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A study of rhodopsin as a potential phospholipid scramblase

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A study of rhodopsin as a potential phospholipid scramblase

Transbilayer phospholipid transfer (flip–flop) is a vital process for all cellular life. This intrinsically slow process is facilitated by integral membrane proteins called flippases and scramblases, which lower the free energy barrier to such a level that phospholipid flip–flop can rapidly occur either with help of external energy sources such as ATP or by thermal fluctuations alone. The existence of flippases has been known for some time, but the identities of the phospholipid translocators are still unknown. The existence of scramblases is less clear, since only related gene sequences have been identified so far. Also, the mechanisms by which phospholipids carry out flip–flops are yet to be identified. Further knowledge on scramblase activities could be helpful in understanding and preventing many diseases. For instance, programmed cell death begins when phosphatidylserine flips in an uncontrollable manner from the cytosolic leaflet to the extracellular side and this process is assumed to take place due to certain membrane proteins. This event in turn creates a signal for extracellular phagocytes by marking the cell for apoptosis. Apoptotic cells are often linked to tumor progression in which it is suggested that mutations in the scramblase genes can facilitate cancer growth. Proper scramblase activation during cancer progression could be used to remove harmful cells. Recent experimental studies have suggested that opsin, one of the G protein- coupled receptors found in photoreceptor cells of the retina, is a phospholipid flip- pase and its counterpart rhodopsin could be a possible scramblase. The purpose of this thesis is to use atomistic molecular dynamics simulations to examine the phos- pholipid scrambling properties of rhodopsin. The results can be used as a basis for further research regarding the subject. The possible flipping routes are investigated using steered MD simulations, and the free energy differences along the translocation paths are calculated by the umbrella sampling method. The results show that rhodopsin significantly lowers the free energy barrier of the membrane, thus functioning as a flippase. The observed flip–flop route taken by the phospholipids is located near the surface of rhodopsin.

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