Molecular dynamics simulation of proteins under high pressure: Structure, function and thermodynamics

Area of Science:

• Biophysics
• Computational Biology
• Protein Science

Background:

• Molecular dynamics (MD) simulation is crucial for studying protein structure, function, and thermodynamics.
• Investigating high-pressure effects on proteins presents challenges, including the need for accurate force fields and water models, and longer simulation timescales.

Purpose of the Study:

• To review recent developments in MD simulation methodologies for high-pressure protein studies.
• To summarize MD simulation studies on proteins in water under high pressure.

Main Methods:

• Development of advanced protein force fields and water models for high-pressure conditions.
• Application of enhanced simulation techniques to capture pressure-induced effects.
• Analysis of MD simulations of proteins in aqueous solutions under elevated pressure.

Main Results:

• MD simulations successfully reproduce experimentally observed high-pressure phenomena in proteins.
• Observed phenomena include hydration changes, water penetration, conformational alterations, helix stabilization, and increased molecular rigidity.
• Simulations highlight distinct protein and water properties under high pressure compared to ambient conditions.

Conclusions:

• MD simulations provide valuable insights into the behavior of proteins under high pressure.
• Comparing simulation results with experimental data can elucidate the mechanisms of biological molecular machines operating with water molecules.