Coarse-grained Martini 3 model for collagen fibrils.

Area of Science:

• Biomolecular modeling
• Computational biophysics
• Materials science

Background:

• Collagen is a crucial structural protein in mammals, vital for connective tissues like bone and ligaments.
• Cross-links significantly influence collagen's mechanical properties, such as stiffness and rigidity.
• Existing simulation methods for collagen with cross-links are either computationally expensive (all-atom) or lack detail (coarse-grained).

Purpose of the Study:

• To develop and validate a novel coarse-grained computational model for fibrillar collagen, incorporating cross-links.
• To bridge the gap between atomistic and simplified coarse-grained simulations for collagen.
• To provide a tool for investigating age-related changes in tissue mechanics and developing biomimetic materials.

Main Methods:

• Development of a computational model using the Martini 3 coarse-grained force field.
• Parametrization of fibrillar collagen structure and cross-links within the model.
• Validation through extensive equilibrium and nonequilibrium molecular dynamics simulations against experimental data and all-atom simulations.

Main Results:

• Successful development and validation of a coarse-grained collagen model that includes cross-links.
• The model accurately reproduces experimental properties and aligns with all-atom simulation results.
• Demonstrated capability to simulate collagen at scales not accessible to fully atomistic methods.

Conclusions:

• The developed Martini 3-based model offers a computationally efficient yet detailed approach to simulating collagen.
• This model can provide insights into the role of cross-links in collagen's mechanical behavior.
• Potential applications include studying aging effects on tissue mechanics and designing advanced biomimetic materials.