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PDBsum entry 1ddb
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* Residue conservation analysis
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DOI no:
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Cell
96:625-634
(1999)
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PubMed id:
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Solution structure of the proapoptotic molecule BID: a structural basis for apoptotic agonists and antagonists.
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J.M.McDonnell,
D.Fushman,
C.L.Milliman,
S.J.Korsmeyer,
D.Cowburn.
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ABSTRACT
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Members of the BCL2 family of proteins are key regulators of programmed cell
death, acting either as apoptotic agonists or antagonists. Here we describe the
solution structure of BID, presenting the structure of a proapoptotic BCL2
family member. An analysis of sequence/structure of BCL2 family members allows
us to define a structural superfamily, which has implications for general
mechanisms for regulating proapoptotic activity. It appears two criteria must be
met for proapoptotic function within the BCL2 family: targeting of molecules to
intracellular membranes, and exposure of the BH3 death domain. BID's activity is
regulated by a Caspase 8-mediated cleavage event, exposing the BH3 domain and
significantly changing the surface charge and hydrophobicity, resulting in a
change of cellular localization.
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Selected figure(s)
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Figure 4.
Figure 4. Comparison of BID and BCL-X[L] BH123 Acceptor
Region(a) The BID and (b) BCL-X[L]–BAK complex (PDB code 1lxl
[[49]) structures were colored according to surface
hydrophobicity (red for hydrophobic, white for hydrophilic)
using GRASP ( [44]). The backbone worms for both BID and the
BCL-X[L]–BAK BH3 peptide complex are colored yellow.
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Figure 5.
Figure 5. Predicted Structural Effects of the Caspase 8
Cleavage of BIDA ribbon diagram of (a) the full-length p22 BID
versus (b) the p15 tBID model (flexible loop BC and amino
terminus not shown). An analysis of the exposed hydrophobic
surface for (c) BID and (d) the tBID model presented in the same
orientation as in (a) and (b). Hydrophobic surfaces were
generated using GRASP ([44]); here the gray and yellow indicate
hydrophobic and hydrophilic surfaces, respectively.
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The above figures are
reprinted
by permission from Cell Press:
Cell
(1999,
96,
625-634)
copyright 1999.
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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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Google scholar
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PubMed id
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Reference
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A.Shamas-Din,
H.Brahmbhatt,
B.Leber,
and
D.W.Andrews
(2011).
BH3-only proteins: Orchestrators of apoptosis.
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Biochim Biophys Acta,
1813,
508-520.
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C.Kantari,
and
H.Walczak
(2011).
Caspase-8 and bid: caught in the act between death receptors and mitochondria.
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Biochim Biophys Acta,
1813,
558-563.
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M.Crimi,
and
M.D.Esposti
(2011).
Apoptosis-induced changes in mitochondrial lipids.
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Biochim Biophys Acta,
1813,
551-557.
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Y.Liu,
C.C.Bertram,
Q.Shi,
and
S.S.Zinkel
(2011).
Proapoptotic Bid mediates the Atr-directed DNA damage response to replicative stress.
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Cell Death Differ,
18,
841-852.
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E.Gavathiotis,
D.E.Reyna,
M.L.Davis,
G.H.Bird,
and
L.D.Walensky
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BH3-triggered structural reorganization drives the activation of proapoptotic BAX.
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Mol Cell,
40,
481-492.
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F.Gonzalvez,
F.Pariselli,
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P.Dupaigne,
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Mechanistic issues of the interaction of the hairpin-forming domain of tBid with mitochondrial cardiolipin.
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PLoS One,
5,
e9342.
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G.J.Rautureau,
C.L.Day,
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Intrinsically disordered proteins in bcl-2 regulated apoptosis.
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Int J Mol Sci,
11,
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L.Bodet,
E.Ménoret,
G.Descamps,
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and
P.Gomez-Bougie
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BH3-only protein Bik is involved in both apoptosis induction and sensitivity to oxidative stress in multiple myeloma.
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Br J Cancer,
103,
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S.Bleicken,
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Molecular details of Bax activation, oligomerization, and membrane insertion.
