Binding affinities controlled by shifting conformational equilibria: opportunities and limitations.

Area of Science:

• Biochemistry and Molecular Biology
• Computational Chemistry
• Structural Biology

Background:

• Conformational selection is a fundamental mechanism explaining molecular recognition and protein-ligand binding.
• Despite its importance, conformational selection is underutilized in rational protein and ligand design strategies.
• Existing methods often struggle to isolate the specific contribution of conformational changes to binding affinity.

Purpose of the Study:

• To explore the potential and limitations of utilizing conformational selection principles in molecular design.
• To develop a thermodynamic approach for predicting the impact of conformational shifts on binding affinity.
• To differentiate the effects of conformational shifts from other factors influencing binding.

Main Methods:

• Application of specialized thermodynamic cycles to model molecular interactions.
• Quantitative prediction of binding affinity changes induced by conformational alterations.
• Analysis of ubiquitin mutants to validate the method's accuracy in diverse complexes.

Main Results:

• The developed thermodynamic approach successfully predicts the influence of conformational shifts on binding affinity.
• The method effectively disentangles the specific contribution of conformational changes from other binding determinants.
• Analysis of six ubiquitin mutants revealed the precise role of conformational selection in their binding affinities.

Conclusions:

• Design strategies can be enhanced by explicitly considering and manipulating conformational selection.
• The thermodynamic framework provides a powerful tool for understanding and engineering molecular recognition.
• This work opens new avenues for optimizing protein-ligand interactions through targeted conformational modulation.