Gaifas, Lorenzo (2019) Modeling alpha-helical pore-forming-protein nanopores in Martini. Master's Research Project 1, Biomolecular Sciences.
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Abstract
In nanopore analytics (NA), individual molecules block the entrance of a single nanopore, generating a blockade of ionic current which can be studied to identify properties of the analyte. Because of its high resolution, low cost and simplicity, this method is gaining popularity, employing both inorganic pores and biological ones. Pore-forming-proteins (PFPs) are often used as biological nanopores, having several advantages on their artificial counterparts, such as being easier to produce and being more customizable in shape and charge. However, our knowledge on PFPs structure and folding is not yet refined enough to allow us to design nanopores with fine-tuned properties. Here, we study the PFP FraC with the use of coarse-grained molecular dynamics, in order to understand the mechanisms of its pore and to find a common ground with experimental data. Knowledge on this protein has already been gathered in the field of NA, which makes it a good candidate for this study. FraC models were created with two different versions of the Martini force field -- v2 and v3 -- to compare the applicability of each version to the study of PFPs. Results indicate that v3 is better than v2 at simulating the behaviour of PFPs, though it still needs some parameters to be tuned properly. With either force field, modeling FraC proved to be not trivial, as there are several factors whose contributions are still poo understood, such as the role of sphingomyelins.
| Item Type: | Thesis (Master's Research Project 1) |
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| Supervisor name: | Marrink, S.J. and Maglia, G. and Bruininks, B.M.H. |
| Degree programme: | Biomolecular Sciences |
| Thesis type: | Master's Research Project 1 |
| Language: | English |
| Date Deposited: | 22 Jan 2020 08:43 |
| Last Modified: | 22 Jan 2020 08:43 |
| URI: | https://fse.studenttheses.ub.rug.nl/id/eprint/21402 |
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