Homology Modeling With High Sequence Identity

Question

[Raghul]

Hi to all, When trying to build a homology modeling for a protein with high sequence identity (>80%)with PDB structure using SwissModel with "alignment mode" option, modeling was not done. Have anybody done something like this? Is it unnecessary to do homology modeling for same protein between very closely related species when there are very few changes between target & template? or on the contrary dont we miss something? I downloaded the original structure & used the "mutate" (SwissPDB Viewer)option to change 5 amino acids (which were the only differences between target & template). I did some model checking with procheck/whatcheck. After these the tool option in SPDBviewer highlighted these particular mutated amino acids have errors or impossible configurations! When mutating, an amino acid can adopt several possible confirmations & configurations, so which confirmation can i give to an amino acid when I mutate it? For eg Proline have very few! I am not a biochemist but I am just interested to see the effect of few changes at structural level in my protein?

thank you raghul

Answer 1

[João Rodrigues]

I never used SwissModel, but I'd reckon you can even use a template with 99% identity. What was the error or problem you experienced? Why do you say the modelling was not done?

You can also try another server like PHYRE2 and see if you get along better with it.

[Raghul]

thanks, I will check again

Answer 2

[Vladimir Chupakhin]

Modeller is the perfect choice. 80% is a high homology but I would recommend to use homology modeling and not a simple "mutate and optimize" strategy, because it will adopt correct conformation of the amino acid and optimize it's orientation (minimization).