I am working on a protein with a distinct conformation. I found out that this conformation is present in many species (by visual inspection and PDB database). I have also observed that the sequences are moderately conserved (from BLAST) and (from ClustalW) - 10% of the residues are highly conserved.
What should I do to study this conformation further?
Well, the conformation can mean many things. I am going to assume that you talk in terms of the solvent accessible surface area. What you can do here is that make sure that the conservation that you detected (residues) in sequence, detect them in the 3-d conformation. Where are they located. If the location (of the residues) is on the surface then you can say with assurity that the sequence conservation correlates to the conformation. Apparently 10% conservation might not be sufficient in this regard, but please do check if the conserved residues make the surface. If they do then publish :)
So you have a crystal structure? You can study it's dynamics by obtain biophysical experimental data on regions of solvent exposure and solvent inaccessibility and stability using hydrogen exchange analysis. There are many papers using this method to understand protein function based on dynamics. If you want any further suggestions let me know since that's my area of expertise and we provide that for many users in our core lab who want to investigate changes or differences in protein conformation.
The Multiple Sequence alignment result shows that the 10% of the residues are IDENTICAL. so can presume the conserved residues helps in structurally maintaining such a conformation ??
@Dennis Pantazatos I am using a crystal structure as a template and modeled 6 protein by homology modeling. So is it valid to use homology models to study the conformation?
No 10% conservation cant dictate alone if the structure would be the same. Functional aspects are usually dictated by the surface of the proteins. The characteristic profile of the surface of the protein is usually made from a few underlying residues. If you detect a conservation across proteins in surface contributing residues, than you can say they help in making the protein carry out similar functions.
In short, look at the conserved residues visually if you are not good with programming, or automate the process using NACCESS to see solvent accissibity of the conserved residues. If the residues are on the surface they should be solvent accessible and thats what is given by NACCESS, See them and if they are on the surface yuo can then say something like all the proteins do similar things.
You can confirm the prediction experimentally without knowing the structure and accurately identify solvent exposed regions of your protein. If you can express it and purify it then as I had mentioned you can perform hydrogen deuterium exchange there is a paper in PNAS where this method was used to identify disordered regions in proteins that failed to crystallize but were successfully crystallized after removing the regions of disorder. By using very short exchange time only surface amide will be labeled and you can identify the regions using MS. The PMID is 14715906 Although I may have it as a download on my profile? I don't remember.
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