IIIT Hyderabad Publications |
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Ion Selectivity and Permeation Mechanism in a Cyclodextrin-based ChannelAuthor: Musunuru Pratyusha Date: 2021-11-18 Report no: IIIT/TH/2021/108 Advisor:Deva U Priyakumar AbstractIon channels are proteins present across the lipid bilayer membrane possessing a pore that selectively allows certain ions to pass through. They control various cellular processes and mechanisms in living organisms that are vital for the functioning of cells. Synthetic ion channels are a promising technology in the medical and materials sciences because of their ability to conduct ions. Synthetic ion channels based on cyclodextrin, a cyclic oligomer of glucose, are of particular interest because of their non-toxicity and bio-compatibility for use in real-life pharmaceutical applications. This study uses the topology from the experimental findings for the construction of the cyclodextrin channels and investigates the permeability and selectivity of each of the three ions proposed. This work employs umbrella samplingbased molecular dynamics simulations in an explicit lipid bilayer environment to probe ion transport through the different kinds of cyclodextrin-based channels and identifies the channel types that are best suited to serve as synthetic ion channels. Free energy profiles show that the connectivity in the channel determines whether the channel is more selective towards cations or anions. The energy barrier for ion transport is governed by the number of glucose molecules constituting the cyclodextrin units of the channel. Furthermore, channels constructed from cyclodextrin units with the highest number of glucose molecules pose the least energy barrier to ion transport, since they facilitate the retention of a large number of coordinating water molecules during the transport process. A detailed mechanism is proposed for ion transport through these channels. An overall picture of how the permeation of the ions is influenced by the different variants of cyclodextrin channels and how the ions respond to different regions of the channels is discussed in this study. Findings from this study will aid in designing cyclodextrin-based channels that could be either cation-selective or anion-selective, by modifying the linkages of the channel or the number of glucose molecules in the cyclodextrin rings. Full thesis: pdf Centre for Computational Natural Sciences and Bioinformatics |
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