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Contents |
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271 a.a.
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246 a.a.
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32 a.a.
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* Residue conservation analysis
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PDB id:
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Complex (thiazolidinedione/receptor)
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Title:
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Ligand-binding domain of the human peroxisome proliferator activated receptor gamma
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Structure:
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Peroxisome proliferator activated receptor gamma. Chain: a, b. Fragment: lbd (ligand binding domain), residues 207-477. Synonym: e domain. Engineered: yes. Nuclear receptor coactivator src-1. Chain: c. Fragment: fragment containing hd1 & hd2 residues 628-703. Engineered: yes.
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Source:
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Homo sapiens. Human. Organism_taxid: 9606. Cellular_location: nucleus. Gene: human ppar gamma cdna. Expressed in: escherichia coli bl21(de3). Expression_system_taxid: 469008. Gene: src-1 cdna.
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Biol. unit:
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Trimer (from
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Resolution:
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2.30Å
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R-factor:
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0.207
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R-free:
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0.264
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Authors:
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R.T.Nolte,G.B.Wisely,M.V.Milburn
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Key ref:
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R.T.Nolte
et al.
(1998).
Ligand binding and co-activator assembly of the peroxisome proliferator-activated receptor-gamma.
Nature,
395,
137-143.
PubMed id:
DOI:
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Date:
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14-Aug-98
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Release date:
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19-Jul-99
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PROCHECK
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Headers
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References
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P37231
(PPARG_HUMAN) -
Peroxisome proliferator-activated receptor gamma from Homo sapiens
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Seq:
Struc:
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505 a.a.
271 a.a.
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Enzyme class:
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Chain C:
E.C.2.3.1.48
- histone acetyltransferase.
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Reaction:
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L-lysyl-[protein] + acetyl-CoA = N6-acetyl-L-lysyl-[protein] + CoA + H+
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L-lysyl-[protein]
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+
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acetyl-CoA
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=
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N(6)-acetyl-L-lysyl-[protein]
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+
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CoA
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+
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H(+)
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Molecule diagrams generated from .mol files obtained from the
KEGG ftp site
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DOI no:
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Nature
395:137-143
(1998)
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PubMed id:
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Ligand binding and co-activator assembly of the peroxisome proliferator-activated receptor-gamma.
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R.T.Nolte,
G.B.Wisely,
S.Westin,
J.E.Cobb,
M.H.Lambert,
R.Kurokawa,
M.G.Rosenfeld,
T.M.Willson,
C.K.Glass,
M.V.Milburn.
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ABSTRACT
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The peroxisome proliferator-activated receptor-gamma (PPAR-gamma) is a
ligand-dependent transcription factor that is important in adipocyte
differentiation and glucose homeostasis and which depends on interactions with
co-activators, including steroid receptor co-activating factor-1 (SRC-1). Here
we present the X-ray crystal structure of the human apo-PPAR-gamma
ligand-binding domain (LBD), at 2.2 A resolution; this structure reveals a large
binding pocket, which may explain the diversity of ligands for PPAR-gamma. We
also describe the ternary complex containing the PPAR-gamma LBD, the
antidiabetic ligand rosiglitazone (BRL49653), and 88 amino acids of human SRC-1
at 2.3 A resolution. Glutamate and lysine residues that are highly conserved in
LBDs of nuclear receptors form a 'charge clamp' that contacts backbone atoms of
the LXXLL helices of SRC-1. These results, together with the observation that
two consecutive LXXLL motifs of SRC-1 make identical contacts with both subunits
of a PPAR-gamma homodimer, suggest a general mechanism for the assembly of
nuclear receptors with co-activators.
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Selected figure(s)
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Figure 1.
Figure 1: Crystal structure of the apo-PPAR- bold gamma- .
a, Ribbons drawing of the apo-PPAR-  LBD,
amino acids 207–476. The nomenclature of the helices is based
on the RXR-  crystal
structure^16. -Helices
are light blue;  -strands
are green; loops are brown. b, A worm backbone tracing of PPAR-
,
with a surface representation of the unoccupied van der Waals
space in the ligand-binding site. We determined the 'unoccupied'
volume by fitting in virtual atoms that did not occupy the van
der Waals surface of the protein. The total unoccupied volume is
 1,300
Å^3. c, Sequence alignment of the human PPAR LBDs. Amino
acids that are conserved between PPARs ,
and
 are
in yellow; the secondary structure that the sequence adopts in
PPAR- is
shown in red boxes for -helices
and blue arrows for -strands.
