Assignment 3 |
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The Nobel prize is never given for a recent discovery so, again, this is not breaking news. The Nobel prize for chemistry was just awarded to the discoverer of green fluorescent protein (GFP) and scientists who developed innovative methods of using it.
1. Go to the protein data bank http://www.rcsb.org/pdb and type in green fluorescent protein. How many structures does the protein data bank have for GFP?
2. Select the third protein on the list (1jby) and read the first three sentences of the abstract. This particular protein has been modified to perform a special function.
a. What is the function?
b. What is the modification?
3. Return to the Structure Summary page for 1jby and locate the Learn More [M] link. Use it to navigate to the Molecule of the Month page.
a. Does GFP require a prosthetic group in order to glow?
b. If so, what is it? If not, what amino acids are involved in creating the glow?
4. What special function does protein 1kys perform?
5. This is my version of the structure shown on "Exploring the Structure."
Label the amino acid side chains and show where the new bond is formed.
To see several examples of applications of this technique, go to http://harvardscience.harvard.edu/featured-image/somewhere-inside-brainbow and www.wired.com/science/discoveries/multimedia/2007/10/gallery_fluorescentneurons
This is due at the beginning of class on Monday, Oct. 13. Answers must be turned in individually.
Answers:
1. 171 structures.
2. a. Sensing a change in pH and changing color (green to blue);
b. Change residue 65 to T and residue 148 and/or residue 203 to C
Comment after grading: "ratiometric emission measurements in vivo" was a very popular answer. Only one person provided an explanation of the phrase, leaving me with the impression that others thought it looked impressive enough to be the answer. If a term or phrase hasn't been introduced in class, you actually should suspect that it is not the answer.
3. a. No; b. S (or T), Y, G
4. Sense (bind) Zn2+ and change intensity
5.
Comment after grading: Several people indicated bond formation between the α-carbon of G and the CHOH part of the T side chain. This clearly is not the structure shown on the specified page.