Homology Modelling with cofactors

[Anonymous]

Hi guys,

Can the RosettaCM protocol include cofactors as residues/restraints in model building?

I am building a cytochrome P450 model and I’d like to include the haem if possible. Without the haem, some of the cofactor-interacting backbone has subtle conformational differences.

[Anonymous]

Here’s what Frank Dimaio recommends for doing cofactors with RosettaCM:

1) generate params and cartesian restraints using Ian’s script:
python ~/rosetta_source/src/python/apps/public/molfile_to_params.py –keep-names –clobber –extra_torsion_output –centroid LIG.mol2 -p LIG -n LIG
2) give the extra params file to Rosetta:
–extra_res_cen LIG.cen.params
–extra_res_fa LIG.fa.params
–extra_improper_file LIG.tors
3) add the ligand(s) in all the template files(*), numbering them sequentially after the chainlength (so if the input fasta has 100 aas, ligands would start at 101).
4) in the section of the xml script, add: “add_hetatm=1”

(*) I presume this would be the *post threading* template files.

[Anonymous]

Thanks Rocco!

I will give this a try.

I have one more question about RosettaCM, but I will add that to the ‘Multiple Templates’ thread.

[Anonymous]

Hi Rocco,

Just to confirm this works *really* well!

Based on your (and Frank’s) recommendations, I recently incorporated S-adenosylmethionine into a model enzyme using RosettaCM. A couple of pointers for anyone else wanting to do this:

– Make sure all threaded parent template files have the ligand coordinates

– Make sure ‘HETATM’ is replaced with ‘ATOM’ in the template files

– No need to add a chain break at the end of the sequence file

 

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