title: Calcium-α-L-guluronate complexes: Ca2+ binding modes from DFT-MD simulations.
abstract: The interactions of divalent calcium ions with a single α-L-guluronate anion and oligo(α-L-guluronate) chain have been studied in terms of the 'hybrid' molecular dynamics technique in which the selected parts of the system are treated with different level of theory (DFT-MD). The simulations were focused on obtaining the free energy profiles designed to clarify the possible calcium binding modes. In all considered cases, the calcium ion is coordinated by carboxyl oxygen atoms and water molecules exclusively. The results allowed for (i) determining the dentacy of calcium binding; (ii) estimating the calcium binding/unbinding-related free energy profiles; and (iii) positive verification of the previously [J. Comput. Chem. 2011, 32, 2988] proposed modification of the egg-box model describing the calcium alginate/guluronate structure. Additionally, the findings indicate that the polarization of the carboxyl group induced by the presence of Ca(2+) ion causes the increase of the free energy barrier separating the 'free' and 'bound' states of Ca(2+), in comparison to the classical biomolecular force fields (GROMOS/SPC and GLYCAM/TIP3P).
authors.affiliation: Institute of Catalysis and Surface Chemistry, Polish Academy of Sciences , ul. Niezapominajek 8, 30-239 Cracow, Poland.
authors.forename: Wojciech
authors.initials: W
authors.lastname: Plazinski
authors.forename: Mateusz
authors.initials: M
authors.lastname: Drach