Science Buddies: "Ask an Expert"

If certain drugs known to bind the protein NPC1 are added to a cell, will they bind proteins that have amino acid sequences with 45% of their bases in common with NPC1?

They might. It depends on a few things.

First, understand that the drug should bind tightly to that target protein. It may also bind 'non-specifically' to any other proteins - this is often dependent on concentration of the target protein and concentration of the drug. If there is LOTS of target protein and little drug, most of the drug will bind to that target. The more drug you add, the more likely it is you will see non-specific binding. You could consider the proteins with 45% homology somewhere in the middle there.

Second, beware 3 dimensional protein structure. Just because there is a common sequence in two proteins, does not mean they will fold in a similar way. This is important because if the protein's binding sequence gets fiolded up inside and the drug can't reach it, there will be no specific binding... so predicting protein binding interactions is more complkicated than just looking at the sequenece.

Good luck with your project. That was a great question
Tonya