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Improving Martini 3 for Disordered and Multidomain Proteins.

F Emil Thomasen¹, Francesco Pesce¹, Mette Ahrensback Roesgaard¹

¹Linderstrøm-Lang Centre for Protein Science, Department of Biology, University of Copenhagen, DK-2200 Copenhagen N, Denmark.

Journal of Chemical Theory and Computation

|April 4, 2022

Summary

Coarse-grained simulations using Martini 3 often underestimate protein size. Adjusting protein-water interactions improves accuracy for intrinsically disordered and multidomain proteins, enhancing simulation reliability.

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Area of Science:

Computational Biology
Structural Biology
Biophysics

Background:

Coarse-grained molecular dynamics (CGMD) simulations are vital for studying protein conformational ensembles.
The Martini 3 force field is widely used but may have limitations in representing protein dimensions.

Purpose of the Study:

To evaluate the accuracy of the Martini 3 force field for intrinsically disordered proteins (IDPs) and multidomain proteins.
To investigate the impact of protein-water interactions on conformational ensembles.
To improve the predictive power of CGMD simulations for soluble proteins.

Main Methods:

Performed coarse-grained molecular dynamics simulations.
Compared simulation results with experimental data, including small-angle X-ray scattering (SAXS) and paramagnetic relaxation enhancement (PRE).
Systematically increased the strength of protein-water interactions in the Martini 3 force field.

Main Results:

Martini 3 underestimates the global dimensions of IDPs and multidomain proteins compared to SAXS data.
A modest increase (approx. 10%) in protein-water interaction strength significantly improves agreement with SAXS data.
The revised force field shows better agreement with experimental data for protein self-association and PRE measurements.

Conclusions:

Adjusting protein-water interactions in Martini 3 offers a substantial improvement for simulating soluble proteins.
This refinement enhances the accuracy of conformational ensemble predictions for IDPs and multidomain proteins.
The modified force field provides a more reliable tool for biophysical studies using CGMD simulations.