Residues involved in rosiglitazone binding are underlined. The
sequence alignment predicts that several residues involved in
direct interactions of PPAR- with
ligand are not conserved in the other PPAR subtypes, and
explains the specificity of TZDs for PPAR- :
residue H323 is not found in PPAR- ,
and Q286 is not found in PPAR- or
PPAR- .
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Figure 3.
Figure 3: SRC-1 interactions with PPAR- bold gamma-.
a, A sigma-weighted 2 F [o]– F [c] omit electron-density
map is shown contoured at 1.0  for
the area surrounding the rosiglitazone ligand. b, A ribbons
drawing of the PPAR- LBD
dimer and SRC-1, including the ligand rosiglitazone. The two
PPAR- monomers
are blue and green and the two SRC-1 interacting helices are
yellow. The structure of SRC-1 was determined from amino acids
628–640 and 684–703 and was crystallographically refined.
Very weak electron density from residues 670 to 684 was visible
but was not crystallographically refined and is shown as a
dashed line. SRC-1 amino acids 642–669 were disordered and not
structurally determined. The diagram shows how one SRC-1
molecule, with two interacting domains, forms a complex with a
PPAR- homodimer.
The dashed line connecting the two structurally determined
domains of SRC-1 is the proposed connection between these two
domains. c, The binding of SRC-1 (amino acids 628–642) to the
LXXLL-binding site of PPAR- .
SRC-1 is coloured: yellow, carbon; blue, nitrogen; red, oxygen.
The ribbon backbone of the PPAR- LBD
is in green. PPAR- amino
acids binding to the LXXLL helix are also shown in green. d,
Residues H631–T640 of SRC-1 are coloured as in c, with an
electrostatic surface of PPAR- showing
the coactivator-binding site. E471 and K301 side chains result
in the red (negative) and blue (positive) charges on the surface
of the coactivator-binding site at the N and C termini of the
SRC-1 helix, respectively. e, Residues H687–E696 of SRC-1 are
coloured as in c, with an electrostatic surface of PPAR- showing
the coactivator-binding site. f, Amino acids L465–K474 of the
PPAR- AF-2
helix of one monomer in the apo structure are shown in: green,
carbon; blue, nitrogen; red, oxygen, with an electrostatic
surface of PPAR- showing
the coactivator-binding site. E471 and K301 side chains result
in the red (negative) and blue (positive) charges on the surface
at the N and C terminus of the other PPAR- monomer.
This figure shows how one monomer in the apo crystal structure
orientates its AF-2 helix into the coactivator-binding site of
another crystallographically related monomer.
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The above figures are
reprinted
by permission from Macmillan Publishers Ltd:
Nature
(1998,
395,
137-143)
copyright 1998.
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Figures were
selected
by an automated process.
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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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D.Vidović,
S.A.Busby,
P.R.Griffin,
and
S.C.Schürer
(2011).
A combined ligand- and structure-based virtual screening protocol identifies submicromolar PPARγ partial agonists.
|
| |
ChemMedChem,
6,
94.
|
|
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|
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|
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H.J.Gim,
Y.J.Cheon,
J.H.Ryu,
and
R.Jeon
(2011).
Design and synthesis of benzoxazole containing indole analogs as peroxisome proliferator-activated receptor-γ/δ dual agonists.
|
| |
Bioorg Med Chem Lett,
21,
3057-3061.
|
|
|
|
|
|
|
J.H.Choi,
A.S.Banks,
T.M.Kamenecka,
S.A.Busby,
M.J.Chalmers,
N.Kumar,
D.S.Kuruvilla,
Y.Shin,
Y.He,
J.B.Bruning,
D.P.Marciano,
M.D.Cameron,
D.Laznik,
M.J.Jurczak,
S.C.Schürer,
D.Vidović,
G.I.Shulman,
B.M.Spiegelman,
and
P.R.Griffin
(2011).
Antidiabetic actions of a non-agonist PPARγ ligand blocking Cdk5-mediated phosphorylation.
|
| |
Nature,
477,
477-481.
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|
|
J.J.Kerrigan,
Q.Xie,
R.S.Ames,
and
Q.Lu
(2011).
Production of protein complexes via co-expression.
|
| |
Protein Expr Purif,
75,
1.
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|
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|
|
J.Zhang,
M.J.Chalmers,
K.R.Stayrook,
L.L.Burris,
Y.Wang,
S.A.Busby,
B.D.Pascal,
R.D.Garcia-Ordonez,
J.B.Bruning,
M.A.Istrate,
D.J.Kojetin,
J.A.Dodge,
T.P.Burris,
and
P.R.Griffin
(2011).
