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PDBsum entry 1gjh
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Contents |
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* Residue conservation analysis
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PDB id:
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Apoptosis
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Title:
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Human bcl-2, isoform 2
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Structure:
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Protein (apoptosis regulator bcl-2 with putative flexible loop replaced with a portion of apoptosis regulator bcl-x protein). Chain: a. Engineered: yes
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Source:
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Homo sapiens. Human. Organism_taxid: 9606. Expressed in: escherichia coli. Expression_system_taxid: 562
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NMR struc:
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1 models
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Authors:
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A.M.Petros,A.Medek,D.G.Nettesheim,D.H.Kim,H.S.Yoon,K.Swift, E.D.Matayoshi,T.Oltersdorf,S.W.Fesik
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Key ref:
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A.M.Petros
et al.
(2001).
Solution structure of the antiapoptotic protein bcl-2.
Proc Natl Acad Sci U S A,
98,
3012-3017.
PubMed id:
DOI:
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Date:
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31-May-01
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Release date:
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13-Jun-01
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Supersedes:
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PROCHECK
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Headers
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References
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P10415
(BCL2_HUMAN) -
Apoptosis regulator Bcl-2 from Homo sapiens
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Seq:
Struc:
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239 a.a.
164 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 14 residue positions (black
crosses)
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DOI no:
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Proc Natl Acad Sci U S A
98:3012-3017
(2001)
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PubMed id:
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Solution structure of the antiapoptotic protein bcl-2.
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A.M.Petros,
A.Medek,
D.G.Nettesheim,
D.H.Kim,
H.S.Yoon,
K.Swift,
E.D.Matayoshi,
T.Oltersdorf,
S.W.Fesik.
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ABSTRACT
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The structures of two isoforms of Bcl-2 that differ by two amino acids have been
determined by NMR spectroscopy. Because wild-type Bcl-2 behaved poorly in
solution, the structures were determined by using Bcl-2/Bcl-x(L) chimeras in
which part of the putative unstructured loop of Bcl-2 was replaced with a
shortened loop from Bcl-x(L). These chimeric proteins have a low pI compared
with the wild-type protein and are soluble. The structures of the two Bcl-2
isoforms consist of 6 alpha-helices with a hydrophobic groove on the surface
similar to that observed for the homologous protein, Bcl-x(L). Comparison of the
Bcl-2 structures to that of Bcl-x(L) shows that although the overall fold is the
same, there are differences in the structural topology and electrostatic
potential of the binding groove. Although the structures of the two isoforms of
Bcl-2 are virtually identical, differences were observed in the ability of the
proteins to bind to a 25-residue peptide from the proapoptotic Bad protein and a
16-residue peptide from the proapoptotic Bak protein. These results suggest that
there are subtle differences in the hydrophobic binding groove in Bcl-2 that may
translate into differences in antiapoptotic activity for the two isoforms.
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Selected figure(s)
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Figure 1.
Fig. 1. Sequence alignment of full-length Bcl-x[L], the
three isoforms of full-length Bcl-2 [denoted Bcl-2(1) (1,2),
Bcl-2(2) (3,4), and Bcl-2(3) (5,6)], and the truncated
Bcl-2/Bcl-x[L] chimeras used in this study. Amino acid
differences between the Bcl-2 isoforms are shown in red, the
truncated loop is shown in green, and the putative
membrane-spanning region is shown in blue.  -helices
previously identified in Bcl-x[L] are denoted above the sequence
in red.
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Figure 3.
Fig. 3. Solvent-accessible surface showing hydrophobic
groove for Bcl-2(1) (A) and Bcl-2(2) (B). Leucine, isoleucine,
valine, tyrosine, phenylalanine, and tryptophan residues are
colored yellow, aspartate and glutamate are colored red, and
lysine, arginine, and histidine are colored blue. All other
residue types are colored gray.
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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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B.Ku,
C.Liang,
J.U.Jung,
and
B.H.Oh
(2011).
Evidence that inhibition of BAX activation by BCL-2 involves its tight and preferential interaction with the BH3 domain of BAX.
