Computational simulation studies of RPE65, alpha crystallin, and ABCR

Includes bibliographical references (pages [286]-294).RPE65, α-crystallin, and ABCR are three important proteins in the visual process. Their dysfunctions cause numerous visual system diseases, such as: autosomal recessive retinitis pigmentosa, cataract, and Stargardt disease. The investigations on their atomic structures and their interactions with ligands are helpful for understanding their functions and the visual system diseases listed above. A combination of computational methods is used to predict protein three-dimensional structures on the basis of their amino acid sequences. The fold recognition method was used to obtain protein templates; molecular mechanics programs were used to carry out optimizations on preliminary models; equilibrated models were obtained from molecular dynamics simulations; and the protein binding sites and their interactions with ligands were investigated by docking programs and the LIGPLOT program. The RPE65 protein is located in the retinal pigment epithelial cells and plays an important role in the visual cycle. Although numerous experimental results demonstrate that it participates in the visual cycle, its detailed structure and function are not clear yet because of difficulties with its isolation and crystallization. Its three-dimensional folding is predicted on the basis of its sequence information. The binding sites of sRPE65 and mRPE65 for their ligands are determined and the main interacting regions are ascertained by using docking methods and steered molecular dynamics simulations. The validity of the models is supported by the experimental observations. α-crystallin is the main structural protein in the mammalian lens. In addition to contributing to the refractive properties of the lens, α-crystallin also exhibits chaperone activity. In solution, it exists as an aggregate with a distribution of different sizes, making crystallization extremely difficult. Therefore, its tertiary and quaternary structures are still unknown. Computational studies on α-crystallin subunits and dimers are useful in the investigation of their structures and aggregation mechanisms. Using these methods, we have identified the most likely interacting regions and key residues in the aggregation process. The α-crystallin subunit models were built up and refined, while the dimer models were built by the docking method based on the subunit models. The dimer models reach an equilibrium state through molecular dynamic simulations, and the interactions between protein subunits were studied. Several interacting regions and key residues which form hydrogen bonds and Van der Waals interactions between the subunits have been identified, The results are in excellent agreement with previously reported experimental determinations of surface residues. These data also support the validity of the present model. ABCR is an intrinsic membrane protein embedded in the membrane of the rod outer segment. Its MSD domains are responsible for transferring all-trans retinal from disc lumen to cytosol. The atomic tertiary structures of MSD-1 and MSD-2 domains were predicted based on their sequence information. The equilibrated models were obtained from the molecular dynamics simulations.Ph.D. (Doctor of Philosophy