Post-Translational Modifications at the Coarse-Grained Level with the SIRAH Force Field

Area of Science:

• Biochemistry and Molecular Biology
• Computational Biology
• Biophysics

Background:

• Post-translational modifications (PTMs) increase protein diversity but are challenging for theoretical models.
• Coarse-grained (CG) models require comprehensive and consistent parameterization for accurate simulations.
• Existing theoretical methods struggle to fully capture the complexity introduced by PTMs.

Purpose of the Study:

• To develop and present a set of topologies and interaction parameters for common PTMs.
• To ensure compatibility of these parameters with the SIRAH force field.
• To expand the chemical scope of CG models for studying protein behavior.

Main Methods:

• Development of new topologies and interaction parameters for common PTMs.
• Integration of these parameters into the existing SIRAH force field.
• Validation of the parameters for structural description.

Main Results:

• A comprehensive set of parameters for common PTMs compatible with the SIRAH force field.
• The new parameters achieve a high level of structural description, consistent with the SIRAH force field.
• Expansion of the chemical spectrum of the SIRAH force field.

Conclusions:

• The developed parameters enhance the capability of CG models to simulate PTMs.
• This work facilitates more accurate modeling of protein dynamics and interactions in complex biological systems.
• The expanded SIRAH force field offers promising applications for studying large-scale protein-protein interactions.