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Cell Res,
21,
627-641.
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PDB code:
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B.Zhou,
X.Li,
Y.Li,
Y.Xu,
Z.Zhang,
M.Zhou,
X.Zhang,
Z.Liu,
J.Zhou,
C.Cao,
B.Yu,
and
R.Wang
(2011).
Discovery and development of thiazolo[3,2-a]pyrimidinone derivatives as general inhibitors of Bcl-2 family proteins.
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ChemMedChem,
6,
904-921.
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S.Malladi,
K.V.Parsa,
D.Bhupathi,
M.A.Rodríguez-González,
J.A.Conde,
P.Anumula,
H.E.Romo,
C.J.Claunch,
R.P.Ballestero,
and
M.González-García
(2011).
Deletion mutational analysis of BMRP, a pro-apoptotic protein that binds to Bcl-2.
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Mol Cell Biochem,
351,
217-232.
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A.Iwata,
V.Morgan-Stevenson,
B.Schwartz,
L.Liu,
J.Tupper,
X.Zhu,
J.Harlan,
and
R.Winn
(2010).
Extracellular BCL2 proteins are danger-associated molecular patterns that reduce tissue damage in murine models of ischemia-reperfusion injury.
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PLoS One,
5,
e9103.
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B.H.Choi,
L.Feng,
and
H.S.Yoon
(2010).
FKBP38 protects Bcl-2 from caspase-dependent degradation.
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J Biol Chem,
285,
9770-9779.
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E.Fire,
S.V.Gullá,
R.A.Grant,
and
A.E.Keating
(2010).
Mcl-1-Bim complexes accommodate surprising point mutations via minor structural changes.
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Protein Sci,
19,
507-519.
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PDB codes:
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E.Gavathiotis,
D.E.Reyna,
M.L.Davis,
G.H.Bird,
and
L.D.Walensky
(2010).
BH3-triggered structural reorganization drives the activation of proapoptotic BAX.
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Mol Cell,
40,
481-492.
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S.Banerjee,
M.Choi,
A.Aboukameel,
Z.Wang,
M.Mohammad,
J.Chen,
D.Yang,
F.H.Sarkar,
and
R.M.Mohammad
(2010).
Preclinical studies of apogossypolone, a novel pan inhibitor of bcl-2 and mcl-1, synergistically potentiates cytotoxic effect of gemcitabine in pancreatic cancer cells.
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Pancreas,
39,
323-331.
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A.Jourdain,
and
J.C.Martinou
(2009).
Mitochondrial outer-membrane permeabilization and remodelling in apoptosis.
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Int J Biochem Cell Biol,
41,
1884-1889.
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H.Dai,
X.W.Meng,
S.H.Lee,
P.A.Schneider,
and
S.H.Kaufmann
(2009).
Context-dependent Bcl-2/Bak interactions regulate lymphoid cell apoptosis.
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J Biol Chem,
284,
18311-18322.
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J.Peng,
J.Ding,
C.Tan,
B.Baggenstoss,
Z.Zhang,
S.M.Lapolla,
and
J.Lin
(2009).
Oligomerization of membrane-bound Bcl-2 is involved in its pore formation induced by tBid.
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Apoptosis,
14,
1145-1153.
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J.Peng,
S.M.Lapolla,
Z.Zhang,
and
J.Lin
(2009).
The cytosolic domain of Bcl-2 forms small pores in model mitochondrial outer membrane after acidic pH-induced membrane association.
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Sheng Wu Yi Xue Gong Cheng Xue Za Zhi,
26,
130-137.
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J.Peng,
S.M.Lapolla,
Z.Zhang,
and
J.Lin
(2009).
The cytosolic domain of Bcl-2 oligomerizes to form pores in model mitochondrial outer membrane at acidic pH.
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Sheng Wu Yi Xue Gong Cheng Xue Za Zhi,
26,
631-637.
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J.Peng,
S.M.Lapolla,
Z.Zhang,
and
J.Lin
(2009).
The Bax BH3 peptide H2-H3 promotes apoptosis by inhibiting Bcl-2's pore-forming and anti-Bax activities in the membrane.
