Decomposition of Protein Experimental Compressibility
into Intrinsic and Hydration Shell Contributions
Voichita M. Dadarlat 1 and Carol Beth Post 1*
1 Purdue Univ.
* To whom correspondence should be addressed. E-mail: cbp{at}purdue.edu.
Submitted on April 24, 2006
Revised on June 1, 2006
Accepted on 31 August 2006
 |
Abstract |
|---|
The experimental determination of protein compressibility reflects both the protein intrinsic compressibility and the difference between the compressibility of water in the protein hydration shell and bulk water. We use molecular dynamics simulations to explore the dependence of the isothermal compressibility of the hydration shell surrounding globular proteins on differential contributions from charged, polar and apolar protein-water interfaces. The compressibility of water in the protein hydration shell is accounted for by a linear combination of contributions from charged, polar and apolar solvent accessible surfaces. The results provide a formula for the deconvolution of experimental data into intrinsic and hydration contributions when a protein of known structure is investigated. The physical basis for the model is the variation in water density shown by the surface-specific radial distribution functions of water molecules around globular proteins. The compressibility of water hydrating charged atoms is lower than bulk water compressibility, the compressibility of water hydrating apolar atoms is somewhat larger than bulk water compressibility, while the compressibility of water around polar atoms is about the same as the compressibility of bulk water. We also assess whether hydration water compressibility determined from small compound data can be used to estimate the compressibility of hydration water surrounding proteins. The results, based on an analysis from four dipeptide solutions, indicate that small compound data can not be used directly to estimate the compressibility of hydration water surrounding proteins.
Key Words:
bound water structure, molecular volume calculation, protein hydration shell, protein intrisic compressibility, solvent radial distribution
