Computational prediction method to decipher receptor-glycoligand interactions in plant immunity

Area of Science:

• Plant immunology and molecular biology
• Computational biochemistry and structural biology

Background:

• Plant immune receptors (PRRs) recognize microbe- and plant damage-associated molecular patterns (MAMPs/DAMPs) via extracellular ectodomains (ECDs).
• Carbohydrate-based ligands (glycans) for PRRs are poorly understood, with few PRR/glycan pairs identified.
• Accurate prediction of PRR-glycan interactions is crucial for understanding plant immunity.

Purpose of the Study:

• To develop and validate a computational screening method for predicting extracellular ectodomain (ECD)-PRR/glycan interactions.
• To investigate the binding of specific glycans to Arabidopsis LysM-PRR members CERK1 and LYK4.
• To accelerate the discovery of novel protein-glycan interactions in plant immunity.

Main Methods:

• Utilized a computational screening method based on molecular dynamics simulations to predict PRR-glycan binding.
• Optimized and validated the method using Arabidopsis LysM-PRR members CERK1 and LYK4 with known MAMPs (chitohexaose, laminarihexaose).
• Confirmed in silico predictions through isothermal titration calorimetry binding assays and genetic analysis of Arabidopsis mutants.

Main Results:

• The computational model accurately predicted CERK1 binding to chitohexaose (1,4-β-d-(GlcNAc)₆) and non-binding to cellohexaose (1,4-β-d-(Glc)₆).
• LYK4 was predicted not to directly bind chitohexaose, and CERK1 was predicted not to directly bind laminarihexaose (1,3-β-d-(Glc)₆).
• Experimental validation confirmed computational predictions, suggesting CERK1 acts as a co-receptor for laminarihexaose recognition.

Conclusions:

• A robust computational method for predicting PRR-glycan interactions has been developed and validated.
• The method provides insights into specific PRR-glycan binding and potential co-receptor roles in plant immunity.
• This approach can significantly accelerate the identification of novel protein-glycan interactions and their roles in plant immune signaling.