Balanced Force Field ff03CMAP Improving the Dynamics Conformation Sampling of Phosphorylation Site

Area of Science:

• Plant biology
• Biochemistry
• Computational biology

Background:

• Phosphorylation is crucial in plant biology, influencing proteome formation.
• Many phosphorylation sites are found in disordered protein regions.
• Existing force fields struggle to accurately model dynamic phosphorylated proteins.

Purpose of the Study:

• Evaluate the ff03CMAP force field for sampling phosphorylated proteins.
• Compare ff03CMAP with other force fields (ff03, CHARMM36m, FB18).
• Identify optimal force field and solvent models for studying phosphorylation dynamics.

Main Methods:

• Tested ff03CMAP on 11 phosphorylated systems (dipeptides, disordered/folded proteins, complexes).
• Assessed performance against ff03 for disordered regions and phosphorylation sites.
• Evaluated ff03CMAP with TIP4PD water model for conformer sampling.
• Compared ff03CMAP with CHARMM36m and FB18 on two systems.

Main Results:

• ff03CMAP demonstrated superior sampling of phosphorylation sites in disordered regions compared to ff03.
• The combination of ff03CMAP and TIP4PD water model yielded the best conformer sampling.
• ff03CMAP showed comparable performance to FB18 and outperformed CHARMM36m.

Conclusions:

• ff03CMAP is a suitable force field for studying phosphorylated proteins, particularly disordered regions.
• The ff03CMAP/TIP4PD combination is recommended for accurate conformer sampling.
• These findings aid researchers in selecting appropriate models for plant phosphorylation dynamics research.