2dm5

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spinqualitylabelsall models 2dm5, resolution 1.7Å Show:Asymmetric Unit Biological Assembly Drag the structure with the mouse to rotate   Export Animated Image

Thermodynamic Penalty Arising From Burial of a Ligand Polar Group Within a Hydrophobic Pocket of a Protein Receptor

Overview

Here, we examine the thermodynamic penalty arising from burial of a polar, group in a hydrophobic pocket that forms part of the binding-site of the, major urinary protein (MUP-I). X-ray crystal structures of the complexes, of octanol, nonanol and 1,8 octan-diol indicate that these ligands bind, with similar orientations in the binding pocket. Each complex is, characterised by a bridging water molecule between the hydroxyl group of, Tyr120 and the hydroxyl group of each ligand. The additional hydroxyl, group of 1,8 octan-diol is thereby forced to reside in a hydrophobic, pocket, and isothermal titration calorimetry experiments indicate that, this is accompanied by a standard free energy penalty of +21 kJ/mol with, respect to octanol and +18 kJ/mol with respect to nonanol. Consideration, of the solvation thermodynamics of each ligand enables the "intrinsic", (solute-solute) interaction energy to be determined, which indicates a, favourable enthalpic component and an entropic component that is small or, zero. These data indicate that the thermodynamic penalty to binding, derived from the unfavourable desolvation of 1,8 octan-diol is partially, offset by a favourable intrinsic contribution. Quantum chemical, calculations suggest that this latter contribution derives from favourable, solute-solute dispersion interactions.

About this Structure

2DM5 is a Single protein structure of sequence from Mus musculus with CD and ODI as ligands. Full crystallographic information is available from OCA.

Reference

Thermodynamic penalty arising from burial of a ligand polar group within a hydrophobic pocket of a protein receptor., Barratt E, Bronowska A, Vondrasek J, Cerny J, Bingham R, Phillips S, Homans SW, J Mol Biol. 2006 Oct 6;362(5):994-1003. Epub 2006 Aug 1. PMID:16935302

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