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Sheng Wu Yi Xue Gong Cheng Xue Za Zhi,
26,
829-835.
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J.Sun,
D.M.Abdeljabbar,
N.Clarke,
M.L.Bellows,
C.A.Floudas,
and
A.J.Link
(2009).
Reconstitution and engineering of apoptotic protein interactions on the bacterial cell surface.
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J Mol Biol,
394,
297-305.
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L.Polzien,
A.Baljuls,
U.E.Rennefahrt,
A.Fischer,
W.Schmitz,
R.P.Zahedi,
A.Sickmann,
R.Metz,
S.Albert,
R.Benz,
M.Hekman,
and
U.R.Rapp
(2009).
Identification of novel in vivo phosphorylation sites of the human proapoptotic protein BAD: pore-forming activity of BAD is regulated by phosphorylation.
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J Biol Chem,
284,
28004-28020.
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M.Orzáez,
A.Gortat,
L.Mondragón,
and
E.Pérez-Payá
(2009).
Peptides and peptide mimics as modulators of apoptotic pathways.
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ChemMedChem,
4,
146-160.
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S.Oda,
M.Schröder,
and
A.R.Khan
(2009).
Structural basis for targeting of human RNA helicase DDX3 by poxvirus protein K7.
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Structure,
17,
1528-1537.
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PDB code:
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Y.P.Rong,
G.Bultynck,
A.S.Aromolaran,
F.Zhong,
J.B.Parys,
H.De Smedt,
G.A.Mignery,
H.L.Roderick,
M.D.Bootman,
and
C.W.Distelhorst
(2009).
The BH4 domain of Bcl-2 inhibits ER calcium release and apoptosis by binding the regulatory and coupling domain of the IP3 receptor.
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Proc Natl Acad Sci U S A,
106,
14397-14402.
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B.Ku,
J.S.Woo,
C.Liang,
K.H.Lee,
H.S.Hong,
X.E,
K.S.Kim,
J.U.Jung,
and
B.H.Oh
(2008).
Structural and biochemical bases for the inhibition of autophagy and apoptosis by viral BCL-2 of murine gamma-herpesvirus 68.
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PLoS Pathog,
4,
e25.
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PDB codes:
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C.Katz,
H.Benyamini,
S.Rotem,
M.Lebendiker,
T.Danieli,
A.Iosub,
H.Refaely,
M.Dines,
V.Bronner,
T.Bravman,
D.E.Shalev,
S.Rüdiger,
and
A.Friedler
(2008).
Molecular basis of the interaction between the antiapoptotic Bcl-2 family proteins and the proapoptotic protein ASPP2.
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Proc Natl Acad Sci U S A,
105,
12277-12282.
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D.Lama,
and
R.Sankararamakrishnan
(2008).
Anti-apoptotic Bcl-XL protein in complex with BH3 peptides of pro-apoptotic Bak, Bad, and Bim proteins: comparative molecular dynamics simulations.
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Proteins,
73,
492-514.
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L.Lins,
and
R.Brasseur
(2008).
Tilted peptides: a structural motif involved in protein membrane insertion?
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J Pept Sci,
14,
416-422.
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L.P.Billen,
A.Shamas-Din,
and
D.W.Andrews
(2008).
Bid: a Bax-like BH3 protein.
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Oncogene,
27,
S93-104.
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M.A.Sani,
S.Castano,
E.J.Dufourc,
and
G.Gröbner
(2008).
Restriction of lipid motion in membranes triggered by beta-sheet aggregation of the anti-apoptotic BH4 domain.
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FEBS J,
275,
561-572.
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N.O.Deakin,
and
C.E.Turner
(2008).
Paxillin comes of age.
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J Cell Sci,
121,
2435-2444.
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R.J.Youle,
and
A.Strasser
(2008).
The BCL-2 protein family: opposing activities that mediate cell death.
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Nat Rev Mol Cell Biol,
9,
47-59.
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A.E.Douglas,
K.D.Corbett,
J.M.Berger,
G.McFadden,
and
T.M.Handel
(2007).
