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PDBsum entry 1qy1
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Transport protein
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PDB id
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1qy1
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Contents |
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* Residue conservation analysis
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PDB id:
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| Name: |
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Transport protein
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Title:
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Thermodynamics of binding of 2-methoxy-3-isopropylpyrazine and 2- methoxy-3-isobutylpyrazine to the major urinary protein
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Structure:
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Major urinary protein. Chain: a. Engineered: yes
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Source:
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Mus musculus. House mouse. Organism_taxid: 10090. Strain: swiss. Gene: mup1. Expressed in: escherichia coli. Expression_system_taxid: 562.
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Resolution:
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1.70Å
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R-factor:
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0.181
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R-free:
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0.210
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Authors:
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R.J.Bingham,J.B.C.Findlay,S.-Y.Hsieh,A.P.Kalverda,A.Kjellberg, C.Perazzolo,S.E.V.Phillips,K.Seshadri,C.H.Trinh,W.B.Turnbull, G.Bodenhausen,S.W.Homans
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Key ref:
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R.J.Bingham
et al.
(2004).
Thermodynamics of binding of 2-methoxy-3-isopropylpyrazine and 2-methoxy-3-isobutylpyrazine to the major urinary protein.
J Am Chem Soc,
126,
1675-1681.
PubMed id:
DOI:
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Date:
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09-Sep-03
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Release date:
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24-Feb-04
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PROCHECK
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Headers
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References
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P11588
(MUP1_MOUSE) -
Major urinary protein 1 from Mus musculus
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Seq:
Struc:
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180 a.a.
157 a.a.*
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Key: |
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PfamA domain |
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Secondary structure |
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CATH domain |
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*
PDB and UniProt seqs differ
at 2 residue positions (black
crosses)
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DOI no:
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J Am Chem Soc
126:1675-1681
(2004)
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PubMed id:
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Thermodynamics of binding of 2-methoxy-3-isopropylpyrazine and 2-methoxy-3-isobutylpyrazine to the major urinary protein.
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R.J.Bingham,
J.B.Findlay,
S.Y.Hsieh,
A.P.Kalverda,
A.Kjellberg,
C.Perazzolo,
S.E.Phillips,
K.Seshadri,
C.H.Trinh,
W.B.Turnbull,
G.Bodenhausen,
S.W.Homans.
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ABSTRACT
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In the present study we examine the thermodynamics of binding of two related
pyrazine-derived ligands to the major urinary protein, MUP-I, using a
combination of isothermal titration calorimetry (ITC), X-ray crystallography,
and NMR backbone (15)N and methyl side-chain (2)H relaxation measurements.
Global thermodynamics data derived from ITC indicate that binding is driven by
favorable enthalpic contributions, rather than the classical entropy-driven
hydrophobic effect. Unfavorable entropic contributions from the protein backbone
and side-chain residues in the vicinity of the binding pocket are partially
offset by favorable entropic contributions at adjacent positions, suggesting a
"conformational relay" mechanism whereby increased rigidity of residues on
ligand binding are accompanied by increased conformational freedom of side
chains in adjacent positions. The principal driving force governing ligand
affinity and specificity can be attributed to solvent-driven enthalpic effects
from desolvation of the protein binding pocket.
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Literature references that cite this PDB file's key reference
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PubMed id
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Reference
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L.Wang,
B.J.Berne,
and
R.A.Friesner
(2011).
Ligand binding to protein-binding pockets with wet and dry regions.
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Proc Natl Acad Sci U S A,
108,
1326-1330.
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C.Diehl,
O.Engström,
T.Delaine,
M.Håkansson,
S.Genheden,
K.Modig,
H.Leffler,
U.Ryde,
U.J.Nilsson,
and
M.Akke
(2010).
Protein flexibility and conformational entropy in ligand design targeting the carbohydrate recognition domain of galectin-3.
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J Am Chem Soc,
132,
14577-14589.
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PDB code:
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N.R.Syme,
C.Dennis,
A.Bronowska,
G.C.Paesen,
and
S.W.Homans
(2010).
Comparison of entropic contributions to binding in a "hydrophilic" versus "hydrophobic" ligand-protein interaction.
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J Am Chem Soc,
132,
8682-8689.
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P.Setny,
R.Baron,
and
J.A.McCammon
(2010).
How Can Hydrophobic Association Be Enthalpy Driven?
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J Chem Theory Comput,
6,
2866-2871.
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S.Perez-Miller,
Q.Zou,
M.V.Novotny,
and
T.D.Hurley
(2010).
