Protein:Ligand binding free energies: A stringent test for computational protein design

Area of Science:

• Computational biology
• Protein engineering
• Biochemistry

Background:

• Tyrosyl-tRNA synthetase (TyrRS) is a key enzyme with a well-studied substrate specificity.
• Experimental redesigns of TyrRS provide benchmarks for computational methods.
• Accurate prediction of binding free energies is crucial for protein design.

Purpose of the Study:

• To extend computational protein design methods for simulating Monte Carlo titrations of multiple ligands.
• To rigorously test the physical model's accuracy in predicting binding free energy differences.
• To validate the computational approach against experimental data for TyrRS variants.

Main Methods:

• Monte Carlo simulations with ligand titration into protein binding pockets.
• Comparison with Molecular Dynamics/Generalized Born Surface Area (MD/GBSA) for validation.
• Sidechain rotamer optimization including energy minimization for accurate contact relaxation.

Main Results:

• The extended computational method accurately predicts binding free energy differences for TyrRS and its mutants.
• Results show good agreement with rigorous MD/GBSA calculations.
• Redesigning amino acid positions successfully recovered experimental outcomes for ligand specificity.

Conclusions:

• The enhanced computational protein design method provides a stringent test of physical models.
• The approach is effective for predicting substrate specificity and guiding protein engineering efforts.
• This method holds promise for accelerating the design of proteins with novel functions.