DNA binding alters coactivator interaction surfaces of the intact VDR-RXR complex.
|
| |
Nat Struct Mol Biol,
18,
556-563.
|
|
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|
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|
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N.Rochel,
F.Ciesielski,
J.Godet,
E.Moman,
M.Roessle,
C.Peluso-Iltis,
M.Moulin,
M.Haertlein,
P.Callow,
Y.Mély,
D.I.Svergun,
and
D.Moras
(2011).
Common architecture of nuclear receptor heterodimers on DNA direct repeat elements with different spacings.
|
| |
Nat Struct Mol Biol,
18,
564-570.
|
|
|
|
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|
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S.M.Hartig,
B.He,
W.Long,
B.M.Buehrer,
and
M.A.Mancini
(2011).
Homeostatic levels of SRC-2 and SRC-3 promote early human adipogenesis.
|
| |
J Cell Biol,
192,
55-67.
|
|
|
|
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|
Y.Bhurruth-Alcor,
T.Røst,
M.R.Jorgensen,
C.Kontogiorgis,
J.Skorve,
R.G.Cooper,
J.M.Sheridan,
W.D.Hamilton,
J.R.Heal,
R.K.Berge,
and
A.D.Miller
(2011).
Synthesis of novel PPARα/γ dual agonists as potential drugs for the treatment of the metabolic syndrome and diabetes type II designed using a new de novo design program protobuild.
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| |
Org Biomol Chem,
9,
1169-1188.
|
|
|
|
|
|
|
A.Bugge,
and
S.Mandrup
(2010).
Molecular Mechanisms and Genome-Wide Aspects of PPAR Subtype Specific Transactivation.
|
| |
PPAR Res,
2010,
0.
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|
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|
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B.M.De Taeye,
C.Morisseau,
J.Coyle,
J.W.Covington,
A.Luria,
J.Yang,
S.B.Murphy,
D.B.Friedman,
B.B.Hammock,
and
D.E.Vaughan
(2010).
Expression and regulation of soluble epoxide hydrolase in adipose tissue.
|
| |
Obesity (Silver Spring),
18,
489-498.
|
|
|
|
|
|
|
C.W.Li,
N.Ai,
G.K.Dinh,
W.J.Welsh,
and
J.D.Chen
(2010).
Human ADA3 regulates RARalpha transcriptional activity through direct contact between LxxLL motifs and the receptor coactivator pocket.
|
| |
Nucleic Acids Res,
38,
5291-5303.
|
|
|
|
|
|
|
E.Benedetti,
R.Galzio,
B.D'Angelo,
M.P.Cerù,
and
A.Cimini
(2010).
PPARs in Human Neuroepithelial Tumors: PPAR Ligands as Anticancer Therapies for the Most Common Human Neuroepithelial Tumors.
|
| |
PPAR Res,
2010,
427401.
|
|
|
|
|
|
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I.Takada,
A.P.Kouzmenko,
and
S.Kato
(2010).
PPAR-gamma Signaling Crosstalk in Mesenchymal Stem Cells.
|
| |
PPAR Res,
2010,
0.
|
|
|
|
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|
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J.Fidelak,
S.Ferrer,
M.Oberlin,
D.Moras,
A.Dejaegere,
and
R.H.Stote
(2010).
Dynamic correlation networks in human peroxisome proliferator-activated receptor-γ nuclear receptor protein.
|
| |
Eur Biophys J,
39,
1503-1512.
|
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|
|
|
|
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J.H.Choi,
A.S.Banks,
J.L.Estall,
S.Kajimura,
P.Boström,
D.Laznik,
J.L.Ruas,
M.J.Chalmers,
T.M.Kamenecka,
M.Blüher,
P.R.Griffin,
and
B.M.Spiegelman
(2010).
Anti-diabetic drugs inhibit obesity-linked phosphorylation of PPARgamma by Cdk5.
|
| |
Nature,
466,
451-456.
|
|
|
|
|
|
|
J.M.Phang,
W.Liu,
and
O.Zabirnyk
(2010).
Proline metabolism and microenvironmental stress.
|
| |
Annu Rev Nutr,
30,
441-463.
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L.Jiang,
J.Wan,
L.Q.Ke,
Q.G.Lü,
and
N.W.Tong
(2010).
Activation of PPARδ promotes mitochondrial energy metabolism and decreases basal insulin secretion in palmitate-treated β-cells.
|
| |
Mol Cell Biochem,
343,
249-256.
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and
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(2010).
Structural and functional insights into nuclear receptor signaling.
