Integrating Explicit and Implicit Fullerene Models into UNRES Force Field for Protein Interaction Studies.

Area of Science:

• Computational chemistry
• Biophysics
• Nanotechnology

Background:

• Fullerenes, like C60, have unique properties for nanomedicine.
• Understanding fullerene-protein interactions is crucial for applications.
• Current methods often require restraints, limiting biological relevance.

Purpose of the Study:

• To implement explicit and implicit C60 models into the UNRES coarse-grained force field.
• To investigate fullerene-protein interactions without protein structure restraints.
• To enable accurate simulations at biologically relevant scales.

Main Methods:

• Utilized the UNRES coarse-grained force field with integrated C60 models.
• Performed molecular dynamics simulations on five model proteins with and without C60.
• Analyzed contact probabilities and protein flexibility.

Main Results:

• Distinct fullerene-protein interaction patterns were observed for different proteins.
• FK506 binding protein showed specific binding sites; others had generalized interactions.
• Explicit C60 model accurately predicted protein flexibility and binding energies compared to all-atom simulations.

Conclusions:

• The UNRES force field with C60 models provides an efficient framework for studying nanoparticle-biomolecule interactions.
• This method allows for simulations of large conformational changes, crucial for understanding biological impacts.
• The computational tools aid in designing safer and more effective nanomaterials for biomedical use.