High resolution X-ray structures of mouse major urinary protein nasal isoform in complex with pheromones.
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Protein Sci,
19,
1469-1479.
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PDB codes:
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B.J.Killian,
J.Y.Kravitz,
S.Somani,
P.Dasgupta,
Y.P.Pang,
and
M.K.Gilson
(2009).
Configurational entropy in protein-peptide binding: computational study of Tsg101 ubiquitin E2 variant domain with an HIV-derived PTAP nonapeptide.
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J Mol Biol,
389,
315-335.
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J.Michel,
J.Tirado-Rives,
and
W.L.Jorgensen
(2009).
Prediction of the water content in protein binding sites.
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J Phys Chem B,
113,
13337-13346.
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K.Teilum,
J.G.Olsen,
and
B.B.Kragelund
(2009).
Functional aspects of protein flexibility.
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Cell Mol Life Sci,
66,
2231-2247.
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S.A.White,
L.Briand,
D.J.Scott,
and
A.J.Borysik
(2009).
Structure of rat odorant-binding protein OBP1 at 1.6 A resolution.
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Acta Crystallogr D Biol Crystallogr,
65,
403-410.
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PDB code:
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V.Ball,
and
C.Maechling
(2009).
Isothermal microcalorimetry to investigate non specific interactions in biophysical chemistry.
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Int J Mol Sci,
10,
3283-3315.
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C.A.MacRaild,
A.H.Daranas,
A.Bronowska,
and
S.W.Homans
(2007).
Global changes in local protein dynamics reduce the entropic cost of carbohydrate binding in the arabinose-binding protein.
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J Mol Biol,
368,
822-832.
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C.Perazzolo,
M.Verde,
S.W.Homans,
and
G.Bodenhausen
(2007).
Evidence of chemical exchange in recombinant Major Urinary Protein and quenching thereof upon pheromone binding.
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J Biomol NMR,
38,
3-9.
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J.Golebiowski,
S.Antonczak,
S.Fiorucci,
and
D.Cabrol-Bass
(2007).
Mechanistic events underlying odorant binding protein chemoreception.
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Proteins,
67,
448-458.
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N.R.Syme,
C.Dennis,
S.E.Phillips,
and
S.W.Homans
(2007).
Origin of heat capacity changes in a "nonclassical" hydrophobic interaction.
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Chembiochem,
8,
1509-1511.
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PDB code:
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A.Ababou,
and
J.E.Ladbury
(2006).
Survey of the year 2004: literature on applications of isothermal titration calorimetry.
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J Mol Recognit,
19,
79-89.
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N.Shimokhina,
A.Bronowska,
and
S.W.Homans
(2006).
Contribution of ligand desolvation to binding thermodynamics in a ligand-protein interaction.
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Angew Chem Int Ed Engl,
45,
6374-6376.
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C.Perazzolo,
J.Wist,
K.Loth,
L.Poggi,
S.Homans,
and
G.Bodenhausen
(2005).
Effects of protein-pheromone complexation on correlated chemical shift modulations.
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J Biomol NMR,
33,
233-242.
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M.Haroun,
C.Ravelet,
A.Ravel,
C.Grosset,
A.Villet,
and
E.Peyrin
(2005).
Thermodynamic origin of the chiral recognition of tryptophan on teicoplanin and teicoplanin aglycone stationary phases.
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J Sep Sci,
28,
409-420.
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S.G.Patching,
S.A.Baldwin,
A.D.Baldwin,
J.D.Young,
M.P.Gallagher,
P.J.Henderson,
and
R.B.Herbert
(2005).
The nucleoside transport proteins, NupC and NupG, from Escherichia coli: specific structural motifs necessary for the binding of ligands.
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Org Biomol Chem,
3,
462-470.
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S.W.Homans
(2005).
Probing the binding entropy of ligand-protein interactions by NMR.
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Chembiochem,
6,
1585-1591.
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J.E.Ladbury,
and
M.A.Williams
(2004).
The extended interface: measuring non-local effects in biomolecular interactions.
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Curr Opin Struct Biol,
14,
562-569.
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J.L.Hurst,
and
R.J.Beynon
(2004).
Scent wars: the chemobiology of competitive signalling in mice.
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Bioessays,
26,
1288-1298.
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The most recent references are shown first.
Citation data come partly from CiteXplore and partly
from an automated harvesting procedure. Note that this is likely to be
only a partial list as not all journals are covered by
either method. However, we are continually building up the citation data
so more and more references will be included with time.
Where a reference describes a PDB structure, the PDB
code is
shown on the right.
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Links
