In wet lab experiment I got the sequences of Heavy chain and the Light chain. I used AlphaFold-2 to generate their the structure PDBs. Now the challenge is how to merge them to get one PDB?
Not sure if it is the correct way to merge, I tried to merge them by copying and paste the coordinates of the Light chain into the Heavy chain's PDB but the generated structure is merged into each other. (attached figures)
Any help regarding this matter would be appreciated.
Read the two .pdb format file in CHIMERA and in save pdb from FILE section.
Check for closely related proteins in the pdb - You may find some structures which can serve as templates for the correct assembly of the two domains. If not, you may have to use protein-protein docking to predict their probable interaction.
Annemarie Honegger
Thanks... Could you please suggest me some article/program by which I can achieve the desired results.
Regarding the docking, I think it will try to interact in a same fashion Antigen-Antibody interacts but I want to arrange Heavy and Light chain as they are in scFv format.
If there is any special kind of protein-protein docking for this pupose, please suggest me.
https://www.rosettacommons.org/docs/latest/application_documentation/docking/sym-dock
https://www.rosettacommons.org/node/11062
Please check the above links
There are many scFv, Fv and Fab structures in the pdb which you can use as templates.
(Do sequence searches on the rcsb advanced search website for the VL and VH sequence separately, and look for structures which are rank highly in both searches)
You can use PyMOL https://pymol.org/2/ for a 3D alignment of the domains (use the "super" command https://pymolwiki.org/index.php/Super rather than "align" to do the alignment to do a sequence-independent structural alignment) . ChimeraX https://www.cgl.ucsf.edu/chimerax/ or DeepView https://spdbv.unil.ch are other possibilities. The program you used to generate the posted image probably also allows to do structural alignment.
Did you try to submit the actual scFv sequence to AlphaFold-2 (one sequence for VL-linker-VH or VH linker-VL)? It would be interesting to see how it deals with the domain interaction. If you do so in SwissModel https://swissmodel.expasy.org, you will get a variety of model, some of which are modelled on actual scFvs, some that are modelled on VL-CL or VH-CH, but usually some good solutions ones are within the best 10 models. Actually, if you do a "Search for Templates" first, you can exclude the VL-CL and VH-CH ones already in the results of this step.
There are so many antibody structures known (>1000) that your best bet is to use an antibody-specific, knowledge-based server. ABodyBuilder http://opig.stats.ox.ac.uk/webapps/newsabdab/sabpred/abodybuilder/ at the SABpred site http://opig.stats.ox.ac.uk/webapps/newsabdab/sabpred/ does a very good job, and also helps you to do a number of antibody-specific analyses.
Try different methods and compare their results. Let us know what works best for you, and why.
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