For example: If I have a wild type protein with 'L' amino acid at 174 position and some researchers have changed it to 'P' amino acid but some researchers have changed it to 'D' amino acid. My question is that on what basis the researchers have selected the amino acid 'D' to study the change in function of the protein? Is it related to the polarity of the amino acid residue or what?
I am hoping to get a reasonable answer.
Thank you.
This is not easy to answer without context. In your example, neither change is particularly conservative. L to P is going to introduce a kink into the backbone. L to D is going to add negative charge where none existed before. Both changes may be appropriate to the experimental aims, but we cannot be sure without the context.
I think you need to consider what it is that you are trying to achieve. Disrupt the protein structure? Make a subtle change in a binding site? The latter type of change is most common, where you try to infer which residues are important by switching them. But you do need to consider if the change makes sense. For example, if you wanted to change C (which often features in enzyme active sites) to see if C is involved in catalysis, you could switch to any one of 19 other amino acids, but not all of them are appropriate . If you switch to a bulky amino acid, you remove the thiol which could be involved in catalysis, but you might also distort and inactivate the binding site simply because of the extra bulk. Thus a conclusion that C is involved in catalysis may not be valid. A better choice would be S, which is almost the same size and also polar. Then, if your enzyme is inactive it is much more likely to be due to the specific elimination of the -SH group of C, as that is effectively the only thing you have switched (to -OH).
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