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| |
Adv Drug Deliv Rev,
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M.M.Musri,
R.Gomis,
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A chromatin perspective of adipogenesis.
|
| |
Organogenesis,
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|
|
M.Moreno,
A.Lombardi,
E.Silvestri,
R.Senese,
F.Cioffi,
F.Goglia,
A.Lanni,
and
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(2010).
PPARs: Nuclear Receptors Controlled by, and Controlling, Nutrient Handling through Nuclear and Cytosolic Signaling.
|
| |
PPAR Res,
2010,
0.
|
|
|
|
|
|
|
N.F.Mistry,
and
S.Cresci
(2010).
PPAR transcriptional activator complex polymorphisms and the promise of individualized therapy for heart failure.
|
| |
Heart Fail Rev,
15,
197-207.
|
|
|
|
|
|
|
P.K.Mishra,
N.Tyagi,
U.Sen,
I.G.Joshua,
and
S.C.Tyagi
(2010).
Synergism in hyperhomocysteinemia and diabetes: role of PPAR gamma and tempol.
|
| |
Cardiovasc Diabetol,
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S.Mukherjee,
and
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Orphan nuclear receptors as targets for drug development.
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| |
Pharm Res,
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|
S.N.Lewis,
J.Bassaganya-Riera,
and
D.R.Bevan
(2010).
Virtual Screening as a Technique for PPAR Modulator Discovery.
|
| |
PPAR Res,
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861238.
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|
|
|
|
|
|
T.Waku,
T.Shiraki,
T.Oyama,
K.Maebara,
R.Nakamori,
and
K.Morikawa
(2010).
The nuclear receptor PPARγ individually responds to serotonin- and fatty acid-metabolites.
|
| |
EMBO J,
29,
3395-3407.
|
|
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PDB codes:
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W.Li,
Y.Yuan,
Z.Luo,
X.Zheng,
L.Zhao,
W.Duan,
and
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(2010).
Bacterial expression, refolding, functional characterization, and mass spectrometric identification of full-length human PPAR-gamma.
|
| |
Biosci Biotechnol Biochem,
74,
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|
Y.H.Peng,
M.S.Coumar,
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W.H.Lin,
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and
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Structural basis for the improved potency of peroxisome proliferator-activated receptor (PPAR) agonists.
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| |
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and
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(2010).
Structural insights into the YAP and TEAD complex.
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| |
Genes Dev,
24,
235-240.
|
|
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PDB code:
|
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|
|
|
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|
|
Z.Zhang,
Q.Li,
F.Liu,
Y.Sun,
and
J.Zhang
(2010).
Prevention of diet-induced obesity by safflower oil: insights at the levels of PPARalpha, orexin, and ghrelin gene expression of adipocytes in mice.
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| |
Acta Biochim Biophys Sin (Shanghai),
42,
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A.Leonardini,
L.Laviola,
S.Perrini,
A.Natalicchio,
and
F.Giorgino
(2009).
Cross-Talk between PPARgamma and Insulin Signaling and Modulation of Insulin Sensitivity.
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| |
PPAR Res,
2009,
818945.
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A.M.Jetten
(2009).
Retinoid-related orphan receptors (RORs): critical roles in development, immunity, circadian rhythm, and cellular metabolism.
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| |
Nucl Recept Signal,
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A.Teichert,
L.A.Arnold,
S.Otieno,
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R.K.Guy,
and
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Quantification of the vitamin D receptor-coregulator interaction.
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Biochemistry,
48,
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A.di Masi,
E.De Marinis,
P.Ascenzi,
and
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(2009).
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Mol Aspects Med,
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B.Relic,
M.Zeddou,
A.Desoroux,
Y.Beguin,
D.de Seny,
and
M.G.Malaise
(2009).
Genistein induces adipogenesis but inhibits leptin induction in human synovial fibroblasts.
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Lab Invest,
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B.Zou,
L.Qiao,
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Current Understanding of the Role of PPARgamma in Gastrointestinal Cancers.
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| |
PPAR Res,
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Cadmium--a metallohormone?
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Toxicol Appl Pharmacol,
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(2009).
C/EBPalpha and the corepressors CtBP1 and CtBP2 regulate repression of select visceral white adipose genes during induction of the brown phenotype in white adipocytes by peroxisome proliferator-activated receptor gamma agonists.
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| |
Mol Cell Biol,
29,
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|
D.A.Elfaki,
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and
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(2009).
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| |
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S.C.Schock,
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T.M.Garcia-Bates,
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Structure of the intact PPAR-gamma-RXR- nuclear receptor complex on DNA.
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PDB codes:
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PDB code:
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Where a reference describes a PDB structure, the PDB
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