I have recently begun an antibody engineering project, in which I am trying to increase the binding affinity of a homology modeled Fab to a TACA (tumor associated carbohydrate antigen). After perusing the literature for some time, I discovered that I need to implement GlycanDock for the initial docking of the carbohydrate ligand to the antibody paratope. After implementing GlycanDock, I intend on using the antibody Affinity Maturation Protocol. I do not think that de novo antibody design is needed because we already have the sequence of an antibody that binds weakly to the target (we have no crystal structure, though). For all of this I am using Rosetta 3.12 installed on a cluster.
In the Meiler Lab workshop protocol for antibody affinity maturation (protocol attached below, link to video: https://www.youtube.com/watch?v=z2kaGqtY5UI), I noticed that it is designed for protein antigens. Is there any way I could make the protocol work with my carbohydrate ligand? What parameters, if any, would I have to change? Ideally, I would like to generate a set of mutations that improve the binding affinity of the modeled Fab to the carbohydrate antigen. Since I do not have a crystal structure to work with, will I still be fine? Should I possibly implement SnugDock (I've read that it works better with homology models) alongside GlycanDock for the initial docking to the antibody structure?
Below I attached some copied of the docking scripts I have been using for the docking of a large library of small molecules (not glycans). I have the following additional questions:
Is there an easy way to change my existing docking XML into one that docks glycans (in terms of weights and other parameters)?
Can I use GlycanDock in Rosetta 3.12? I saw a script titled dock_glycans.static.linuxgccrelease in the bin directory. Is this the one I should use?
Does anyone here have a script that modifies the existing affinity maturation protocol into one that works with carbohydrate antigens?
What flags should I use in both the glycan docking and the affinity maturation?
If the affinity maturation protocol in Rosetta won't work on a carbohydrate antigen, what else can I do computationally in order to generate sequences with improved binding?
Thank you in advance for your suggestions. Any example scripts for GlycanDock and/or Affinity Maturation would be greatly appreciated.
Useful references for GlycanDock:
|Meiler Lab Affinity Maturation Tutorial||238.32 KB|
|XML example file used for my standard protein-ligand docking.||45.45 KB|