Find a primary literature review describing the protein/enzyme.
Find and load a pdb file in Swiss pbdviewer
If there are several types of enzymes select the best picture.
Find the active site if identified.
Get the protein sequence from NCBI or other data base.
Blast (using blastP) the data base and retrieve 5 sequences from other organisms and align them in the BioEdit program**. (You should already have Bioedit working). Highlight conserved amino acids.
In your structure find the conserved amino acids and identify where they are (highlight them on the structure. Pick 5 areas of identity and if possible describe their function. Determine if other structures of the same protein exists with substrates or inhibitors bound. Locate the small molecule binding site in the protein and report which amino acids in the aligned sequences that interact with the small molecule(substrate, inhibitor or modulator).
You should have at least three primary research articles that you reference more may be helpful. Write a five page description of your project. Support your data with graphs pictures and alignments (not included in the page limit).
A 5 page double spaced written report and as many figures as required is minimum for a grade. Reference all literature used and use a bibliography that is compatible with the journal Cell Minimum of 3 references. Remember-do not copy the text. This is plagiarism and a zero will be assigned if plagiarized. Use your own words to explain. To find out how to use cell references go the web page for Cell- Instructions for authors. And get examples from there.
If your enzyme or protein is part of a multi subunit complex or interacts with other proteins instead of small molecules, describe the interaction motif and treat the other protein binding site as a small molecule binding site. Report the interaction sites as describe on the previous page. Any other interesting facts, biochemistry and superfamily relationships please include.
Grading will be on the degree of detail and completeness of the project. This assignment is a learning tool so spend quality time in the completion of it and demonstrate your own initiative in the scholarship of the project.
** When aligning the sequences pick homologous sequences that are some what distant at least 20% sequence dissimilar. If you pick E. coli and use Salmonella or Shigella which are very closely related there maybe no differences in the sequences to determine conserved and non conserved domains. When using BlastP select sequences down the list (select 500 hits). With lower BLAST scores.
