Hi Armando At the risk of appearing flippant, why not submit the sequence of the full-length protein to something like Alphafold (readily available to all via ColabFold (see https://colab.research.google.com/github/sokrypton/ColabFold/blob/main/AlphaFold2.ipynb)?
I suspect that each of the two domains may be modelled well (provided your sequence is less than 2000 residues, I think) and correspond to what you have found experimentally, but the region between the two would have poorer statistics (PAE matrix would show low values and lDDT would be lower between the two domains). An alternative would be to use one of the traditional homology modelling tools like Phyre2 in “intensive" mode (which is designed for multi domain proteins), but the results would probably not be as good (you can make of that what you will); the advantage of Phyre2 is that it’s very, very easy to run (submitting a job would take less time than it’s taken me to type this sentence), and has very helpful user support (see http://www.sbg.bio.ic.ac.uk/phyre2/html/page.cgi?id=index) It would at least give you something to think about before spending time in the lab. Harry > On 26 Jul 2023, at 09:14, Armando Albert <xalb...@iqfr.csic.es> wrote: > > Dear all, > We are trying to characterize a protein consisting of two domains. We have > successfully produced, purified and crystallized both domains independently. > However, we are unable to overexposes a soluble form of the full-length > protein. Can anyone provide a strategy to merge back the independent domains > into a single protein chain or to modify the construct to succeed in the > overproduction of the full-length protein? > Armando > > ######################################################################## > > To unsubscribe from the CCP4BB list, click the following link: > https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1 > > This message was issued to members of www.jiscmail.ac.uk/CCP4BB, a mailing > list hosted by www.jiscmail.ac.uk, terms & conditions are available at > https://www.jiscmail.ac.uk/policyandsecurity/ ######################################################################## To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1 This message was issued to members of www.jiscmail.ac.uk/CCP4BB, a mailing list hosted by www.jiscmail.ac.uk, terms & conditions are available at https://www.jiscmail.ac.uk/policyandsecurity/
