1yp6: Difference between revisions

Revision as of 17:07, 21 February 2008

Van der Waals Interactions Dominate Hydrophobic Association in a Protein Binding Site Occluded From Solvent Water

OverviewOverview

In the present study we examine the enthalpy of binding of 2-methoxy-3-isobutylpyrazine (IBMP) to the mouse major urinary protein (MUP), using a combination of isothermal titration calorimetry (ITC), NMR, X-ray crystallography, all-atom molecular dynamics simulations, and site-directed mutagenesis. Global thermodynamics data derived from ITC indicate that binding is driven by favorable enthalpic contributions, rather than a classical entropy-driven signature that might be expected given that the binding pocket of MUP-1 is very hydrophobic. The only ligand-protein hydrogen bond is formed between the side-chain hydroxyl of Tyr120 and the ring nitrogen of the ligand in the wild-type protein. ITC measurements on the binding of IBMP to the Y120F mutant demonstrate a reduced enthalpy of binding, but nonetheless binding is still enthalpy dominated. A combination of solvent isotopic substitution ITC measurements and all-atom molecular dynamics simulations with explicit inclusion of solvent water suggests that solvation is not a major contributor to the overall binding enthalpy. Moreover, hydrogen/deuterium exchange measurements suggest that there is no significant contribution to the enthalpy of binding derived from "tightening" of the protein structure. Data are consistent with binding thermodynamics dominated by favorable dispersion interactions, arising from the inequality of solvent-solute dispersion interactions before complexation versus solute-solute dispersion interactions after complexation, by virtue of poor solvation of the binding pocket.

About this StructureAbout this Structure

1YP6 is a Single protein structure of sequence from Mus musculus with , and as ligands. Full crystallographic information is available from OCA.

ReferenceReference

Van der Waals interactions dominate ligand-protein association in a protein binding site occluded from solvent water., Barratt E, Bingham RJ, Warner DJ, Laughton CA, Phillips SE, Homans SW, J Am Chem Soc. 2005 Aug 24;127(33):11827-34. PMID:16104761

Page seeded by OCA on Thu Feb 21 16:07:38 2008

Proteopedia Page Contributors and Editors (what is this?)Proteopedia Page Contributors and Editors (what is this?)

OCA

@@ Line 1: / Line 1: @@
-[[Image:1yp6.gif|left|200px]]<br /><applet load="1yp6" size="450" color="white" frame="true" align="right" spinBox="true"
+[[Image:1yp6.gif|left|200px]]<br /><applet load="1yp6" size="350" color="white" frame="true" align="right" spinBox="true"
 caption="1yp6, resolution 1.80&Aring;" />
 '''Van der Waals Interactions Dominate Hydrophobic Association in a Protein Binding Site Occluded From Solvent Water'''<br />
 ==Overview==
-In the present study we examine the enthalpy of binding of, 2-methoxy-3-isobutylpyrazine (IBMP) to the mouse major urinary protein, (MUP), using a combination of isothermal titration calorimetry (ITC), NMR, X-ray crystallography, all-atom molecular dynamics simulations, and, site-directed mutagenesis. Global thermodynamics data derived from ITC, indicate that binding is driven by favorable enthalpic contributions, rather than a classical entropy-driven signature that might be expected, given that the binding pocket of MUP-1 is very hydrophobic. The only, ligand-protein hydrogen bond is formed between the side-chain hydroxyl of, Tyr120 and the ring nitrogen of the ligand in the wild-type protein. ITC, measurements on the binding of IBMP to the Y120F mutant demonstrate a, reduced enthalpy of binding, but nonetheless binding is still enthalpy, dominated. A combination of solvent isotopic substitution ITC measurements, and all-atom molecular dynamics simulations with explicit inclusion of, solvent water suggests that solvation is not a major contributor to the, overall binding enthalpy. Moreover, hydrogen/deuterium exchange, measurements suggest that there is no significant contribution to the, enthalpy of binding derived from "tightening" of the protein structure., Data are consistent with binding thermodynamics dominated by favorable, dispersion interactions, arising from the inequality of solvent-solute, dispersion interactions before complexation versus solute-solute, dispersion interactions after complexation, by virtue of poor solvation of, the binding pocket.
+In the present study we examine the enthalpy of binding of 2-methoxy-3-isobutylpyrazine (IBMP) to the mouse major urinary protein (MUP), using a combination of isothermal titration calorimetry (ITC), NMR, X-ray crystallography, all-atom molecular dynamics simulations, and site-directed mutagenesis. Global thermodynamics data derived from ITC indicate that binding is driven by favorable enthalpic contributions, rather than a classical entropy-driven signature that might be expected given that the binding pocket of MUP-1 is very hydrophobic. The only ligand-protein hydrogen bond is formed between the side-chain hydroxyl of Tyr120 and the ring nitrogen of the ligand in the wild-type protein. ITC measurements on the binding of IBMP to the Y120F mutant demonstrate a reduced enthalpy of binding, but nonetheless binding is still enthalpy dominated. A combination of solvent isotopic substitution ITC measurements and all-atom molecular dynamics simulations with explicit inclusion of solvent water suggests that solvation is not a major contributor to the overall binding enthalpy. Moreover, hydrogen/deuterium exchange measurements suggest that there is no significant contribution to the enthalpy of binding derived from "tightening" of the protein structure. Data are consistent with binding thermodynamics dominated by favorable dispersion interactions, arising from the inequality of solvent-solute dispersion interactions before complexation versus solute-solute dispersion interactions after complexation, by virtue of poor solvation of the binding pocket.
 ==About this Structure==
-YP6 is a [http://en.wikipedia.org/wiki/Single_protein Single protein] structure of sequence from [http://en.wikipedia.org/wiki/Mus_musculus Mus musculus] with CD, CL and PRZ as [http://en.wikipedia.org/wiki/ligands ligands]. Full crystallographic information is available from [http://ispc.weizmann.ac.il/oca-bin/ocashort?id=1YP6 OCA].
+YP6 is a [http://en.wikipedia.org/wiki/Single_protein Single protein] structure of sequence from [http://en.wikipedia.org/wiki/Mus_musculus Mus musculus] with <scene name='pdbligand=CD:'>CD</scene>, <scene name='pdbligand=CL:'>CL</scene> and <scene name='pdbligand=PRZ:'>PRZ</scene> as [http://en.wikipedia.org/wiki/ligands ligands]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1YP6 OCA].
 ==Reference==
@@ Line 14: / Line 14: @@
 [[Category: Single protein]]
 [[Category: Barratt, E.]]
-[[Category: Bingham, R.J.]]
+[[Category: Bingham, R J.]]
-[[Category: Homans, S.W.]]
+[[Category: Homans, S W.]]
-[[Category: Laughton, C.A.]]
+[[Category: Laughton, C A.]]
-[[Category: Phillips, S.E.V.]]
+[[Category: Phillips, S E.V.]]
-[[Category: Warner, D.J.]]
+[[Category: Warner, D J.]]
 [[Category: CD]]
 [[Category: CL]]
@@ Line 24: / Line 24: @@
 [[Category: lipocalin; beta-barrel; mup1; 2-methoxy-3-isobutylpyrazine]]
-''Page seeded by [http://ispc.weizmann.ac.il/oca OCA ] on Wed Nov 21 06:57:39 2007''
+''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Thu Feb 21 16:07:38 2008''