure of RPs in days using a desktop computer, which also gives clear physical picture for the packing, tilting, and orientation of transmembrane helices. A high-resolution protein structure is obtained from the AA molecular dynamics simulations by refining the predicted CG structure. The root mean square deviation in coordinates of backbone atoms from the X-ray structure is 1.89 Å for HR, 1.92 Å for SRII, 2.64 Å for BR, and 5.54 Å for rhodopsin. Reasonable predictions of HR structure can be obtained by this approach in the case of using predicted secondary structures with certain alignment error. Since the crystal structure of SRI is not available in the protein data bank, the predicted structure of SRI from our dual-scale approach is compared to that obtained from homology modeling.
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