I am trying to dock a protein onto nucleosome, as it was done in Frontiers | MARTINI-Based Protein-DNA Coarse-Grained HADDOCKing . I am asking for help in trying to perform similar docking with another nucleosome-binding protein using the web server.
Coarse-graining input error: I first used PDB-tools web to tidy up the crystal structure of nucleosome, PDBID 1KX5. To preserve the multi chain structure, I used ‘delhetatm’ followed by ‘reres’. I uploaded this to the HADDOCK web server, and checked coarse-grain option. This resulted in an error: “An error occurred during CG conversion: Chain is mixed nucleic/protein, not supported. split into different chains and try again”. However, the DNA and protein components are in different chains, only renumbered.
Peptide flexibility: I just proceeded with all-atom docking. Here, I am expecting my protein to bind histone tail, DNA, and the nucleosome body, so I wanted to make the histone tails flexible in order to accomodate binding to my protein, as was discussed in Step 3 of HADDOCKing of the p53 N-terminal peptide to MDM2 – Bonvin Lab . However, I couldn’t find the option for this–do I need higher access level? Pushing through without changing the basic parameters resulted in my protein barely holding on to the edge of histone H3 tail without changing its conformation.
In sum, I am having problems with coarse-graining and making the histone peptide flexible. And I am wondering if I should increase the sampling parameters as said in the paper. My post became quite lengthy–any advice would be appreciated.