Structure determination of proteins is vital for the understanding of their function. It often relies on techniques that use intense X-ray pulses to create diffraction patterns of protein crystals, which then contain information on the three-dimensional structure of the crystallised protein. An emerging technique called Single Particle Imaging (SPI) aims to make possible the structure determination without the need for crystallisation of the proteins, by taking diffraction patterns from many individual proteins. Translating the diffraction patterns to spatial geometry is a daunting task that requires sophisticated algorithms which are not always able to determine the structure because of fundamental uncertainties in the recovery process. To improve the structure determination process, one can try to rotate the protein to a known orientation using electric fields before the measurement takes place. However, as a result of how these experiments are performed, the proteins may have water around them during this orientation phase. Using molecular dynamics (MD) on ubiquitin, a small protein found in all eukaryotic cells, it is shown that a layer of water around a protein does not only help to achieve orientation faster (compared to an identical protein without this layer), the water also provides the protein with increased structural stability.
| Identifer | oai:union.ndltd.org:UPSALLA1/oai:DiVA.org:uu-473458 |
| Date | January 2022 |
| Creators | Elfrink, Gideon |
| Publisher | Uppsala universitet, Institutionen för fysik och astronomi |
| 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 ; FYSMAS1176 |
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