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Chapter Five Exercises
1. Build a zinc-finger protein profile and execute a PSI-BLAST exercise.
Use NCBI resources to identify a sequence containing a zinc finger binding domain. Run a BLAST query using that sequence in an effort to identify other zinc finger proteins. Next, repeat the exercise but use PSI-BLAST instead of regular BLAST. Comment on the effectiveness of the two approaches for finding zinc fingers. Include discussion about both the success of the search methods and the ease of carrying out the two methods.
2. Characterize the secondary structure and modification sites of several related proteins.
Use the Protein Data Bank (PDB) to find a protein whose crystal structure has been solved and submitted within the past month. Submit the amino acid sequence of that protein to at least two different structure prediction servers (you can find a useful list of servers, along with evaluations of the underlying methods, at http://cubic.bioc.columbia.edu/eva). Inspect the predictions, compare them to the structure from PDB, and comment on your findings.
3. Perform a simple threading exercise.
4. Identify the complementation groups in a hypothetical genetic data set.
Suppose six mutations, a, b, c, d, e, and f, for a phenotype have been identified, and that heterozygotes for each pair of mutations have been developed by appropriate crosses of homozygous parents. In the table below, the wildtype phenotype is indicated by +, while - denotes mutant phenotypes. Organize the six mutations into complementation groups.
| Mutation 2 | |||||||
|---|---|---|---|---|---|---|---|
| Mutation 1 | a | b | c | d | e | f | |
| a | + | - | + | - | + | ||
| b | + | + | + | + | |||
| c | + | - | + | ||||
| d | + | - | |||||
| e | + | ||||||
| f | |||||||
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