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Poisson-Boltzmann Calculations: van der Waals or Molecular Surface?
Xiaodong Pang1, Huan-Xiang Zhou
1Department of Physics and Institute of Molecular Biophysics, Florida State University, Tallahassee, Florida 32306, USA.
Communications in Computational Physics
|January 8, 2013
Summary
The Poisson-Boltzmann equation
Area of Science:
- Biophysics
- Computational Chemistry
- Structural Biology
Background:
- The Poisson-Boltzmann equation (PBE) is crucial for modeling biomolecular electrostatics.
- PBE calculations are sensitive to the dielectric boundary definition (molecular vs. van der Waals surface).
Purpose of the Study:
- To review studies comparing molecular and van der Waals surfaces for PBE calculations.
- To assess the validity of assigning high dielectric constants to internal voids.
Main Methods:
- Review of recent studies comparing dielectric boundary definitions.
- Comparison against experimental data and explicit-solvent simulations.
- Analysis of NMR data regarding solvent accessibility.
Main Results:
- The choice of dielectric boundary significantly impacts PBE results.
- Van der Waals surfaces, when considering solvent accessibility, show promise.
- Internal protein voids may be accessible to solvent, challenging previous assumptions.
Conclusions:
- Re-evaluation of dielectric boundary definitions in PBE is necessary.
- Van der Waals surfaces may be a viable alternative, especially considering solvent penetration.
- Protein interior is not entirely isolated from the solvent environment.
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