Self-assembling dipeptides: including solvent degrees of freedom in a coarse-grained model

Area of Science:

• Computational chemistry
• Biomolecular modeling
• Multiscale simulations

Background:

• Previous work outlined a solvent-free coarse-grained peptide model based on atomistic descriptions.
• This model captured molecular flexibility and peptide interactions in solution.

Purpose of the Study:

• To develop a coarse-grained model that explicitly includes solvent degrees of freedom.
• To accurately represent peptide-peptide interactions and thermodynamic association in water.
• To enable efficient multiscale simulations of peptide self-assembly.

Main Methods:

• Structure-based coarse graining methodology to preserve solvation structure.
• Devising nonbonded potentials for peptide beads to represent interactions in water.
• Development of both implicit- and explicit-solvent models.

Main Results:

• Successfully created coarse-grained models with explicit solvent degrees of freedom.
• The models accurately reproduce peptide-peptide interactions and thermodynamic association.
• Demonstrated efficient simulation of long time-scale and large length-scale peptide self-assembly.

Conclusions:

• The developed coarse-grained models are powerful tools for multiscale and scale-bridging simulations.
• These models facilitate efficient simulation of complex biomolecular processes like peptide self-assembly.
• Combined with backmapping, atomistic structures of aggregates can be obtained efficiently.