I have sequenced an important part of a variant of the DHPS gene containing 500bp encoding the important domain part of protein, but not the full gene, by Applied Biosystem 16 capillary. Now I want to obtain the structure of the full protein contained in my sequenced domain.
Can I use bioinformatics modelling approaches to model the full protein?
I have the template structure of this protein as wild type.
Hi Priyanka
In my opinion you can theoretically attempt this problem and as far as modelling is concerned there should not be any probleb....you have a template molecule to design the structure and you have sequenced 500 bp of the gene you want to model.....but how much sequence is remaining and if you are planning (as you said) to model full length protein (though you have only 500 bp sequence),,,what sequence you will use for the non sequenced region.......you can use the sequence from a closest hit or from the template it self....and design the 3D structure......if there are no/only few variations are expected between the non-sequenced regions of the gene and the template....it may work out fine....but if later you find variations (between presently non-sequenced regions and the sequence you used for modelling)....then your model may not fit...but it will be a good attempt
Hi Priyanka
In my opinion you can theoretically attempt this problem and as far as modelling is concerned there should not be any probleb....you have a template molecule to design the structure and you have sequenced 500 bp of the gene you want to model.....but how much sequence is remaining and if you are planning (as you said) to model full length protein (though you have only 500 bp sequence),,,what sequence you will use for the non sequenced region.......you can use the sequence from a closest hit or from the template it self....and design the 3D structure......if there are no/only few variations are expected between the non-sequenced regions of the gene and the template....it may work out fine....but if later you find variations (between presently non-sequenced regions and the sequence you used for modelling)....then your model may not fit...but it will be a good attempt
I believe that I have a similar problem. I have the full sequence of a gene for a molecule from Drosophila which is closely related to and also d shares common domain structures with yeast proteins from with solved crystal structures.. However my protein (and homologs from other higher eukaryotes) is expanded by about 200 amino acids in the C-terminal domain, Some of the last few amino acids (far C-terminus) are similar and represent a common protein-protein interaction motif. Therefore the additional amino acids lie in the middle of the C-terminal domain needs to be modeled and fitted into the other regions of the molecule.
Is there any program which will fit the additional residues (predicted secondary structure mostly helix) to the gap in the
c-terminal domain. My guess is that most of the additional amino acids extend the yeast structure (helix), however it might also contain enough loop character to fold and interact with other parts of the molecule.
I have tried, i-Tasser, Swiss modler (alignment mode) , Phyer [sic] and other protein structure prediction programs. The only programs that were so bold as to predict structures came up with structures that were ridiculous either by inspection or low probability. This seems to be a simple problem but it has frustrated me for some time. I hope this adds to the general discussion.
-Doug
Sounds good. Rick, Thank you! I expect that one must deal with the bulk of the side groups of the amin acids in the non template segments and orient them in a way that minimizes free energy. Is this a capability of Moeller or Chimera? I guess this is really something I must find out for myself ;-) I will try this approach. I probably will be back to this forum again. Thanks to all of you.
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