Hello All,
I want to patch two templates into one. Each of it is a homodimer. They are; TMH and a periplasmic protein. There are no missing residues, and I want to patch them both into a single protein.
I have tried multi-chain modeling into one, but the resultant molecule is very wired and lot of unfolded area. Any suggestions?
Regards,
I don't know about your protein. So commenting on your protein may not the perfect. How you conform that the result was wired? Do you have any complete structure of same family protein where you can do superimposed? You can do loop refinement or md simulation to fold correctly the unfolded region.
Or, you can do modelling from itasser, then that itasser model as one of the template for multitemplete modelling along with other templates you are using for modelling. I think this can improve your results.
Thanks Bera,
One of my domain is a periplasmic domain solved by X-ray in daimeric state. I have TMH region obtained from modeling. I tried Modeller for multitemplate modeling but MOdeller is unable to fix the TMH region correctly. Currently, I have got a monomeric model by itasser which seems good but i am unable to build a complete dimer now, though I tried symdock and cluspro.
You can just build complete dimer using I-TASSER. Then you'll have some initial template for complete protein which you can further model using other templates in Modeller. I-TASSER can able to model upto 1500 residues.
I want to build a dimer by using online server of I-TASSER. If I am not mistaken, I-TASSER server generates a monomeric model even if the available template is a dimmer. Just like Swiss-Model, it will tells you that the template is a dimmer but will generate a monomeric model.
Hi,
You can use the complete monomeric protein as template to model the dimer using MODELLER, for your ref:
https://salilab.org/modeller/manual/node29.html
Thanks Sucharita,
Primarily, I tried Modeller using model-multiple.py, but Modeller is some how unable to locate exact spatial arrangement and keep the TMHs in an unfolded state. :-(
Model the individual parts the best you can, then fit the parts to the dimeric template to make a raw model of the dimer (e.g. in Swissmodel, pymol, etc) and arrange the TM domains in a reasonable way - now make sure that the two chains have different chain labels and correct residue numbers, before fine-tuning the model through repacking, energy minimization etc.
@Annemarie Honegger
Thank you so much, I did last night as you explained above. There is still a slight problem that both the monomers are relatively more closer to each other (< 1 angstrom). I hope to fix it soon.
Regards and thanks to all.
you can use modeller to build homodimer protein. the manual for do this is https://salilab.org/modeller/manual/node29.html
i did it before without any problem.
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