Structure of M11L: A myxoma virus structural homolog of the apoptosis inhibitor, Bcl-2.
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Protein Sci,
16,
695-703.
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PDB code:
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A.L.Nouvion,
J.Thibaut,
O.D.Lohez,
S.Venet,
P.Colas,
G.Gillet,
and
P.Lalle
(2007).
Modulation of Nr-13 antideath activity by peptide aptamers.
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Oncogene,
26,
701-710.
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A.Mukhopadhyay,
and
H.Weiner
(2007).
Delivery of drugs and macromolecules to mitochondria.
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Adv Drug Deliv Rev,
59,
729-738.
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C.Xing,
L.Wang,
X.Tang,
and
Y.Y.Sham
(2007).
Development of selective inhibitors for anti-apoptotic Bcl-2 proteins from BHI-1.
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Bioorg Med Chem,
15,
2167-2176.
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D.Westphal,
E.C.Ledgerwood,
M.H.Hibma,
S.B.Fleming,
E.M.Whelan,
and
A.A.Mercer
(2007).
A novel Bcl-2-like inhibitor of apoptosis is encoded by the parapoxvirus ORF virus.
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J Virol,
81,
7178-7188.
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G.Tang,
C.Y.Yang,
Z.Nikolovska-Coleska,
J.Guo,
S.Qiu,
R.Wang,
W.Gao,
G.Wang,
J.Stuckey,
K.Krajewski,
S.Jiang,
P.P.Roller,
and
S.Wang
(2007).
Pyrogallol-based molecules as potent inhibitors of the antiapoptotic Bcl-2 proteins.
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J Med Chem,
50,
1723-1726.
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G.Tang,
K.Ding,
Z.Nikolovska-Coleska,
C.Y.Yang,
S.Qiu,
S.Shangary,
R.Wang,
J.Guo,
W.Gao,
J.Meagher,
J.Stuckey,
K.Krajewski,
S.Jiang,
P.P.Roller,
and
S.Wang
(2007).
Structure-based design of flavonoid compounds as a new class of small-molecule inhibitors of the anti-apoptotic Bcl-2 proteins.
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J Med Chem,
50,
3163-3166.
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K.W.Kinnally,
and
B.Antonsson
(2007).
A tale of two mitochondrial channels, MAC and PTP, in apoptosis.
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Apoptosis,
12,
857-868.
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L.Banadyga,
J.Gerig,
T.Stewart,
and
M.Barry
(2007).
Fowlpox virus encodes a Bcl-2 homologue that protects cells from apoptotic death through interaction with the proapoptotic protein Bak.
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J Virol,
81,
11032-11045.
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M.Zhang,
Y.Ling,
C.Y.Yang,
H.Liu,
R.Wang,
X.Wu,
K.Ding,
F.Zhu,
B.N.Griffith,
R.M.Mohammad,
S.Wang,
and
D.Yang
(2007).
A novel Bcl-2 small molecule inhibitor 4-(3-methoxy-phenylsulfannyl)-7-nitro-benzofurazan-3-oxide (MNB)-induced apoptosis in leukemia cells.
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Ann Hematol,
86,
471-481.
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P.E.Czabotar,
E.F.Lee,
M.F.van Delft,
C.L.Day,
B.J.Smith,
D.C.Huang,
W.D.Fairlie,
M.G.Hinds,
and
P.M.Colman
(2007).
Structural insights into the degradation of Mcl-1 induced by BH3 domains.
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Proc Natl Acad Sci U S A,
104,
6217-6222.
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PDB codes:
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S.Cooray,
M.W.Bahar,
N.G.Abrescia,
C.E.McVey,
N.W.Bartlett,
R.A.Chen,
D.I.Stuart,
J.M.Grimes,
and
G.L.Smith
(2007).
Functional and structural studies of the vaccinia virus virulence factor N1 reveal a Bcl-2-like anti-apoptotic protein.
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J Gen Virol,
88,
1656-1666.
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PDB code:
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T.J.Malia,
and
G.Wagner
(2007).
