Exploring volume, compressibility and hydration changes of folded proteins upon compression

Area of Science:

• Biophysics
• Physical Chemistry
• Computational Biology

Background:

• Protein structure, stability, and function are influenced by volumetric properties in solution.
• Temperature and pressure-dependent volumetric properties are crucial for understanding proteins, especially under extreme conditions.
• Partial molar volume and its pressure dependence in proteins remain poorly understood.

Purpose of the Study:

• To investigate the pressure dependence of apparent volume (Vapp) and its components for a model protein, staphylococcal nuclease (SNase).
• To analyze the contribution of molecular volume (VM), intrinsic volume, solvent contribution, and boundary voids to the observed pressure effects.
• To compare pressure-dependent volumetric behavior with temperature-dependent behavior and with results for unfolded polypeptides.

Main Methods:

• Molecular dynamics simulations of aqueous solutions of staphylococcal nuclease (SNase).
• Application of the Voronoi-Delaunay method to analyze apparent volume and its components.
• Quantification of pressure-dependent changes in intrinsic volume, solvent contribution, and boundary voids.

Main Results:

• Apparent volume (Vapp) shows a strong decrease with increasing pressure, consistent with experimental data (βT = 0.95 × 10⁻⁵ bar⁻¹).
• The primary driver for Vapp decrease is the compression of molecular volume (VM), particularly internal voids (V).
• Detailed quantification of pressure effects on intrinsic volume, solvent, and boundary void contributions was achieved.

Conclusions:

• The compressibility of internal protein voids is the dominant factor in the pressure dependence of protein apparent volume.
• The study provides a detailed molecular-level understanding of protein volumetric properties under pressure.
• Findings offer insights into protein behavior in solution across different environmental conditions and for various protein states.