how to design binding interface?

[Anonymous]

Dear ALL,
I have a complex with two chains. Now I am going to design the binding interface of Chain A while fix everything in the chain B.
Which application should I use? Thank you!

[Anonymous]

rosetta_scripts is the application to use. The drawback is that you’ll have to put together an XML file which outlines the procedure you want to do. The best documentation we have publicly available at the moment is the 3.4 documentation (section “Rosetta Scripts”), but everything there should more-or-less be relevant to any more recent release.

What I might recommend, though, is to take a look at some of the recent Rosetta binding interface design papers, and crib the script from the Supplemental Material. “RosettaScripts: A Scripting Language Interface to the Rosetta Macromolecular Modeling Suite” ( http://dx.doi.org/10.1371/journal.pone.0020161 ) has a simple protein interface design example in the main text. “Computational Design of Novel Protein Binders and Experimental Affinity Maturation” ( http://dx.doi.org/10.1016/j.jmb.2013.06.035 ) gives a good overview with references, though it doesn’t seem to have an example script itself. “Hotspot-Centric De Novo Design of Protein Binders” ( http://dx.doi.org/10.1016/j.jmb.2011.09.001 ) and “Computational Design of a Protein-Based Enzyme Inhibitor” ( http://dx.doi.org/10.1016/j.jmb.2013.06.035 ) are other good papers with examples of RosettaScripts for protein interface design. Other examples are likely out there as well.

[Anonymous]

Hi,
I want to enhance the binding affinity of a protein-protein complex(crystal structure is available).
For this, I am simultaneously changing my interface residues from the resfile(using ALLAA). Now, I want to iteratively do this(using LoopOver) till my ddg for mutant becomes less than that for WT.I am (fast)relaxing and repacking after every step.
I wanted to know how can I apply this filter to compare ddg_mutant with ddg_WT. Also, is this a correct approach or is there a better way to achieve my goal?
Any help would be great appreciated.

p.s- I am using the rosetta script in ‘calculate_protein_protein_ddg’

[Anonymous]

Thank you! I have read those paper and I think I have something different from them.
I already have an known protein protein binding complex. I just want to redesign the binding interface of chain A while fixing chain B. As I mentioned in https://www.rosettacommons.org/node/3486″. Right now I fix the chain B (I tried NATRO and trying NATAA now) and none-interface region of chain A, and design the binding interface in chain A. But I am not sure whether this is the right way to design the interface. Thanks!

[Anonymous]

That approach will work, but the advantage of looking into some of the RosettaScripts based protocols is that you can start to do some limited backbone and rigid body degrees of freedom sampling along with the sidechain sampling.

The protocols referenced might be a little more extensive than you need, as you are already starting with a known protein-protein interaction, but you can certainly cut down those protocols by eliminating the interaction search steps, and just using the part of the protocol which designs the interface after a putative interface has been identified.

If you don’t want to sample backbone or rigid body degrees of freedom, the fixbb approach with an appropriate resfile will certainly work for a design methodology.

[Anonymous]

I got your point! Thanks very much!

[Anonymous]

Hello

I exactly want to do that job.so by what you said in this comment, would fix bb be a correct methodology for designing interface complex ??

[Anonymous]

A Delta filter (https://www.rosettacommons.org/docs/latest/Filters-RosettaScripts.html#Delta) will allow you to compare a filter’s value to the filter’s value on the input structure or some other reference structure.

[Anonymous]

fixbb could certainly work to design an interface of a protein-protein complex. Just make sure the resfile you provide to fixbb has the correct behavior set for the particular residues you want to design.

The big limitation of fixbb is that it’s a fixed backbone design process. Rosetta won’t attempt to reoptimize the backbone structure or the rigid body alignment of the two binding partners with the new protein sequence. You can potentially get better design results if you use a more advanced protocol which allows some backbone or rigid body orientation changes during the design process. But fixbb will certainly work as a simple, first pass approach.

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