Second-contact shell mutation diminishes streptavidin-biotin binding affinity through transmitted effects on...

Area of Science:

• Biochemistry
• Structural Biology
• Protein Dynamics

Background:

• The streptavidin-biotin complex is a model system for high-affinity protein-ligand interactions.
• Understanding the molecular basis of streptavidin's high affinity is crucial for biotechnological applications.

Purpose of the Study:

• To investigate the impact of a specific point mutation (Y54F) in streptavidin on binding affinity and dynamics.
• To elucidate the role of distal protein dynamics in modulating ligand binding affinity.

Main Methods:

• Characterization of the Y54F streptavidin mutant's binding affinity, enthalpy, and entropy.
• Structural analysis of the Y54F mutant in complex with biotin.
• Molecular dynamics simulations to assess atomic fluctuation amplitudes and water-mediated interactions.

Main Results:

• The Y54F mutation caused a 75-fold decrease in binding affinity, primarily due to faster dissociation.
• A significant loss of binding enthalpy and a small gain in binding entropy were observed.
• Molecular dynamics revealed increased atomic fluctuations in key biotin contact residue W79, linked to the loss of water-mediated hydrogen bonds.

Conclusions:

• Changes in protein dynamics distal to the binding site can profoundly affect ligand binding affinity.
• The Y54F mutation perturbs the 'tryptophan collar' dynamics, compromising the streptavidin-biotin interaction.
• Equilibrium structure changes are not always necessary to explain altered binding affinity.