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J Biol Chem,
285,
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Y.Guillemin,
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L.Blum,
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J.Salgado,
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and
A.Aouacheria
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Active fragments from pro- and antiapoptotic BCL-2 proteins have distinct membrane behavior reflecting their functional divergence.
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PLoS One,
5,
e9066.
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A.Manara,
J.Lindsay,
M.Marchioretto,
A.Astegno,
A.P.Gilmore,
M.D.Esposti,
and
M.Crimi
(2009).
Bid binding to negatively charged phospholipids may not be required for its pro-apoptotic activity in vivo.
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Biochim Biophys Acta,
1791,
997.
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K.Sakamaki,
and
Y.Satou
(2009).
Caspases: evolutionary aspects of their functions in vertebrates.
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J Fish Biol,
74,
727-753.
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L.J.Wee,
J.C.Tong,
T.W.Tan,
and
S.Ranganathan
(2009).
A multi-factor model for caspase degradome prediction.
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BMC Genomics,
10,
S6.
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M.D.Shortridge,
and
R.Powers
(2009).
Structural and functional similarity between the bacterial type III secretion system needle protein PrgI and the eukaryotic apoptosis Bcl-2 proteins.
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PLoS One,
4,
e7442.
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P.E.Czabotar,
P.M.Colman,
and
D.C.Huang
(2009).
Bax activation by Bim?
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Cell Death Differ,
16,
1187-1191.
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Y.Yao,
A.A.Bobkov,
L.A.Plesniak,
and
F.M.Marassi
(2009).
Mapping the interaction of pro-apoptotic tBID with pro-survival BCL-XL.
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Biochemistry,
48,
8704-8711.
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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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E.Lomonosova,
and
G.Chinnadurai
(2008).
BH3-only proteins in apoptosis and beyond: an overview.
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Oncogene,
27,
S2-19.
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G.Chinnadurai,
S.Vijayalingam,
and
R.Rashmi
(2008).
BIK, the founding member of the BH3-only family proteins: mechanisms of cell death and role in cancer and pathogenic processes.
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Oncogene,
27,
S20-S29.
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I.Galindo,
B.Hernaez,
G.Díaz-Gil,
J.M.Escribano,
and
C.Alonso
(2008).
A179L, a viral Bcl-2 homologue, targets the core Bcl-2 apoptotic machinery and its upstream BH3 activators with selective binding restrictions for Bid and Noxa.
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Virology,
375,
561-572.
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J.Hutcheson,
and
H.Perlman
(2008).
BH3-only proteins in rheumatoid arthritis: potential targets for therapeutic intervention.
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Oncogene,
27,
S168-S175.
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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.Giam,
D.C.Huang,
and
P.Bouillet
(2008).
BH3-only proteins and their roles in programmed cell death.
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Oncogene,
27,
S128-S136.
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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.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.L.Pauleau,
N.Larochette,
F.Giordanetto,
S.R.Scholz,
D.Poncet,
N.Zamzami,
V.S.Goldmacher,
and
G.Kroemer
(2007).
Structure-function analysis of the interaction between Bax and the cytomegalovirus-encoded protein vMIA.
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Oncogene,
26,
7067-7080.
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A.Rasola,
and
P.Bernardi
(2007).
The mitochondrial permeability transition pore and its involvement in cell death and in disease pathogenesis.
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Apoptosis,
12,
815-833.
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E.Riddle-Taylor,
K.Nagasaki,
J.Lopez,
C.O.Esquivel,
O.M.Martinez,
and
S.M.Krams
(2007).
Mutations to bid cleavage sites protect hepatocytes from apoptosis after ischemia/reperfusion injury.
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Transplantation,
84,
778-785.
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E.Schmitt,
C.Paquet,
M.Beauchemin,
and
R.Bertrand
(2007).
DNA-damage response network at the crossroads of cell-cycle checkpoints, cellular senescence and apoptosis.
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J Zhejiang Univ Sci B,
8,
377-397.
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J.C.Timmer,
and
G.S.Salvesen
(2007).
Caspase substrates.
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Cell Death Differ,
14,
66-72.
