how to repacking loop while freezing other residues?

[Anonymous]

Hello,

I rebuilded two missing loops in a crystal structure and tried to use Rosetta to refine these loops. I want to refine the loops but keep the rest of the native structure (both backbone and side chain) “freeze”. However,each time the loops were repacked, the neighbor residues connect to the loops will also move. I tried to fix the native structure with -loops:fix_natsc, and also try to set the neighbor distant to 0, but all failed.

The command was:
./loopmodel.linuxgccrelease -database ../rosetta_database/ -loops:input_pdb 2wuy.pdb -loops:loop_file 2wuy.loop -loops:remodel perturb_kic -loops:refine refine_kic -ex1 -ex2 -nstruct 10 -loops.max_kic_build_attempts 100 -in:file:fullatom -loops:fix_natsc true -loops:neighbor_dist 0.0

and the loop file was:
LOOP 31 49 40 0 1
LOOP 173 187 180 0 1

If I want to fix the original structure and optimize the rebuilded loops, what should I do?

Thank you very much!

[Anonymous]

I’m not 100% sure it will let you prevent repacking on the nearby residues.

Try using a resfile that specifies NATRO for all non-loop positions? (I’m also not sure this will work).

[Anonymous]

I’m not too familiar with the loopmodel code, but I’m assuming that it automatically extends the loops to the residue just outside the cutpoint – likely not in the full loopmodel sense, but just to fix up the joining points. (Are you getting significant movement, or is it just subtle changes in most coordinates, with perhaps significant changes in the atoms directly next to the cutpoints?)

The quick and dirty solution is to simply recognize that the loopmodel application will tweak the adjacent residues, and trim your loop definitions accordingly. If you shorten the loop by one residue on each end, when the loopmodel application extends it by one residue, you’ll get the limited movement you expected.

[Anonymous]

For your loop definition file: you are aware that you need to use “rosetta numbering”, numbering residues from 1, rather than PDB numbering in that loops file? (Rocco, didn’t you or someone tweak that?) Is it possible that it’s moving the wrong residues because the window of residues to move is slightly off?

[Anonymous]

Thanks for comment!

I tried to refine a loop with resfile,but still fail. The resfile is:

NATRO

start
32 A PIKAA K EX 1 EX 2 EX 3
33 A PIKAA R EX 1 EX 2 EX 3
34 A PIKAA K EX 1 EX 2 EX 3
35 A PIKAA K EX 1 EX 2 EX 3
36 A PIKAA H EX 1 EX 2 EX 3
37 A PIKAA F EX 1 EX 2 EX 3
38 A PIKAA A EX 1 EX 2 EX 3
39 A PIKAA E EX 1 EX 2 EX 3
40 A PIKAA H EX 1 EX 2 EX 3
41 A PIKAA E EX 1 EX 2 EX 3
42 A PIKAA I EX 1 EX 2 EX 3
43 A PIKAA E EX 1 EX 2 EX 3
44 A PIKAA E EX 1 EX 2 EX 3
45 A PIKAA A EX 1 EX 2 EX 3
46 A PIKAA T EX 1 EX 2 EX 3
47 A PIKAA L EX 1 EX 2 EX 3
48 A PIKAA D EX 1 EX 2 EX 3

And here is the command:
./loopmodel.linuxgccrelease -database ../rosetta_database/ -loops:input_pdb 2wuy.pdb -loops:loop_file 2wuy.loop -resfile resfile -loops:remodel perturb_kic -loops:refine refine_kic -ex1 -ex2 -nstruct 1 -loops.max_kic_build_attempts 100 -in:file:fullatom -loops:fix_natsc 1

I put an image here, protein in gold is from PDB, and the blue one is loops-rebuilded. One of the loop is show on the left. The helix connect to this loop was extended while refining.

[Anonymous]

Thank you for your reply!

Actually, I don’t quite understand how the cutpoint influence the result. I tried to put the cutpoint to the last reside of the rebuilded loop, the result seem similar.

I have tried different loop file for a loop, the original one is:
LOOP 31 49 40 0 1

and the new one is:
LOOP 33 47 40 0 1

for the new loop file, the loop still being extended, as show in the picture in the attachments.

[Anonymous]

Sorry, I was flubbing my termonology. I didn’t actually mean “cutpoint”, I meant the transition point between loop and non-loop. Basically, I was suggesting you do what you just did – shrink the size of the loop by one.

Unfortunately, I’m not quite sure what I’m supposed to be seeing from the image you show. What are the two proteins you’re comparing? What are you expecting to see if everything went as you hoped?

[Anonymous]

Sorry for hasn’t added any note on that image. The protein in gold is native crystal structure, and on the left of it,there is a dash line represent a missing loop, so I rebuild the loop and refine it by Rosetta, then I got the blue protein. As could be seen, several residues which should form helix in gold protein (on the left,on top of the dash line) became loop in the blue one.

[Anonymous]

Yes, that is why I couldn’t get the result! I always use the PDB numbering. I have tried the rosetta numbering, it works.
Thank you so much!

So the rosetta numbering should always been used in any operation?

[Anonymous]

If the residue number is accompanied by a chain ID, assume it is in PDB numbering.

If the residue number is NOT accompanied by a chain ID, assume it is Rosetta numbering (from 1).

[Anonymous]

OK, so loop model is Rosetta numbering, and resfile is in PDB numbering.

Thanks in advance!

[Author]

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