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Entropy Rules: Molecular Dynamics Simulations of Model Oligomers for Thermoresponsive Polymers.

ABSTRACT: We attempted to attain atomic-scale insights into the mechanism of the heat-induced phase transition of two thermoresponsive polymers containing amide groups, poly(N-isopropylacrylamide) (PNIPAM) and poly(2-isopropyl-2-oxazoline) (PIPOZ), and we succeeded in reproducing the existence of lower critical solution temperature (LCST). The simulation data are in accord with experimental findings. We found out that the entropy has an important contribution to the thermodynamics of the phase separation transition. Moreover, after decomposing further the entropy change to contributions from the solutes and from the solvent, it appeared out that the entropy of the solvent has the decisive share for the lowering of the free energy of the system when increasing the temperature above the LCST. Our conclusion is that the thermoresponsive behavior is driven by the entropy of the solvent. The water molecules structured around the functional groups of the polymer that are exposed to contact with the solvent in the extended conformation lower the enthalpy of the system, but at certain temperature the extended conformation of the polymer collapses as a result of dominating entropy gain from "released" water molecules. We stress also on the importance of using more than one reference molecule in the simulation box at the setup of the simulation.

SUBMITTER: Kantardjiev A

PROVIDER: S-EPMC7597358 | biostudies-literature | 2020 Oct

REPOSITORIES: biostudies-literature

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Entropy Rules: Molecular Dynamics Simulations of Model Oligomers for Thermoresponsive Polymers.

Kantardjiev Alexander A Ivanov Petko M PM

Entropy (Basel, Switzerland) 20201021 10

We attempted to attain atomic-scale insights into the mechanism of the heat-induced phase transition of two thermoresponsive polymers containing amide groups, poly(<i>N</i>-isopropylacrylamide) (PNIPAM) and poly(2-isopropyl-2-oxazoline) (PIPOZ), and we succeeded in reproducing the existence of lower critical solution temperature (LCST). The simulation data are in accord with experimental findings. We found out that the entropy has an important contribution to the thermodynamics of the phase sepa ...[more]

PMID: 33286955

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Project description:Molecular recognition by enzymes is a complicated process involving thermodynamic energies governing protein-ligand interactions. In order to aid the estimation of inhibitory activity of compounds targeting an enzyme, several computational methods can be employed to dissect this intermolecular contact. Herein, we report a structural dynamics investigation of an epigenetic enzyme HDAC2 in differentiating its binding to various inhibitors within the sub-sites of its active site. Molecular dynamics (MD) simulation was employed to elucidate the intermolecular interactions as well as the dynamics behavior of ligand binding. MD trajectories of five distinct HDAC2-inhibitor complexes reveal that compounds lacking adequate contacts with the opening rim of the active site possess high fluctuation along the cap portion, thus weakening the overall affinity. Key intermolecular interactions determining the effective binding of inhibitors include hydrogen bonds with Gly154, Asp181, and Tyr308; hydrophobic interactions between Phe155/Phe210 and the linker region; and a pi-stacking with Arg39 at the foot pocket. Decomposition of the binding free energy calculated per-residue by MM/PBSA also indicates that the interactions within the internal foot pocket, especially with residues Met35, Leu144, Gly305, and Gly306, can contribute significantly to the ligand binding. Additionally, configurational entropy of the binding was estimated and compared to the scale of the binding free energy in order to assess its contribution to the binding and to differentiate various ligand partners. It was found that the levels of entropic contribution are comparable among a set of structurally similar carbamide ligands, while it is greatly different for the set of unrelated ligands, ranging from 2.75 to 16.38 kcal/mol for the five inhibitors examined. These findings exemplify the importance of assessing molecular dynamics as well as estimating the entropic contribution in evaluating the ligand binding mechanism.

Dataset Information

Entropy Rules: Molecular Dynamics Simulations of Model Oligomers for Thermoresponsive Polymers.

Publications

Entropy Rules: Molecular Dynamics Simulations of Model Oligomers for Thermoresponsive Polymers.

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