Effective atom volumes for implicit solvent models: comparison between Voronoi volumes and minimum fluctuation...

Area of Science:

• Computational Chemistry
• Molecular Modeling
• Biophysics

Background:

• Implicit solvent models, such as the generalized Born method, require accurate atomic volumes for solute representation.
• The accurate determination of atomic volumes is critical for the performance of these models in molecular simulations.

Purpose of the Study:

• To describe and compare two novel approaches for determining atomic volumes for the generalized Born model.
• To evaluate the impact of including or excluding hydrogen atoms on solute volume calculations.

Main Methods:

• Development of two distinct methods for atomic volume calculation: Voronoi polyhedra and volume fluctuation minimization.
• Application of these methods to determine atomic volumes for proteins and nucleic acids using the CHARMM force field.
• Comparative analysis of the two approaches based on structural parameters like size and solvent accessibility.

Main Results:

• Both Voronoi polyhedra and volume fluctuation minimization methods provide viable atomic volumes for implicit solvent models.
• The choice of method and inclusion of hydrogen atoms can influence the resulting atomic volumes.
• Volumes derived from known protein and nucleic acid structures show variations based on the chosen method.

Conclusions:

• The study provides a framework for selecting appropriate atomic volumes for generalized Born calculations.
• The findings contribute to improving the accuracy of implicit solvent models in computational chemistry.
• Understanding atomic volume contributions is key to refining molecular simulations of biological systems.