Hi everyone,
I am working with a protein whose first ~20 residues are missing. Experiment evidence suggest that these residues are crucial. So, Intend to model them. However, with so many server available QUARK, I-TESSER etc. I am bit confused, what to choose. Also, these artificially modeled residues comes with added uncertainty. Different servers usually result in different structure. I can probably try a sanity check using ubiquitin as a test protein on different servers but what are the that methods beside modelling from the server can be used ?
Thanks,
Vikas
First of all you need to determine whether your missing residues are disordered or not. I suggest using d2p2. If they are disordered then by definition they will not have a stable structure. Otherwise you can use a structure prediction server such as iTasser - the result will be based primarily on homology, your model will show you the most likely structure based on the closest known structure available in databases.
Also, if the 20 missing residues are disordered but definitely play a crucial role, try seeing if they match any short linear motifs for example in the eukaryotic linear motif database.
Mr. Dubey,
How many and the amino acid residues in your protein?
Thanks everyone for their answers :
Jan : I am uncertain about those residues being structured or unstructured. I have tried using QUARK, which predicts a mix of both structured and unstructured. I will look in the motif database. Thanks for your suggestion.
Mis. Ivanova : There are 1316 residues in my protein. It's sodium potassium pump.
Saravanan : How and where can I get this hybrid approach ?
@Vikas Dubey Hope your protein is a membrane protein, if so, the first 20 residue might be sandwiched inside the membrane. In that case you need to model along with the membrane . You may try Memoir http://opig.stats.ox.ac.uk/webapps/memoir/php/index.php. I have not tried but might be helpful to you.
You can model this disordered active region based on carbon distribution. Carbon optimised domains are playing for stability/order in protein structure. Mutants of this 20 amino acid long stretch is stable somewhere in other proteins. You can fix up there and do further modeling.
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