The work in this thesis is divided into two aims. The first aim is to provide a detailed analysis of water molecules at protein-protein interfaces as well as quantifying their contributions with respect to different residue types. To achieve this aim a data set of 4741 water molecules abstracted from 179 high-resolution (≤ 2.30 Å) X-ray crystal structures of protein-protein complexes was analyzed with a suite of modeling tools based on HINT. The second aim is to observe the effect of adding interfacial water molecules in developing a model for the protein-protein interaction between pyridoxal kinase and serine hydroxymethyltransferase. This model was created to explore the possibility of the formation of a channel between the two proteins upon interaction providing a safe way to transport the substrate pyridoxal 5’-phosphate (active form of vitamin B6). This work demonstrates a substantial progress in the understanding of the role of water molecules in protein-protein binding.
| Identifer | oai:union.ndltd.org:vcu.edu/oai:scholarscompass.vcu.edu:etd-3577 |
| Date | 15 August 2011 |
| Creators | Ahmed, Mostafa H. |
| Publisher | VCU Scholars Compass |
| Source Sets | Virginia Commonwealth University |
| Detected Language | English |
| Type | text |
| Format | application/pdf |
| Source | Theses and Dissertations |
| Rights | © The Author |
Page generated in 0.0039 seconds