disulfide bridges in loop modeling

[Anonymous]

Hi!

What is the easiest way to incorporate disulfide bridges in loop modeling protocole? What flags should I add to loopmodeling protocole?

I used the “detect_disulfide_before_relax” – didn’t work.
I added constraints file like below:

AtomPair CB 264 CB 257 HARMONIC 3.85 1.0

or

AtomPair SG 264 SG 257 HARMONIC 3.85 1.0

together with flags:

add -constraints::cst_fa_file input/file.cst and -constraints::cst_fa_weight 1000.0

didn’t work….
Despite the fact, that I already have disulfide bridge in the input structure…And I wanted only to refine the loop with disufide.

I am sure there is an easy explanation, I just didn’t worked it out myself. Anybody did?

D.

[Anonymous]

Here are some ideas:

A) The disulfides in 3.1 are known to be problematic. They’re being rebuilt from the ground up for 3.2.

It might not have worked if it used CYS residue types instead of CYD residues. The former retains the sulfur’s hydrogen; it will clash horribly even with the constraints and probably overrule the constraint.

C) It’s fairly likely that none of the loop code is written to respect disulfides in the loops anyway – the two loop closure algorithms are intolerant of that sort of secondary loop restraint (or at least, they aren’t written to know about it)

D) I would try regular relax mode instead of trying to loop model with a disulfide in the loop.

[Anonymous]

Thanks, I will test it all!

cheers,

D.

> Hi!
>
> What is the easiest way to incorporate disulfide bridges in loop modeling protocole? What flags should I add to loopmodeling protocole?
>
> I used the “detect_disulfide_before_relax” – didn’t work.
> I added constraints file like below:
>
> AtomPair CB 264 CB 257 HARMONIC 3.85 1.0
>
> or
>
> AtomPair SG 264 SG 257 HARMONIC 3.85 1.0
>
> together with flags:
>
> add -constraints::cst_fa_file input/file.cst and -constraints::cst_fa_weight 1000.0
>
> didn’t work….
> Despite the fact, that I already have disulfide bridge in the input structure…And I wanted only to refine the loop with disufide.
>
> I am sure there is an easy explanation, I just didn’t worked it out myself. Anybody did?
>
> D.
>

[Author]

Posts