Solvent reaction field potential inside an uncharged globular protein: a bridge between implicit and explicit solvent...

Area of Science:

• Computational chemistry
• Molecular dynamics
• Biophysics

Background:

• Proteins interact with surrounding solvent molecules.
• Understanding these interactions is crucial for predicting protein behavior and function.
• Implicit solvent models simplify these interactions but may lack accuracy.

Purpose of the Study:

• To compute the solvent reaction field potential for an uncharged protein.
• To analyze the contribution of solvation shells to this potential.
• To assess the impact of these findings on implicit solvent models.

Main Methods:

• Molecular dynamics simulations of an uncharged protein in explicit solvent.
• Calculation of solvent reaction field potential.
• Analysis of charge density and solvation shell structure.
• Comparison with implicit solvent models (Poisson).

Main Results:

• A finite, positive potential (13-24 kBT) was observed inside the protein.
• This potential is geometry-dependent and primarily from the first solvation shell.
• Ordered first and second solvation shells significantly influence the potential.
• Explicit solvent simulations show high correlation with implicit models when reaction field energy is included.

Conclusions:

• The ordered structure of water molecules near a protein surface creates a significant internal potential.
• Accurate implicit solvent models must account for the solvent reaction field.
• Findings enhance the accuracy of computational models for protein-solvent interactions.