The thesis presented here describes the steps that were taken in an attempt to solve the protein structure of MenD via molecular replacement and multiple wavelength anomalous dispersion. The introduction provides background on menaquinone biosynthesis and the role of MenD in this metabolic pathway. Also, a detailed discussion of the DC Family of enzymes, a subgroup of ThDP dependent enzymes, which MenD is a part of, is included.<p>
Utilizing various software packages a 1.9 Å data set was processed and analyzed in an attempt to provide a molecular replacement result. When molecular replacement was deemed incapable of solving the phase problem of the data set, the production of SeMet protein was attempted to allow for MAD phasing.<p>
A homology model of MenD was produced using the program Modeller with benzaldehyde lyase as a template. A structure based sequence alignment was done with all DC Family enzymes with structures published. Then a second structure based sequence alignment was done to compare the same set to the Modeller model. This was done to gain a deeper understanding of MenD and how it interacts with its cofactors ThDP and Mg2+. Furthermore, these results were used to implicate potential active site residues.
| Identifer | oai:union.ndltd.org:LACETR/oai:collectionscanada.gc.ca:SSU.etd-04092009-161657 |
| Date | 15 April 2009 |
| Creators | Toogood, Ronald Daniel |
| Contributors | Sanders, David A. R., Palmer, David |
| Publisher | University of Saskatchewan |
| Source Sets | Library and Archives Canada ETDs Repository / Centre d'archives des thèses électroniques de Bibliothèque et Archives Canada |
| Language | English |
| Detected Language | English |
| Type | text |
| Format | application/pdf |
| Source | http://library.usask.ca/theses/available/etd-04092009-161657/ |
| Rights | restricted, I hereby certify that, if appropriate, I have obtained and attached hereto a written permission statement from the owner(s) of each third party copyrighted matter to be included in my thesis, dissertation, or project report, allowing distribution as specified below. I certify that the version I submitted is the same as that approved by my advisory committee. I hereby grant to University of Saskatchewan or its agents the non-exclusive license to archive and make accessible, under the conditions specified below, my thesis, dissertation, or project report in whole or in part in all forms of media, now or hereafter known. I retain all other ownership rights to the copyright of the thesis, dissertation or project report. I also retain the right to use in future works (such as articles or books) all or part of this thesis, dissertation, or project report. |
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