Supramolecular Assembly of a Biomineralizing Antimicrobial Peptide in Coarse-Grained Monte Carlo Simulations
Physics and Astronomy
Monte Carlo simulations are used to model the self-organizing behavior of the biomineralizing peptide KSL (KKVVFKVKFK) in the presence of phosphate. Originally identified as an antimicrobial peptide, KSL also directs the formation of biosilica through a hypothetical supramolecular template that requires phosphate for assembly. Specificity of each residue and the interactions between the peptide and phosphate are considered in a coarse-grained model. Both local and global physical quantities are calculated as the constituents execute their stochastic motion in the presence and absence of phosphate. Ordered peptide aggregates develop after simulations reach thermodynamic equilibrium, wherein phosphates form bridging ligands with lysines and are found interdigitated between peptide molecules. Results demonstrate that interactions between the lysines and phosphate drive self-organization into lower energy conformations of interconnected peptide scaffolds that resemble the supramolecular structures of polypeptide-and polyamine-mediated silica condensation systems. Furthermore, the specific phosphate-peptide organization appears to mimic the zwitterionic structure of native silaffins (scaffold proteins of diatom shells), suggesting a similar template organization for silica deposition between the in vitro KSL and silaffin systems.
Physical Chemistry Chemical Physics
Eby, D. M.,
Johnson, G. R.,
Farmer, B. L.,
Pandey, R. B.
(2011). Supramolecular Assembly of a Biomineralizing Antimicrobial Peptide in Coarse-Grained Monte Carlo Simulations. Physical Chemistry Chemical Physics, 13(3), 1123-1130.
Available at: https://aquila.usm.edu/fac_pubs/546