Improved Protein Dynamics and Hydration in the Martini3 Coarse-Grain Model

Area of Science:

• Computational biology
• Biophysics
• Molecular dynamics simulations

Background:

• The Martini force field is crucial for simulating biological systems at large scales.
• Rigorous benchmarking of Martini3Go̅ for globular proteins is lacking.

Purpose of the Study:

• To evaluate the Martini3Go̅ force field's performance for small globular proteins.
• To compare simulation results with experimental data and all-atom simulations.

Main Methods:

• Coarse-grain molecular dynamics simulations using Martini3Go̅.
• Analysis of protein structural integrity (contact maps, Rg, SAXS).
• Comparison of predicted chemical shifts and hydration with experimental and all-atom data.

Main Results:

• Martini3Go̅ accurately models structural and dynamic features of ubiquitin, lysozyme, and cofilin.
• Protein structural integrity is maintained, consistent with experimental observables.
• Protein-water interaction energetics and hydration levels align well with atomistic simulations.

Conclusions:

• Martini3Go̅ shows promise for simulating globular proteins.
• Protein-water interaction dynamics need improvement, depending on protein complexity and residue specificity.
• Further refinement of Martini models is needed for enhanced solvation effects.