Question

Imagine that you’ve cloned something that you think is a cadherin, but you know very little about it (and hopefully nobody knows anything about it, otherwise it wouldn’t be “research”). You think it is attached to the cytoskeleton, hypothetically through its cytoplasmic tail. Your goal is to identify the part(s) of the cytoplasmic tail that is/are responsible for binding. Luckily, if you’ve cloned a gene, it is easy to make sub-clones that have specific portions of the polypeptide strand deleted. This is usually denoted by “delta” (ΔCx would be missing region #x of the cytoplasmic tail).

To achieve this goal, you would use a technique called immunoprecipitation, followed by SDS-PAGE (western blotting). The new part is immunoprecipitation, but do not worry; below the problem setup is a video for more info on this technique – which is like an add-on to the beginning parts of the SDS-PAGE/western procedure that you are already familiar with.

Basically, you use an antibody that binds to your cadherin (you can design an antibody for it, once you know the DNA sequence from the cloning step) to “pull down” your cadherin. Anything directly attached to your cadherin though, will also get pulled down with your antibody. Then you can throw away all of the other cell components – next you release the proteins from the antibody and make a liquid out of this “precipitated protein” that you pulled down – and finally you load the liquid on an SDS-PAGE gel just as we did with the “total protein” from the cytoplasm of the yeast cells. The difference (compared to what we did in lab) is that if we now use another antibody (like anti-GFP) at the end of the procedure to find the detectable proteins in our experimental system – only other proteins that were pulled down with the cadherin could possibly show up, not just any-and-all proteins that contain GFP that were in the cell lysate (liquid cell mash). Assume that we have GFP tags and antibody labelling abilities, for all candidate binding partners of the cadherin.

From the results, you can see that three proteins pull down. An approximately 110 kilodalton (kDa), a 97 kDa, and an 80 kDa protein all seem to bind with our cadherin (based on the “intact” experiment on the left; with cells that express the normal cadherin that can bind to everything that it normally wants to bind). Answer the questions below regarding the other experiments. Use panel (B) to understand what is in the lanes (the thin parts are the regions deleted, TM means “transmembrane”, the numbers are not relevant but they correspond to the number of amino acids that are deleted).

Linear Diagram of

our Cadherin

1. Which region (give a number 6, 7, 8, 9 or 10) is responsible for binding to the 97 kDa partner of the cadherin?

2. How do you explain the fact that deleting region #6 abolishes all three binding interactions? Think of protein structure/function from the in-person classes as well as the ECM lecture about cadherins (what would be the role of the transmembrane region in the overall protein structure and its ability to bind to partners).

3. Explain how the results from mutant ΔC9 (in which all three binding sites are deleted) is different than the explanation in part ii. In other words, where does the 110 kDa protein bind, and where does the 80 kDa protein bind on the cadherin? How do you explain the results from lanes 2 and 5 being the same, even though the experiments were different?

4. mOsT EXtreme ScIEntIfIc cHaLLeNge: How do you explain the results in lane 6, which seem to suggest that mutant ΔC10 still has binding to the 97 kDa partner – even though mutant ΔC10 is missing regions 7, 8, 9, and 10? Again, think of protein structure/function – and be creative.

Answer 1

1. The region number 7 is responsible for the binding to the 97kDa partner of the cadherin, as the deletion of the 7 portion excluded the 97kDa band on the gel in lane number 3. Hence it is responsible to bind to the 97kDa partner.

2. Cadherin is a protein involved in forming the adherens junction in a calcium dependent manner by dimerization process. The transmembrane zone of the cadherin protein is essential as it is required for the dimer formation and hence if the cadherin doesn't dimerize then it cannot interact with any protein and hence there are no bands on the gel in lane number 2.

3. The mutant deltaC9 has all of the protein binding zones deleted and hence no protein is able to bind to the cadherin inspite of cadherin dimerization. The 80kDa protein is binding in the zone of 8-31 of the deltaC8 mutant and the 110kDa protein is binding in the zone of 31-70 of the deltaC9 mutant. The results from lanes 2 and 5 are same because both of them are inhibiting the protein interaction by altering the structural characteristics of proteins.

4. The mutant deltaC10 is able to bind to the 97kDa protein. There maybe a possible explaination when one considers the protein structure/function mechanism. The cadherin protein is dimerising in deltaC10 mutant and the deleted region in the cytoplasmic face may contain the binding site of 97kDa protein, but the amino acids that are present in the cytoplasmic face may create a structure that is homologous to the protein binding site of 97kDa and hence the 97kDa protein is able to bind to that deltaC10 mutant.

If you have any query kindly comment before giving thumbs up. Thank you.