Computational Elucidation of Recombinant Fusion Protein Effect on Peptide-Directed Nanoparticles

Nanoparticles synthesized using various peptides have optimized properties and functional abilities which can be achieved via peptide flexibility and site specificity. Using peptide Pd4 and other alanine substitution combinations of Pd4 attached to a green fluorescent protein (GFPuv), nanoparticles with well-defined sizes that are soluble in aqueous solutions can be produced. In this study, extensive molecular dynamics simulations explored the structural and functional differences between the free peptides and the peptides bound to the GFPuv used in nanoparticle production. Binding affinities of histidines of Pd4 peptide and its two mutants A6 and A11 to a palladium atom were calculated using the free energy perturbation method. Interestingly, the average particle sizes obtained from transmission electron microscopy (TEM) images correlated with our calculated free energies of different peptide sequences. Remarkably, when the peptide was bound to GFPuv, the free energies of histidine were very similar in the wild-type and other mutated peptides. However, this trend is not observed with free peptide simulations, where binding affinities differ by mutation of histidine residues. This study describes, at a molecular level, the role of amino acid sequence on binding affinity of the peptide to the surface of the palladium particles, and the functional ability of the GFPuv protein controlling these free energies irrespective of peptide sequence. Our study will provide a framework for designing free and protein attached peptides that facilitate peptide-mediated nanoparticle formation with well-regulated properties.