Modeling of Biological Membranes by a Coarse-grained Approach
Date
2018-03-07
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Abstract
In this thesis, Martini coarse-grained simulations were performed to investigate the dynamic behavior of lipids and proteins in two different membrane-protein systems. In the first study, I simulated a chromatophore membrane. The model consists of the cytochrome-bc1 from Rhodobacter sphaeroides embedded in an asymmetric distribution of three lipid species. Analyses of a simulation carried out over 40 microseconds highlight specific lipid-protein interactions that are of biological relevance for ongoing research. The second study works towards the modeling of biological membranes at a larger scale. We developed a protocol to build and simulate complex models more representative of physiological membranes, in terms of crowdedness of proteins and lipid diversity. Several eukaryotic plasma membrane models were generated. Analyses of a system consisting of 150 proteins with more than 60 lipid species and simulated for 6 microseconds are discussed.
Description
Keywords
biological membranes, coarse-grained simulation, molecular dynamics simulation, large-scale membrane models, Martini model, lipid-protein interactions
Citation
Delgado-Magnero, K. H, (2018). Modeling of Biological Membranes by a Coarse-grained Approach (Master's thesis, University of Calgary, Calgary, Canada). Retrieved from https://prism.ucalgary.ca. doi:10.11575/PRISM/20521