Protein folding affected by neg. cahrges amino acids? - (Nov/21/2011 )
How much does a neg. charge amino acid (aspartate) affect the protein folding? I'm curious as to whether 5 aa substitution (ser/thr -> asp) to mimic phosphorylation can affect the protein folding enough to render the
protein useless. By the way, these aa subs would be between aa 15-46 of a ~400 aa long protein and the
central DNA-binding core domain is not near these subs.
Btw, one will see a faster running band for the modified protein when compared to a wt protein, right?
1) There's no way to tell for sure how it will affect protein structure. It may do nothing or completely destroy everything. There are techniques available to evaluate that, though.
2) The difference in running would be so miniscule that you won't see any difference on SDS-PAGE. The switch to negative charge should also have no effect, since the SDS is supposed to make the charges of all proteins essentially uniform.
Phosphorylation of Ser-Pro and Thr-Pro sites often causes a significant SDS-PAGE mobility shift (upwards). Ser/Thr to Asp substitition likely do the same. I have been told that this shift is caused by reduced SDS binding.
I agree with Deadaly. One can not tell for sure if the Asp you have substituted affect folding unless and other wise it is proven by experiments.
I am currently working with novel protein and substituted Asp to Ala (in contrary to what you did) in order to see the role of Asp. But now I am struggling to get this mutated protein expressed. I tried too many times with different conditions, but no protein Anyhow, I am thinking that the Asp that I mutated has something with the protein's structure.
If the secondary structure of your protein is known, you can check the position and role of those amino acids you have mutated.
Btw, have you considered the molecular weight difference of your modified protein from the WT?? The modified might have been lighter as you see fast running bands.
Increased negative charge on a protein, such as phosphorylation can slow the migration of your band on a SDS-PAGE. The increased negative charge causes it to bind less SDS therefore changes its charge:mass ratio