A molecular dynamics study of solvent behavior around a protein

Area of Science:

• Biophysics
• Computational Chemistry
• Structural Biology

Background:

• Understanding protein-solvent interactions is crucial for deciphering protein function and dynamics.
• Molecular dynamics (MD) simulations provide a powerful tool to investigate these interactions at an atomic level.

Purpose of the Study:

• To analyze the structure and behavior of water solvent around the trp-holorepressor protein.
• To investigate the mobility and distribution of water molecules in proximity to the protein surface.

Main Methods:

• Analysis of a molecular dynamics simulation trajectory of the trp-holorepressor in a water environment.
• Calculation of self-diffusion coefficients to assess solvent mobility.
• Distribution analysis and radial distribution functions to determine water-protein interactions.

Main Results:

• Solvent within 10 Angstroms of the protein displayed significantly lower mobility.
• No general tendency was observed in solvent diffusion around different atom types or residues.
• Two distinct water oxygen distribution peaks were identified: one near polar/charged atoms (2.8 A) and another near apolar atoms (approx. 3.4 A).
• These distributions suggest the formation of a hydrophobic shell stabilized by water-water hydrogen bonds around apolar regions.

Conclusions:

• Solvent mobility near proteins is reduced, particularly within a 10 Angstrom radius.
• The type of atom or residue does not significantly influence local solvent mobility.
• Distinct hydration shells form around proteins, characterized by hydrogen bonding patterns that differ between polar/charged and apolar regions.