maintaining dimer integrity

[wangsuhaoshabi]

Dear Rosetta Developers ,

I hope this email finds you well.
I am writing to ask for advice regarding a molecular docking task I am currently performing. My system involves docking a homodimer ligand to a receptor.
System Details:
Ligand: A homodimer composed of two chains (let's say Chain A and Chain B).
Disulfide Bonds: The ligand contains both intra-chain disulfide bonds and inter-chain disulfide bonds (connecting Chain A and Chain B).
The Problem:
During the docking simulation, I observed that the two chains of the homodimer ligand tend to separate/dissociate from each other. My goal is to treat the homodimer as a single rigid body (or at least maintain the inter-chain interaction) while docking it to the receptor.
My Questions:
Disulfide Specification: How should I correctly format the disulfide file to explicitly define the inter-chain disulfide bonds? I want to ensure Rosetta recognizes that these two chains are covalently linked.
Command / Flags: Which specific command-line flags or options should I use to prevent the dimer from falling apart? Do I need to manually adjust the Fold Tree or use specific constraints to fix the relative position of the two ligand chains?
Any guidance or example command lines would be greatly appreciated.
Thank you very much for your time and help.
Best regards,

[roccomoretti]

For standard protein-protein docking, the two partners (individually) are generally treated as more-or-less rigid bodies. There's some internal flexibility, but there's not really any internal sampling that should lead to the two chains dissociating -- whether or not they're covalently bonded. All you need to do is properly set the docking partners to annotate which chains are on which side of the docked interface (e.g. "AB_C"), and the docking code will automatically set up the FoldTree for you. (If you're putting together your own docking protocol in RosettaScripts or the like, you'll have to set up the FoldTree yourself, though the default FoldTree should work if the movable chain is only a single chain.)

(Note that Rosetta protein/protein docking is generally a two-body docking approach, even when there are multiple chains within each partner. To actively dock more than one interface, you'll typically need to do multiple rounds of two-body docking.)

Upon read-in, Rosetta should run code to autodetect disulfide bonds, so if you have CYS residues in the correct disulfide bonding geometry, Rosetta should properly annotate them as covalently bonded, and will treat them as such during docking. As an alternative, there's also an -in:obey_ssbond option, which tells Rosetta to skip the autodetection and use the information in the SSBOND records of the input PDB file to place the disulfides, even if the geometry isn't right.

[wangsuhaoshabi]

For standard protein-protein docking, the two partners (individually) are generally treated as more-or-less rigid bodies. There's some internal flexibility, but there's not really any internal sampling that should lead to the two chains dissociating -- whether or not they're covalently bonded. All you need to do is properly set the docking partners to annotate which chains are on which side of the docked interface (e.g. "AB_C"), and the docking code will automatically set up the FoldTree for you. (If you're putting together your own docking protocol in RosettaScripts or the like, you'll have to set up the FoldTree yourself, though the default FoldTree should work if the movable chain is only a single chain.)

(Note that Rosetta protein/protein docking is generally a two-body docking approach, even when there are multiple chains within each partner. To actively dock more than one interface, you'll typically need to do multiple rounds of two-body docking.)

Upon read-in, Rosetta should run code to autodetect disulfide bonds, so if you have CYS residues in the correct disulfide bonding geometry, Rosetta should properly annotate them as covalently bonded, and will treat them as such during docking. As an alternative, there's also an -in:obey_ssbond option, which tells Rosetta to skip the autodetection and use the information in the SSBOND records of the input PDB file to place the disulfides, even if the geometry isn't right.

Thank you very much. I'm using rosettasurface and I want to modify its source code. Specifically, I want to disable the fragment part and make it support multi-chain docking (the source code can only support single-chain). So, how should I set up its FoldTree?

[roccomoretti]

Generally with docking, you want to set things up such that the "fixed" portion of the molecule is on one side of a jump, and the movable portion(s) are downstream of the jump(s). For multi-chain docking, each independent moving piece should be downstream of its own jump. The reason for this is that docking movers generally manipulate the 6 degrees of freedom of a jump, and when they do, you want just the "movable" portions of the docking to move. For multi-body docking, you generally want each body to be independently movable.

There's certainly refinements over-and-above this basic requirement. For example, you can alter the foldtree such that it's the center of mass of each of the docking components which are directly linked by the jump, rather than their N termini. This doesn't change the accessible space of the docking, it just changes how the rigid body degrees of freedom are sampled for small changes to each DOF. (e.g. changing the rotation angle is applied at a different location.)