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Simulations of peptide-graphene interactions in explicit water
Aerial N Camden1, Stephen A Barr, Rajiv J Berry
1Air Force Research Laboratory, Materials & Manufacturing Directorate , 2941 Hobson Way, WPAFB, Ohio 45433, United States.
The Journal of Physical Chemistry. B
|August 23, 2013
Summary
Graphene-peptide interactions were studied using molecular dynamics. Arginine, glutamine, and asparagine showed the strongest binding, influenced by solvent effects, highlighting the importance of explicit water in simulations.
Area of Science:
- Materials Science
- Biochemistry
- Computational Chemistry
Background:
- Graphene's unique properties enable applications in biochemical sensors.
- Peptide-graphene interactions offer insights into larger biomolecule binding.
- Understanding these interactions is crucial for designing advanced biosensing platforms.
Purpose of the Study:
- To compute binding enthalpies of GXG tripeptides with graphene.
- To investigate the influence of solvent on peptide-graphene interactions.
- To analyze conformational changes of peptides upon binding to graphene.
Main Methods:
- Classical molecular dynamics simulations were employed.
- Explicit water molecules were included to model solvent effects.
- Binding enthalpies of various tripeptides with graphene were calculated.
Main Results:
- Arginine, glutamine, and asparagine exhibited the strongest binding affinities.
- Peptide conformation changed significantly at the graphene interface compared to solution.
- Hydrophilic residues showed stronger binding, driven by solvent influence.
Conclusions:
- Explicit solvent inclusion is essential for accurate peptide-graphene system modeling.
- The study provides a framework for validating surface interaction parameters.
- Findings are applicable to diverse molecular fragments and computational methods.
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