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J.Choi,
D.Zhai,
X.Zhou,
A.Satterthwait,
J.C.Reed,
and
F.M.Marassi
(2007).
Mapping the specific cytoprotective interaction of humanin with the pro-apoptotic protein bid.
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Chem Biol Drug Des,
70,
383-392.
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J.Zhu,
Y.Yang,
and
J.Wu
(2007).
Bcl-2 cleavages at two adjacent sites by different caspases promote cisplatin-induced apoptosis.
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Cell Res,
17,
441-448.
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K.Hamacher
(2007).
Information theoretical measures to analyze trajectories in rational molecular design.
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J Comput Chem,
28,
2576-2580.
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K.Sakamaki,
M.Nozaki,
K.Kominami,
and
Y.Satou
(2007).
The evolutionary conservation of the core components necessary for the extrinsic apoptotic signaling pathway, in Medaka fish.
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BMC Genomics,
8,
141.
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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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M.G.Hinds,
C.Smits,
R.Fredericks-Short,
J.M.Risk,
M.Bailey,
D.C.Huang,
and
C.L.Day
(2007).
Bim, Bad and Bmf: intrinsically unstructured BH3-only proteins that undergo a localized conformational change upon binding to prosurvival Bcl-2 targets.
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Cell Death Differ,
14,
128-136.
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S.W.Tait,
E.de Vries,
C.Maas,
A.M.Keller,
C.S.D'Santos,
and
J.Borst
(2007).
Apoptosis induction by Bid requires unconventional ubiquitination and degradation of its N-terminal fragment.
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J Cell Biol,
179,
1453-1466.
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S.Ying,
M.Pettengill,
D.M.Ojcius,
and
G.Häcker
(2007).
Host-Cell Survival and Death During Chlamydia Infection.
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Curr Immunol Rev,
3,
31-40.
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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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V.G.Veresov,
and
A.I.Davidovskii
(2007).
Monte Carlo simulations of tBid association with the mitochondrial outer membrane.
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Eur Biophys J,
37,
19-33.
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V.Stoka,
V.Turk,
and
B.Turk
(2007).
Lysosomal cysteine cathepsins: signaling pathways in apoptosis.
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Biol Chem,
388,
555-560.
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B.B.Olsen,
J.Petersen,
and
O.G.Issinger
(2006).
BID, an interaction partner of protein kinase CK2alpha.
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Biol Chem,
387,
441-449.
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B.Becattini,
C.Culmsee,
M.Leone,
D.Zhai,
X.Zhang,
K.J.Crowell,
M.F.Rega,
S.Landshamer,
J.C.Reed,
N.Plesnila,
and
M.Pellecchia
(2006).
Structure-activity relationships by interligand NOE-based design and synthesis of antiapoptotic compounds targeting Bid.
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Proc Natl Acad Sci U S A,
103,
12602-12606.
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D.White,
A.A.Musse,
J.Wang,
E.London,
and
A.R.Merrill
(2006).
Toward elucidating the membrane topology of helix two of the colicin E1 channel domain.
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J Biol Chem,
281,
32375-32384.
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G.Häcker,
S.Kirschnek,
and
S.F.Fischer
(2006).
Apoptosis in infectious disease: how bacteria interfere with the apoptotic apparatus.
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Med Microbiol Immunol,
195,
11-19.
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H.Ji,
A.Shekhtman,
R.Ghose,
J.M.McDonnell,
and
D.Cowburn
(2006).
NMR determination that an extended BH3 motif of pro-apoptotic BID is specifically bound to BCL-XL.
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Magn Reson Chem,
44,
S101-S107.
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J.A.Caruso,
and
J.J.Reiners
(2006).
Proteolysis of HIP during apoptosis occurs within a region similar to the BID loop.
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Apoptosis,
11,
1877-1885.
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K.Hamacher,
A.Hübsch,
and
J.A.McCammon
(2006).
A minimal model for stabilization of biomolecules by hydrocarbon cross-linking.
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J Chem Phys,
124,
164907.
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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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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.
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Cell Death Differ,
13,
1250-1255.
