Peripheral membrane protein modeling

[Anonymous]

Is it possible to model peripheral membrane proteins?

I know RosettaMP is  useful to model transmembrane proteins, but I don’t know whether it is applicable for peripheral membrane proteins or not.

 

Thanks.

[Anonymous]

Sorry, there really isn’t support for membrane proteins which don’t have at least one transmembrane span.

I do know there’s work in the RosettaCommons community to add such support, but it might be a bit before that work is ready for public release.

[Anonymous]

I see. Thanks for your reply.

[Anonymous]

I am just a user, but I use Charmm-GUI (online) to add a DPPC bilayer and then use the output in Rosetta. Charmm-GUI is great and let’s you choose the orientation etc. Then I remove the solvent and relax works fine albeit a tad slower.

Say I have an iTasser model of the protein, I got to http://www.charmm-gui.org/?doc=input/membrane and add a dipalmitoylphosphatidylcholine bilayer, which is a fairly normal lipid. Then I tweak the output in PyMol –say fix a floopy loop sticking into the membrane say– and do something like the following…

remove solvent

alter resn DPPC, resn='FAT'

sort

alter resn FAT, chain='X'

sort

alter all, segi=''

sort

alter resn FAT, type='HETATM'

sort

pwd

#save xxx.pdb

And use the attached FAT.params like:

$ROSETTA/relax.$ROSETTAEXT -database $ROSETTADB -s protein.pdb -no_optH false -ex1 -ex2 -ex1aro -mute basic -relax:jump_move true -relax:thorough -in:file:extra_res_fa FAT.params -nstruct 10

[Author]

Posts