Stability of protein mutants: I'm trying to design thermostable variants of a protein. Is it possible to theoretically differentiate them without doing simulation? What would be the parameters I should look into?
iSTABLE
http://predictor.nchu.edu.tw/istable/about.php
iMUTANT
http://folding.uib.es/i-mutant/i-mutant2.0.html
popMUSIC
http://babylone.ulb.ac.be/popmusic/
FOLDX
http://foldx.crg.es/
autoMUTE
http://proteins.gmu.edu/automute/
Thank you very much Jeffrey. I have tried couple of those like iMUTANT, HUNTER etc and findings are not very satisfactory in terms of our problem. I had gone through literature where people using their own scripts, are they better in comparison to these available servers. Do you have any further suggestions. Please help.
You might try a program specific for thermostability (AUTO-MUTE for example). Many of the programs are support vector machines trained to test stability without reference to temperature, or are knowledge based forcefields parameterized without (or with weak) temperature dependence.
Some things to consider:
1.For the structure dependent methods like FOLDX, the accuracy is highly dependent on the side-chain conformations. You will need high quality side-chain optimization to alleviate side-chain clashes in the mutant, which are one of the largest energy terms in the force fields used.
2. The accuracy of both types of methods is limited somewhat by the spread in experimental values. For example, many of the programs do not handle changes in pH.
ok wonderful. That make a lot of sense to me. Thanks again. I would go through those program with the protein of my interest with a std one (I have experimental result for the std one). I would get back to you after that.
I'm working on a similar thing right now (mutant stability at room temperature ). I'' let you know what I find...
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