One focus goal that science always works towards is an understanding of biological structures, with proteins being one of the main research goals. Sequencing proteins is currently a time-exhausting task, so focus is being put on trying to use nanopores in a similar way as in DNA sequencing for proteins. In this report, the neighbouring amino acids in the same peptide as the amino acid being sequenced are varied and the change in ionic current from the pore based on the neighbouring amino acids is analysed. This was done by using Molecular Dynamics program NAMD. A peptide was placed in the center of different silicon nitride pore structures inside a water box with ions and was simulated with an added electric field. The drop in current was checked for 4 different peptide systems and one check for the empty pores. The results presented in the report show that changing the neighbouring amino acids increases the current measured, therefore making the current blocking worse when mixing nearby amino acids. However, the differences are very small and similar amino acids give wildly different values. A larger evaluation with more computational power seems reasonable for a more definitive result.
| Identifer | oai:union.ndltd.org:UPSALLA1/oai:DiVA.org:uu-531502 |
| Date | January 2024 |
| Creators | Freedman, Victor |
| Publisher | Uppsala universitet, Kemisk och biomolekylär fysik, Uppsala universitet, Materialteori |
| Source Sets | DiVA Archive at Upsalla University |
| Language | English |
| Detected Language | English |
| Type | Student thesis, info:eu-repo/semantics/bachelorThesis, text |
| Format | application/pdf |
| Rights | info:eu-repo/semantics/openAccess |
| Relation | FYSAST ; FYSMAS1232 |
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