Last Updated on 09/30/03
By Philip Bourne
Students are expected to develop an annotated Web resource which focuses on their protein of choice. The Web resource is the sole assessment and will be submitted by 12/13/03. An example of a resource can befound here. Students should have chosen their protein by the start of the second class.
The objective is to use the Web resources we have studied in class to create a detailed profile of the protein under study. In general terms this study should focus on the protein as a member of a larger family and details of the structure-function relationship that exists. The Web resource will be written using the BioEditor. The computers in the PC training room have copies of BioEditor available. Copies of BioEditor for use outside of the class can be downloaded for Win2000, Win2000Me, and Windows XP from http://bioeditor.sdsc.edu
Students should begin from the following template:
| Contents | Description |
| 1. Summary | Summarize the family to which the protein belongs, its biological function in relationship to known biochemistry and the relationship between sequence, structure and function. This should convey the maximum amount of information you can and should not be simply the abstract of an associated paper on structure function - show that you have accumulated some knowledge from your Web analysis. [200 words max] |
| 2. Disease | Provide details of any diseases of adverse physiological effects associated with the protein. [200 words max] |
| 3. Family | Characterize the protein family to which the specific protein belongs. [200 words max] |
| 4. Function | Provide a description of the function of the protein, including diagrams (eg pathways, mode of interaction) that illustrate the role of the protein.[ no limit] |
| 5. Structure | Provide a synopsis of the structure, including secondary structure, tertiary structure, bound ligands, unusual features (e.g., disulphide linkages, salt bridges, surface pockets. active sites etc.) [no limit] |
| 6. Properties | Provide physicochemical properties, MW, Isoelectric point, amino acid composition [brief] |
| 7. Sequence-function | Describe any known sequence signatures for the protein family [200 words max] |
| 8. Structure-function | Describe in detail the known relationship between structure and function [no limit] |
| 9. Evolution | Describe any sequence homology (local, global, close distant) include representative sequence alignments and a phylogenetic tree. [200 words max] |
| 10. Structure comparison | Describe any interesting structure comparisons [200 words max] |
Publicly accessible (non-copyrighted) materials may be used, but must be acknowledged.