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This paper presents a detailed protocol for modeling protein-glycan interactions using the HADDOCK3 integrative modeling platform, which incorporates experimental or predicted interaction restraints and allows for flexible refinement. The protocol is demonstrated on the interaction between a 4-beta-glucopyranose glycan and the Humicola grisea Cel12A enzyme, using an X-ray structure for validation. Applying this protocol from unbound structures yields models with interface-ligand RMSD values below 3 angstroms, demonstrating its effectiveness.
Accurately modeling notoriously flexible protein-glycan interactions is now more tractable thanks to a refined HADDOCK3 protocol that achieves sub-3 angstrom RMSD.
Glycans are structurally diverse and flexible biomolecules that play key roles in many biological processes. Their conformational variability makes the modeling of their interactions with proteins particularly challenging. This chapter presents a step-by-step protocol for modeling protein-glycan interactions using HADDOCK3, an integrative modeling platform that supports the inclusion of experimental or predicted interaction restraints and allows for flexible refinement of the solutions. The workflow is illustrated using the interaction between a linear homopolymer glycan, 4-beta-glucopyranose, and the catalytic domain of the Humicola grisea Cel12A enzyme, for which an experimental X-ray structure is available as a reference. Detailed instructions are provided for input structure preparation, restraint definition, docking setup, execution, and result analysis. Application of the protocol starting from unbound structures yields models of acceptable to medium quality, with interface-ligand RMSD values below 3 angstroms. Although illustrated on a specific system, the protocol has been optimized and benchmarked on multiple protein-glycan complexes and is broadly applicable to similar systems, providing a framework for integrative modeling of protein-glycan interactions.
