This old version of Proteopedia is provided for student assignments while the new version is undergoing repairs. Content and edits done in this old version of Proteopedia after March 1, 2026 will eventually be lost when it is retired in about June of 2026.

Apply for new accounts at the new Proteopedia. Your logins will work in both the old and new versions.


2dm5

From Proteopedia

(Difference between revisions)
Jump to: navigation, search
Line 1: Line 1:
-
[[Image:2dm5.gif|left|200px]]
+
{{Seed}}
 +
[[Image:2dm5.png|left|200px]]
<!--
<!--
Line 9: Line 10:
{{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==
+
<!--
-
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.
+
The line below this paragraph, {{ABSTRACT_PUBMED_16935302}}, adds the Publication Abstract to the page
 +
(as it appears on PubMed at http://www.pubmed.gov), where 16935302 is the PubMed ID number.
 +
-->
 +
{{ABSTRACT_PUBMED_16935302}}
==About this Structure==
==About this Structure==
Line 30: Line 34:
[[Category: Beta barrel]]
[[Category: Beta barrel]]
[[Category: Lipocalin]]
[[Category: Lipocalin]]
-
''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Sun May 4 00:43:25 2008''
+
 
 +
''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Mon Jul 28 16:06:44 2008''

Revision as of 13:06, 28 July 2008

Image: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

Page seeded by OCA on Mon Jul 28 16:06:44 2008

Proteopedia Page Contributors and Editors (what is this?)

OCA

Retrieved from "http://52.214.119.220/wiki/index.php/2dm5"
Personal tools