Sequestered water and binding energy are coupled in complexes of lambda Cro repressor with non-consensus binding...

Area of Science:

• Biophysics
• Molecular Biology
• Structural Biology

Background:

• Lambda Cro repressor is a key protein in phage lambda genetic regulation.
• Protein-DNA interactions are crucial for biological processes and are influenced by solvation.
• Understanding water's role in molecular recognition is vital for drug design and biotechnology.

Purpose of the Study:

• To quantify the role of sequestered water in the binding affinity of lambda Cro repressor to various DNA sequences.
• To investigate the relationship between binding free energy and the number of water molecules involved in protein-DNA complex formation.
• To determine if sequestered water is sterically driven or influenced by other factors.

Main Methods:

• Utilizing osmotic pressure dependence of dissociation rates and relative binding constants.
• Analyzing changes in binding free energy and sequestered water molecules for lambda Cro repressor-DNA complexes.
• Comparing experimental data with thermodynamic parameters like heat capacity, enthalpy, and entropy.

Main Results:

• A linear correlation was observed between the number of sequestered water molecules and binding free energy across a 1000-fold change in association constant.
• Each additional sequestered water molecule in non-cognate complexes corresponds to a loss of approximately 150 cal/mol in binding free energy.
• The number of sequestered water molecules showed relative insensitivity to the type of osmolyte used, indicating steric sequestration.

Conclusions:

• The study infers that steric effects play a significant role in sequestering water within lambda Cro repressor-DNA complexes.
• Thermodynamic analysis suggests that changes in complex structure extend beyond simple water molecule incorporation.
• The findings provide insights into the energetic contributions of solvation to protein-DNA recognition specificity.