NMR structural investigation of the mitochondrial outer membrane protein VDAC and its interaction with antiapoptotic Bcl-xL.
|
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Biochemistry,
46,
514-525.
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A.A.Fiebig,
W.Zhu,
C.Hollerbach,
B.Leber,
and
D.W.Andrews
(2006).
Bcl-XL is qualitatively different from and ten times more effective than Bcl-2 when expressed in a breast cancer cell line.
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BMC Cancer,
6,
213.
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C.Tan,
P.J.Dlugosz,
J.Peng,
Z.Zhang,
S.M.Lapolla,
S.M.Plafker,
D.W.Andrews,
and
J.Lin
(2006).
Auto-activation of the apoptosis protein Bax increases mitochondrial membrane permeability and is inhibited by Bcl-2.
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J Biol Chem,
281,
14764-14775.
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D.P.Frazier,
A.Wilson,
R.M.Graham,
J.W.Thompson,
N.H.Bishopric,
and
K.A.Webster
(2006).
Acidosis regulates the stability, hydrophobicity, and activity of the BH3-only protein Bnip3.
|
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Antioxid Redox Signal,
8,
1625-1634.
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J.Peng,
C.Tan,
G.J.Roberts,
O.Nikolaeva,
Z.Zhang,
S.M.Lapolla,
S.Primorac,
D.W.Andrews,
and
J.Lin
(2006).
tBid elicits a conformational alteration in membrane-bound Bcl-2 such that it inhibits Bax pore formation.
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J Biol Chem,
281,
35802-35811.
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L.D.Walensky
(2006).
BCL-2 in the crosshairs: tipping the balance of life and death.
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Cell Death Differ,
13,
1339-1350.
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L.Khemtémourian,
M.A.Sani,
K.Bathany,
G.Gröbner,
and
E.J.Dufourc
(2006).
Synthesis and secondary structure in membranes of the Bcl-2 anti-apoptotic domain BH4.
|
| |
J Pept Sci,
12,
58-64.
|
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M.F.van Delft,
and
D.C.Huang
(2006).
How the Bcl-2 family of proteins interact to regulate apoptosis.
|
| |
Cell Res,
16,
203-213.
|
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P.H.Schlesinger,
and
M.Saito
(2006).
The Bax pore in liposomes, Biophysics.
|
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Cell Death Differ,
13,
1403-1408.
|
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P.S.Schwartz,
and
D.M.Hockenbery
(2006).
Bcl-2-related survival proteins.
|
| |
Cell Death Differ,
13,
1250-1255.
|
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U.M.Moll,
N.Marchenko,
and
X.K.Zhang
(2006).
p53 and Nur77/TR3 - transcription factors that directly target mitochondria for cell death induction.
|
| |
Oncogene,
25,
4725-4743.
|
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W.D.Fairlie,
M.A.Perugini,
M.Kvansakul,
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PDB code:
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T.Oltersdorf,
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A.R.Shoemaker,
R.C.Armstrong,
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C.Li,
M.J.Mitten,
D.G.Nettesheim,
S.Ng,
P.M.Nimmer,
J.M.O'Connor,
A.Oleksijew,
A.M.Petros,
J.C.Reed,
W.Shen,
S.K.Tahir,
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PDB codes:
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M.Li,
E.R.Rayburn,
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PDB code:
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PDB code:
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Design and Evolution of a Miniature Bcl-2 Binding Protein We thank the HHMI Biopolymer/Keck Foundation Biotechnology Resource Laboratory (Yale University School of Medicine, New Haven, CT) for oligonucleotide and peptide synthesis and amino acid analysis and Professor Jennifer Doudna (Yale University) for use of a Perseptive Voyager-DE (MALDI-TOF) mass spectrometer. We are grateful also to Dr. Junying Yuan and Dr. Alexi Degterev (Harvard Medical School) for a generous gift of Bcl-X(L)-His(6) and Stacey E. Rutledge for helpful comments. This work was supported by the National Institutes of Health.
|
| |
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The most recent references are shown first.
Citation data come partly from CiteXplore and partly
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only a partial list as not all journals are covered by
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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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