Implementation and Validation of Titratable Cysteine in GROMACS-Based Constant-pH Molecular Dynamics

Area of Science:

• Biomolecular Simulation
• Computational Chemistry
• Biophysics

Background:

• Cysteine's protonation state is crucial for biological functions.
• Existing constant-pH molecular dynamics (CpHMD) methods lack titratable cysteine.
• Accurate simulation of cysteine requires specialized force-field parameters.

Purpose of the Study:

• To develop and implement a titratable cysteine residue for GROMACS CpHMD.
• To integrate this new residue into the phbuilder workflow.
• To enable accurate simulation of cysteine protonation states in biomolecular systems.

Main Methods:

• Introduced a titratable cysteine residue (CYST) for GROMACS λ-dynamics.
• Integrated CYST into the phbuilder workflow.
• Calibrated the model using an ALA-CYS-ALA tripeptide and validated on proteins (ACBP, DJ-1).

Main Results:

• The CYST residue accurately reproduces sigmoidal titration behavior and a target pKa of 8.33.
• Simulations of ACBP mutants show a high pKa regime for noncatalytic cysteines.
• The reactive Cys106 of DJ-1 is correctly placed in an acidic regime.

Conclusions:

• This work provides a practical extension for simulating titratable cysteines in biomolecular systems using GROMACS CpHMD.
• The new CYST residue enhances the capabilities of molecular dynamics for studying cysteine's role in biological processes.
• Accurate modeling of cysteine protonation states is now feasible for diverse protein environments.