Coarse-Grained Simulation of Protein-Imprinted Hydrogels
I Zadok and S Srebnik, JOURNAL OF PHYSICAL CHEMISTRY B, 122, 7091-7101 (2018).
The MARTINI force-field is adapted for acrylic functional monomers and used to simulate protein-imprinted polymers, including complexation in solution, cross-linking reaction, washing, and rebinding of the protein. A globally controlled grand canonical Monte Carlo simulation combined with molecular dynamics is used to achieve proper hydration and swelling of the gel. Two gel formulations are compared, one with only polar functional monomers and one with additional small number of charged monomers. Imprinted hydrogels are evaluated for two proteins, lysozyme, and cytochrome c and chosen due to their similarity in size and isoelectric point, though it is known that their imprinting behavior is very different. Analysis of diffusion of the proteins within the gel shows that their interaction with functional monomers and their diffusion mechanism differ substantially and hence affect their specific and nonspecific interactions with the gel.
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