Structural determinants of trypsin affinity and specificity for cationic inhibitors

Area of Science:

• Biochemistry
• Computational Chemistry
• Molecular Modeling

Background:

• Understanding enzyme-inhibitor interactions is crucial for drug design.
• Bovine beta-trypsin is a well-studied serine protease with a defined S1 specificity site.

Purpose of the Study:

• To calculate binding free energies of four inhibitors to bovine beta-trypsin.
• To elucidate the contributions of electrostatic and nonpolar interactions to binding affinity.
• To investigate the role of the S1 specificity site's molecular architecture in recognition.

Main Methods:

• Finite difference Poisson-Boltzmann equation for electrostatic contributions.
• Free energy-surface area relationship for nonpolar interactions.
• Estimation of conformational entropy loss for enzyme and ligand.

Main Results:

• Calculated binding free energies were reasonable, correctly predicting relative inhibitor affinities.
• Electrostatic interactions generally opposed binding, but salt bridges stabilized complexes.
• Partially buried Asp189 and immobile specificity site residues reduced desolvation and entropic penalties.

Conclusions:

• The trypsin binding site's architecture promotes specific recognition by minimizing desolvation and entropic costs.
• Like-charged molecules can exhibit favorable electrostatic binding due to solvent interactions in charged complexes.
• Findings offer insights into molecular recognition and binding principles.