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Issue 11, 2012
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Exploring the properties of small molecule protein binding via molecular simulations: the TRSH–p53 core domain complex

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Abstract

Molecular dynamics simulations have been performed to investigate the binding of tris(hydroxymethyl)-aminomethane to the surface of the core domain of the mouse cellular tumor antigen p53 employing the GROMOS 45A4 and 53A6 force field parameter sets. A close investigation of the crystal structure reported by Ho et al. revealed that the protonated form is bound to the protein, i.e. a tris(hydroxymethyl)-methylammonium ion (TRSH). Molecular Dynamics (MD) simulations indicate that the p53 protein gains stability upon binding the ligand. In addition to MD simulations of the p53 protein with and without the TRSH compound, thermodynamic integration was utilised to estimate the free enthalpy of binding of the TRSH–p53 complex, which was estimated to be −49 and −54 kJ mol−1 utilising the 45A4 and 53A6 force fields, respectively.

Graphical abstract: Exploring the properties of small molecule protein binding via molecular simulations: the TRSH–p53 core domain complex

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Publication details

The article was received on 30 Apr 2012, accepted on 06 Jul 2012 and first published on 11 Jul 2012


Article type: Paper
DOI: 10.1039/C2MB25166C
Mol. BioSyst., 2012,8, 2891-2900

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    Exploring the properties of small molecule protein binding via molecular simulations: the TRSH–p53 core domain complex

    T. S. Hofer and W. F. van Gunsteren, Mol. BioSyst., 2012, 8, 2891
    DOI: 10.1039/C2MB25166C

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