sequence mistake-how will it affect my folding! - (Dec/12/2008 )

Hey all,

I have a protein sequence which has a changed amino acid from the original sequence... is there any way i can predict how this will affect the folding of the protein and if so how?

I was trying to change a word document into a pdb file but it wont display the protein in pdb veiwer...

Thanks in advance guys

---

What exactly is the mutation? (i.e. the intended amino acid and the mutant amino acid). A conservative change from one simila aa to another (e.g. leucine to isoleucine, or glycine to alanine) generally won't affect folding, but if you add or remove a proline, or change to something completely different (e.g. polar to non-polar, or uncharged to charged) things can get messy.

Ginger

---

its a leucine to serine change

---

Then this could be a bit of a problem. You have changed both the shape and polarity of the amino acid, going from a branched aliphatic aa to a tiny polar aa. I would not trust a protein with this mutation to have the same physical properties as a non-mutant, and would go through the effort of finding a non-mutated clone, or performing mutagenesis to get the intended sequence.

---

It also depends on where the mutation is. If it's in a transmembrane region, it may not matter, but if it affects the formation of a catalytic site, it probably will matter.

---

Why not run the sequence through modeler and see what happens*.

If you have a template to do it with.

---

Could do that, but a computer model is still an estimate. I feel it is best to rebuild now than to continue further work with this problem in your protein.

---

Yes that's true. I am not sure what the original poster was attempting to do.

---