A coil-to-globule transition capable coarse-grained model for poly(N-isopropylacrylamide)

Control of polymer-protein interactions by tuning the composition and length of polymer chains

Nanomoduling the 3D shape and chemical functionalities in a synthetic polymer may create recognition cavities for biomacromolecule binding, which serves as an attractive alternative to natural antibodies with much less cost. To obtain fundamental understanding and predict molecular design rules of the polymer antibody, we analyze the complex structure between the biomarker protein epithelial cell adhesion molecule (EpCAM) and a series of polymer ligands via molecular dynamics (MD) simulations. For monomeric ligands, strong enrichment of aromatic residues in protein binding sites is revealed, in line with the reported observations for natural antibodies. Yet, for linear polymers with a growing degree of polymerization, for the first time, a drastic change is revealed on the type of enriched protein residues and the location of protein binding sites, driven by the increasing steric hindrance effect that makes the adsorption of the polymer in the protein exterior feasible. Varying the polymer length and monomeric composition also significantly affects the ligand binding affinity. Here, we have captured three distinct dependences of the ligand binding free energy on the degree of polymerization: for NIPAm based hydrophilic polymers, TBAm dominated hydrophobic polymers and AAc dominated charged polymers. These results can be rationalized by the complex structure and the composition of protein residues at the binding interface. The entire analysis demonstrates unique binding features for polymer ligands and the possibility to modulate their binding sites and affinity by engineering the polymer structure.

Molecular insights on poly(N-isopropylacrylamide) coil-to-globule transition induced by pressure

By using extensive all-atom molecular dynamics simulations of an atactic linear polymer chain, we provide microscopic insights into poly(N-isopropylacrylamide) (PNIPAM) coil-to-globule transition addressing the roles played by both temperature and pressure. We detect a coil-to-globule transition up to large pressures, showing a reentrant behavior of the critical temperature with increasing pressure in agreement with experimental observations. Furthermore, again confirming the experimental findings, we report the existence at high pressures of a new kind of globular state. It is characterized by a more structured hydration shell that is closer to PNIPAM hydrophobic domains, as compared to the globular state observed at atmospheric pressure. Our results highlight that temperature and pressure induce a PNIPAM coil-to-globule transition through different molecular mechanisms, opening the way for a systematic use of both thermodynamic variables to tune the location of the transition and the properties of the associated swollen/collapsed states.

Coarse-grained force-field for large scale molecular dynamics simulations of polyacrylamide and polyacrylamide-gels based on quantum mechanics

Developing a coarse-grained force field for polyacrylamide based on quantum mechanics equation of state.