The goal of this assignment is to determine which amino acids are important for the functionality of your protein and to find
out how that was determined.
2.For your protein, which functional aspect of the protein are you going to investigate? For example, suppose you are
studying an enzyme whose catalytic ability is controlled by glucose. In this case, there would be at least two potential
functional components to investigate; the glucose-sensing portion and the active site of the catalytic portion of the enzyme.
3. How will you be able to tell that an amino acid or string of amino acids contributes to the function you are
investigating? This means, which experimental variables can you measure for different protein variants in order to assess
whether they are changing the function that you are interested in? You may need to check out some papers before being able to
answer this.
4. Describe in your own words the techniques that were used to identify functionally important amino acids in the articles
that you looked at. Please cite the articles. For instance, the example of the NMDA receptor that I discussed in class used
site-directed mutagenesis and two-electrode voltage clamp, so you should look up and briefly describe those techniques.
5.Describe in your own words the mechanisms, either those demonstrated or postulated to occur, by which the functionally
important amino acids contributed to the protein function under investigation. Please cite the articles from which you
obtained this information.
6.How far apart are the important amino acids in terms of the primary amino acid sequence? Use the letter symbol (slide 18 in
9/21 lecture) to denote what the amino acids are. Is the protein composed of multiple similar subunits with similar important
amino acids in each one? For instance, you can see in the summary figure on slide 22 of the 9/21 lecture that there are
multiple amino acids, particularly those labeled in blue and red, that contribute to ion flux and selectivity. These amino
acids, such as P557 (proline 557) and L657 (leucine 657), are separated by 100 amino acids in the primary sequence but are in
very close proximity in the folded protein. Also, there are two different subunits with important amino acids, the NR1 and
NR2B subunits.
