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Issue 5, 2012
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Molecular theory of solvation for supramolecules and soft matter structures: application to ligand binding, ion channels, and oligomeric polyelectrolyte gelators

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Abstract

We combine the statistical–mechanical 1D/3D-RISM-KH molecular theory of solvation with DFT electronic structure calculations and MD and coarse-grained DPD simulations, and apply them to study association phenomena in synthetic organic soft matter and biomolecular systems. This combined approach from electronic to molecular structure and coarse-graining allows us to address complex processes occurring in solution on very long timescales, such as proteinligand binding, distributions of electrolyte solution species in ion channels, and oligomeric polyelectrolyte gelation. The statistics of rare events involving supramolecular solute and solvent is accounted for analytically within the 3D-RISM-KH molecular theory of solvation. The hybrid MD/3D-RISM-KH method for molecular dynamics of the biomolecule in the potential of mean force obtained with the molecular theory of solvation has been implemented in the Amber package. The 3D molecular theory of solvation also replaces MM/GB(PB)SA post-processing using empirical treatment of non-polar contributions with MM/3D-RISM-KH evaluation of the solvation thermodynamics. The 3D-RISM-KH theory accurately yields the solvation structure for biomolecular systems as large as the GroEL chaperonin complex, GLIC ion channel, and 3D maps of ligand binding affinity of antiprion compound to mouse PrPC prion protein at once without phenomenological approximations. We apply the DFT/1D-3D-RISM-KH/DPD multiscale approach to investigate the structural and dynamical properties and gelation ability of oligomeric polyelectrolyte gelators, towards understanding of the gelation mechanism.

Graphical abstract: Molecular theory of solvation for supramolecules and soft matter structures: application to ligand binding, ion channels, and oligomeric polyelectrolyte gelators

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Publication details

The article was received on 11 Aug 2011, accepted on 03 Nov 2011 and first published on 12 Dec 2011


Article type: Paper
DOI: 10.1039/C1SM06542D
Citation: Soft Matter, 2012,8, 1508-1520
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    Molecular theory of solvation for supramolecules and soft matter structures: application to ligand binding, ion channels, and oligomeric polyelectrolyte gelators

    A. Kovalenko, A. E. Kobryn, S. Gusarov, O. Lyubimova, X. Liu, N. Blinov and M. Yoshida, Soft Matter, 2012, 8, 1508
    DOI: 10.1039/C1SM06542D

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