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Y.K.Verma,
G.U.Gangenahalli,
V.K.Singh,
P.Gupta,
R.Chandra,
R.K.Sharma,
and
H.G.Raj
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Cell death regulation by B-cell lymphoma protein.
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Apoptosis,
11,
459-471.
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A.J.García-Sáez,
M.Coraiola,
M.Dalla Serra,
I.Mingarro,
G.Menestrina,
and
J.Salgado
(2005).
Peptides derived from apoptotic Bax and Bid reproduce the poration activity of the parent full-length proteins.
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Biophys J,
88,
3976-3990.
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A.Strasser
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The role of BH3-only proteins in the immune system.
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Nat Rev Immunol,
5,
189-200.
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D.Zhai,
F.Luciano,
X.Zhu,
B.Guo,
A.C.Satterthwait,
and
J.C.Reed
(2005).
Humanin binds and nullifies Bid activity by blocking its activation of Bax and Bak.
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| |
J Biol Chem,
280,
15815-15824.
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F.Gonzalvez,
J.J.Bessoule,
F.Rocchiccioli,
S.Manon,
and
P.X.Petit
(2005).
Role of cardiolipin on tBid and tBid/Bax synergistic effects on yeast mitochondria.
|
| |
Cell Death Differ,
12,
659-667.
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K.J.Oh,
S.Barbuto,
N.Meyer,
R.S.Kim,
R.J.Collier,
and
S.J.Korsmeyer
(2005).
Conformational changes in BID, a pro-apoptotic BCL-2 family member, upon membrane binding. A site-directed spin labeling study.
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| |
J Biol Chem,
280,
753-767.
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N.Van Mau,
A.V.Kajava,
C.Bonfils,
J.C.Martinou,
and
M.C.Harricane
(2005).
Interactions of Bax and tBid with lipid monolayers.
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J Membr Biol,
207,
1-9.
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N.Yan,
and
Y.Shi
(2005).
Mechanisms of apoptosis through structural biology.
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Annu Rev Cell Dev Biol,
21,
35-56.
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R.G.Hibbert,
P.Teriete,
G.J.Grundy,
R.L.Beavil,
R.Reljic,
V.M.Holers,
J.P.Hannan,
B.J.Sutton,
H.J.Gould,
and
J.M.McDonnell
(2005).
The structure of human CD23 and its interactions with IgE and CD21.
|
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J Exp Med,
202,
751-760.
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PDB codes:
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S.Ying,
B.M.Seiffert,
G.Häcker,
and
S.F.Fischer
(2005).
Broad degradation of proapoptotic proteins with the conserved Bcl-2 homology domain 3 during infection with Chlamydia trachomatis.
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Infect Immun,
73,
1399-1403.
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A.B.Werner,
S.W.Tait,
E.de Vries,
E.Eldering,
and
J.Borst
(2004).
Requirement for aspartate-cleaved bid in apoptosis signaling by DNA-damaging anti-cancer regimens.
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| |
J Biol Chem,
279,
28771-28780.
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A.J.Valentijn,
and
A.P.Gilmore
(2004).
Translocation of full-length Bid to mitochondria during anoikis.
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| |
J Biol Chem,
279,
32848-32857.
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B.Becattini,
S.Sareth,
D.Zhai,
K.J.Crowell,
M.Leone,
J.C.Reed,
and
M.Pellecchia
(2004).
Targeting apoptosis via chemical design: inhibition of bid-induced cell death by small organic molecules.
|
| |
Chem Biol,
11,
1107-1117.
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C.Claveria,
C.Martinez-A,
and
M.Torres
(2004).
A Bax/Bak-independent mitochondrial death pathway triggered by Drosophila Grim GH3 domain in mammalian cells.
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| |
J Biol Chem,
279,
1368-1375.
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C.M.Franzin,
J.Choi,
D.Zhai,
J.C.Reed,
and
F.M.Marassi
(2004).
Structural studies of apoptosis and ion transport regulatory proteins in membranes.
|
| |
Magn Reson Chem,
42,
172-179.
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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
codes are
shown on the right.
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|
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