I have to accomplish an homology modeling task in which the reference template does not cover very large loops of the query sequence (20-30 residues). I have not found any reliable alternative template for that disordered regions. Fortunately, they are located far away from the site of interest for my project. Nevertheless, the softwares (ie MODELLER, GROMACS) and the analyses I have to carry on need an entire ungapped protein model. I thought about substituting the large missing loops with short ex-novo peptidic patches (such as a poly-ala sequence). In such way I will reduce the background noise generated by sub-optimal flexible regions created ab-initio. I am looking for any suggestion that could corroborate such an idea (ie a validated method and/or literature references)
Offhand, I do not know of a paper that describes the oligo-Ala loop substitution you propose, but it seems like a good idea that I would probably try in your situation as well.
Another approach could be actually to not put in the loops, but leave the protein split into several chains. You'd want capped/uncharged termini to avoid major artefacts. Many proteins would be perfectly stable without their loops.
If you would like to validate either of the options as a method, you could look for crystal structures with large loops, take them out and/or replace them by short(er) Ala loops and see that the dynamics of the protein core remains unaffected. This will very likely vary between different (types of) proteins. It would be best if you could verify this on some (remote) homologue of your protein of interest, if you are so lucky to find such a structure.
Unfortunately there is not any remote homologue structure where that large loop are structured (even perform iterate PSI-Blast runs or trying a threading approach).
I will try the ARCHPRED tool proposed by Narcis Fernandez-Fuentes, but I feel that trying FRAGRUS is more suitable.
I want to obtain an ungapped structure in order to have minimal trouble with MODELLER or GROMACS.
Another approach I have found just now is to graft structured shorter loops from an homologue domain. I performed a Ca superposition over the core structure (without loops) of my domain vs homologue and I have obtained an RMSD of 1.6A. It seems to sound good to try a grafting approach, does not it?
This may help:
Journal of Molecular Biology
Volume 273, Issue 1, 17 October 1997, Pages 330–337
Glutamine, alanine or glycine repeats inserted into the loop of a protein have minimal effects on stability and folding rates
Andreas G. Ladurnera, Alan R. Fersht
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