Extracting hydrophobicity parameters from solute partition and protein mutation/unfolding experiments

Area of Science:

• Biochemistry
• Physical Chemistry

Background:

• Hydrophobicity is crucial for protein structure and function.
• Existing hydrophobicity scales derived from octanol-water partitioning and protein unfolding experiments show significant discrepancies.

Purpose of the Study:

• To investigate the reasons for the large difference in hydrophobicity values obtained from protein unfolding versus octanol-water partitioning.
• To propose and validate a more suitable model for the protein interior's hydrophobic environment.

Main Methods:

• Reanalysis of solute partitioning data with introduced volume dependence.
• Reanalysis of protein unfolding data using a full free energy analysis.
• Analysis of pure hydrocarbon solubilities in water.
• Examination of hydrophobic side-chain contact environments in mutation/unfolding experiments.

Main Results:

• Octanol-water partitioning yields a hydrophobicity parameter of 22 cal/mol/Ų, while protein unfolding yields 31.2 cal/mol/Ų after reanalysis.
• Hydrocarbon solubilities in water yield a hydrophobicity parameter of 30.8 cal/mol/Ų.
• Analysis of hydrophobic side chains in proteins reveals minimal polar contact (<2%), supporting a hydrocarbon-like environment.

Conclusions:

• Octanol is an inadequate model for the hydrophobic environment within a protein's interior.
• Hydrocarbons provide a more accurate model for protein interior hydrophobicity.
• The discrepancy in hydrophobicity scales is largely due to the limitations of the octanol model.