Disulfide Bonds in Loop Modeling

[Anonymous]

Good Morning,

I was implementing the NGK loop modeling to fill the missing loops in the PDB structure, but the disulfide bonds in the PDB were broken and converted to regular cystines after the modeling. These disulfide bonds are not in the remodeled loop region and I specified ‘-loops:fix_natsc true’. From the output, it says: 

core.conformation.Conformation: Found disulfide between residues 76 166

core.conformation.Conformation: current variant for 76 CYS

core.conformation.Conformation: current variant for 166 CYS

core.conformation.Conformation: current variant for 76 CYD

core.conformation.Conformation: current variant for 166 CYD

core.conformation.Conformation: Found disulfide between residues 278 287

core.conformation.Conformation: current variant for 278 CYS

core.conformation.Conformation: current variant for 287 CYS

core.conformation.Conformation: current variant for 278 CYD

core.conformation.Conformation: current variant for 287 CYD

core.pose.extra_pose_info_util: [ WARNING ] Cannot open psipred_ss2 file tt

protocols.loops.loops_main: can not open DSSP file tt

Can I ask how to keep these disulfide bonds fixed? Thank you!

 

[Anonymous]

Hello, 

have you tried the suggestions in https://www.rosettacommons.org/node/10108?

Depending on the exact question you are working on, you can also try skipping the centroid (perturb_kic) stage, which may be where the disulfides are lost.

Amelie

 

[Anonymous]

Hi Amelie,

I have implemented NGK with restraints on the disulfide bonds. The distances between the SG atoms were maintained, but H atoms were still added onto the SG atoms, do I need to take extra steps to add the disulfide bonds? 

Sometimes, it failed to build loop with kinematic mover during the initial kinematic perturbation after 10000 trial and got stuck, is there a way to avoid this?

Can I ask another question? In some tutorials, the option: -loops:outer_cycles was used, but seems it was not valid anymore, should I replace it with -loops:refine_outer_cycles?

I’m trying to fill the missing loop regions and proceed with MD simulation. I’m including the flags file, loop file and constraint file here, can you kindly give me some suggestions? 

Flags flie:

-s input.pdb

-loops:loop_file input.loop

-out:pdb

-out:path:all output/

-database /home/progs/rosetta_src_2020.50.61505_bundle/main/database

-in:file:native input.pdb

-constraints:cst_fa_file disulfide.cst

-constraints:cst_fa_weight 10000

-nstruct 1000

-in:file:fullatom

-in:detect_disulf true

-loops:fix_natsc true              

-loops:remodel perturb_kic

-loops:refine refine_kic

-loops:refine_outer_cycles 5

-kic_bump_overlap_factor 0.36

-legacy_kic false

-kic_min_after_repack true

-corrections:score:use_bicubic_interpolation false

-loops:kic_rama2b

-loops:kic_omega_sampling

-allow_omega_move

-loops:ramp_fa_rep

-loops:ramp_rama

-ex1

-ex2

-extrachi_cutoff 0

-extra_res_cen lig.cen.params

-extra_res_fa  lig.fa.params

 

Loop file:

LOOP 149 164 0 0 1

LOOP 221 242 0 0 1

LOOP 279 286 0 0 1

 

Constraint file:

AtomPair SG 76 SG 166 HARMONIC 2.03 .5

AtomPair SG 278 SG 287 HARMONIC 2.03 .5

 

Thank you!

[Author]

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