2dm5: Difference between revisions

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[[Image:2dm5.gif|left|200px]]
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[[Image:2dm5.png|left|200px]]


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{{STRUCTURE_2dm5|  PDB=2dm5  |  SCENE=  }}  
{{STRUCTURE_2dm5|  PDB=2dm5  |  SCENE=  }}  


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




==Overview==
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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.
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{{ABSTRACT_PUBMED_16935302}}


==About this Structure==
==About this Structure==
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[[Category: Beta barrel]]
[[Category: Beta barrel]]
[[Category: Lipocalin]]
[[Category: Lipocalin]]
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Revision as of 13:06, 28 July 2008

File:2dm5.png

Template:STRUCTURE 2dm5

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

Template:ABSTRACT PUBMED 16935302

About this Structure

2DM5 is a Single protein structure of sequence from Mus musculus. 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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