I have a couple of peptides (epitopes) with corresponding HLA alleles. Any possibility that I can visualise the structure of HLA alleles along with the bound epitope and to see how the epitope is accommodated in side the pocket utilising some bioinformatic tools?
As discussed above by Maurício, you cannot just "align" your desired peptide in the cleft of a given MHC allele, the structure would not be reliable. There is one webserver to provide initial structures of desired pMHC complexes, MHCSim, but these structures are obtained by mutating available crystal structures and need to be further refined after modeling.
There are other prediction methods already described, such as D1-EM-D2 and pDOCK. The D1-EM-D2 was developed by our group and was used to make structure-based predictions on T cell cross-reactivity. It was also used to model several complexes presenting virus-derived epitopes, which are avaliable through the CrossTope Data Bank. Maybe your complexes of interest were already predicted using our approach.
http://igrid-ext.cryst.bbk.ac.uk/MHCsim/
http://www.crosstope.com.br/
Article PDOCK: A new technique for rapid and accurate docking of pep...
Article Structural in silico analysis of cross-genotype-reactivity a...
Article CrossTope: A curate repository of 3D structures of immunogen...
The one I use for that kind of stuff is Chimera (from the ECSF)
https://www.cgl.ucsf.edu/chimera/
Below is the link of 10 Free Software for protein 3D structure visualization.I think this may solve your problem.
Best of luck..
http://www.bioinformatics-made-simple.com/2012/09/10-free-software-for-protein-3d.html
First you need to find and download the structure of the desired allele in the "pdb" format, from the Protein Data Bank. Unfortunately, just few alleles have structures already available. After download the pdb file, you need to download a software to visualize the structure, such as PyMOL or Chimera. You can find online tutorials for both softwares (see links below).
Using Chimera, you can even skip the part of downloading the pdb file. You can use the "Fech by ID" option to just provide the pdb code of a desired peptide:MHC complex, such as 1WBY, and the program will download and show the structure in your screen.
www.rcsb.org/pdb/home/home.do
http://www.pymol.org/
https://www.cgl.ucsf.edu/chimera/
https://www.cgl.ucsf.edu/chimera/current/docs/UsersGuide/
http://www.pymolwiki.org/index.php/Main_Page
You may look for in the PDB (protein Data Bank) http://www.rcsb.org/pdb/home/home.do
You will find a lot of HLA alleles that have been crystallyzed and the structure have been solved! For different alleles you will also find some molecules (ligands) interacting with them.
Thanks everyone. Assuming the structure of the HLA I'm interested in has been crystallised with an epitope which differs from what I want to check, what are the possibilities that I can visualise how my peptide would fit in to that particular HLA? Especially with Chimera? Thanks
HI,
I'm not an expert, but in this case, I believe you will have to apply a molecular modeling approach. We have been working with this issue for some time and also published a paper about modeling new epitopes (that weren't crystallized) into different HLA alleles. You can check the article in this link: http://www.plosone.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.0010353
After you have modeled, you can visualize whatever you want (chimera, pymol, ...). As far as I know, you can't just pick an epitope and fit inside the HLA cleft, without any structure refinement.
As discussed above by Maurício, you cannot just "align" your desired peptide in the cleft of a given MHC allele, the structure would not be reliable. There is one webserver to provide initial structures of desired pMHC complexes, MHCSim, but these structures are obtained by mutating available crystal structures and need to be further refined after modeling.
There are other prediction methods already described, such as D1-EM-D2 and pDOCK. The D1-EM-D2 was developed by our group and was used to make structure-based predictions on T cell cross-reactivity. It was also used to model several complexes presenting virus-derived epitopes, which are avaliable through the CrossTope Data Bank. Maybe your complexes of interest were already predicted using our approach.
http://igrid-ext.cryst.bbk.ac.uk/MHCsim/
http://www.crosstope.com.br/
Article PDOCK: A new technique for rapid and accurate docking of pep...
Article Structural in silico analysis of cross-genotype-reactivity a...
Article CrossTope: A curate repository of 3D structures of immunogen...
You can model the peptide into the groove roughly using side chain packing then evaluate for atomic clash and interaction...
http://www.ncbi.nlm.nih.gov/pubmed/10773348
http://www.ncbi.nlm.nih.gov/pubmed/10703604
http://www.ncbi.nlm.nih.gov/pubmed/17597847
http://www.bioinformation.net/ted
You can use TED it is fairly generic in nature ...
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