Hofma, Julia Bo (2021) Backmapping of Coarse-Grained Ezrin-Membrane Complexes. Bachelor's Thesis, Physics.
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Abstract
The proteins ezrin and merlin have opposite roles in glioblastoma. Since their tumor-influencing function is located in the FERM domain, it is interesting to investigate the FERM domain. In all-atom Molecular Dynamics simulations, the ezrin FERM domain showed a binding mode which we call the primary binding mode, when bound to a PIP2 containing POPC membrane. Coarsegrain Molecular Dynamics simulations showed, next to the primary binding mode, another binding mode which we call the secondary binding mode. That binding mode was investigated in this paper. Backmapping using an established routine was performed to get from the coarse-grained system to an all-atom system. The resulting all-atom structures were investigated in detail. (...) Despite its shortcomings, the obtained all-atom systems may be used to validate the binding mode in subsequent all-atom simulations. This validation was done in this project for one of the backmapped systems. Although we have to be careful with drawing conclusions since the backmapping was only partly correct, the outcome of the validation simulation was that the secondary binding mode is not a stable binding mode in all-atom.
| Item Type: | Thesis (Bachelor's Thesis) |
|---|---|
| Supervisor name: | Giessen, E. van der and Onck, P.R. and Stadtmuller, T.H.J. |
| Degree programme: | Physics |
| Thesis type: | Bachelor's Thesis |
| Language: | English |
| Date Deposited: | 02 Jul 2021 11:24 |
| Last Modified: | 02 Jul 2021 11:24 |
| URI: | https://fse.studenttheses.ub.rug.nl/id/eprint/24875 |
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