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A near atomic structure of the active human apoptosome
2016
eLife
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Funding
Funder Grant reference number Author National Institutes of Health GM063834 Christopher W Akey The funders had no role in study design, data collection and interpretation ...
The sequential addition of further subunits would then overcome entropic barriers to favor apoptosome assembly reviewed in Yuan and Akey, 2013) . ...
W Akey, http://orcid.org/0000-0002-3059-3121
Additional files
Major datasets The following datasets were generated: ...
doi:10.7554/elife.17755
pmid:27697150
pmcid:PMC5050015
fatcat:27ldsuq6szggfgpol2k5qd2ohm
Apoptosome Structure, Assembly, and Procaspase Activation
2013
Structure
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Apaf-1-like molecules assemble into a ring-like platform known as the apoptosome. This cell death platform then activates procaspases in the intrinsic cell death pathway. In this review, crystal structures of Apaf-1 monomers and CED-4 dimers have been combined with apoptosome structures to provide insights into the assembly of cell death platforms in humans, nematodes, and flies. In humans, the caspase recognition domains (CARDs) of procaspase-9 and Apaf-1 interact with each other to form a
doi:10.1016/j.str.2013.02.024
pmid:23561633
pmcid:PMC3644875
fatcat:b324tjnunbenvogvsxd4b4x2re
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... -CARD disk, which interacts with the platform to create an asymmetric proteolysis machine. The disk tethers multiple pc-9 catalytic domains to the platform to raise their local concentration, and this leads to zymogen activation. These findings have now set the stage for further studies of this critical activation process on the apoptosome.
Crystal Structure and Function of Human Nucleoplasmin (Npm2): A Histone Chaperone in Oocytes and Embryos
2011
Biochemistry
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Human Npm2 is an ortholog of Xenopus nucleoplasmin (Np), a chaperone that binds histones. We have determined the crystal structure of a truncated Npm2-core at 1.9Å resolution and show that the N-terminal domains of Npm2 and Np form similar pentamers. This allowed us to model an Npm2 decamer which may be formed by hydrogen bonds between quasi-conserved residues in the interface between two pentamers. Interestingly, the Npm2 pentamer lacks a prototypical A1-acidic tract in each of its subunits.
doi:10.1021/bi2006652
pmid:21863821
pmcid:PMC3172369
fatcat:t73qssjyvzbwlb6ilb42r2zu3u
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... is feature may be responsible for the inability of Npm2-core to bind histones. However, Npm2 with a large acidic tract in its C-terminal tail (Npm2-A2) is able to bind histones and form large complexes. Fluorescence resonance energy transfer experiments and biochemical analysis of loop mutations support the premise that nucleoplasmins form decamers when they bind H2A-H2B dimers and H3-H4 tetramers simultaneously. In the absence of histone tetramers, these chaperones bind H2A-H2B dimers with a single pentamer forming the central hub. When taken together, our data provide insights into the mechanism of histone binding by nucleoplasmins.
The NPC-Transporter, A Ghost in the Machine
2010
Structure
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Reproduced from Akey and Radermacher (1993). ...
., 1998; Akey and Radermacher, 1993) , as well as in FEISEM images (Allen et al., 2000) . ...
doi:10.1016/j.str.2010.09.005
pmid:20947011
pmcid:PMC2966715
fatcat:vrgl6vzb7jb7ppgp5wbgy55zj4
The Crystal Structure of Drosophila NLP-Core Provides Insight into Pentamer Formation and Histone Binding
2003
Structure
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., Akey, I.V., Dingwall, C., Hartman, K.L., Laue, T., Nolte, Thermal stability assays were carried out on the purified proteins R.T., Head, J.F., and Akey, C.W. (2001). ...
doi:10.1016/s0969-2126(03)00007-8
pmid:12575937
fatcat:4el7kmiswzdafbr2jzezeqzqae
Oxidized or Reduced Cytochrome c and Axial Ligand Variants All Form the Apoptosome in Vitro
2017
Biochemistry
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NIH GM063834 to Christopher W. Akey. ...
doi:10.1021/acs.biochem.7b00309
pmid:28510448
pmcid:PMC5551479
fatcat:lgmpzy6obreedadre2q2fztqsa
The Structure and Function of Xenopus NO38-Core, a Histone Chaperone in the Nucleolus
2004
Structure
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References Chaperone histone complexes were made with a rapid desalting method, by mixing the components at a final concentration of 01ف Akey, C.W., and Luger, K. (2003). ...
doi:10.1016/j.str.2004.09.017
pmid:15576029
fatcat:w7zmgdqwsfcejc5jsz73qswoae
IcmQ in the Type 4b Secretion System Contains an NAD+ Binding Domain
2013
Structure
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Trypsin (1,000:1 w/w; Sigma) was added to the complex for 2 hr, prior to protease removal by passage over agarose-linked benzamidine. ...
doi:10.1016/j.str.2013.05.017
pmid:23850453
pmcid:PMC3816012
fatcat:uzrv3ecjobaetjnh6qrftiiw6a
Three-Dimensional Structure of the Apoptosome
2002
Molecular Cell
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Correspondence: akey@med-biophm.bu.edu ...
doi:10.1016/s1097-2765(02)00442-2
pmid:11864614
fatcat:oqfh5t5kwfasfcq5qdcgqs5lry
Changes in Apaf-1 Conformation That Drive Apoptosome Assembly
2013
Biochemistry
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Apoptosome assembly is highly regulated in the intrinsic cell death pathway. To better understand this step, we created an improved model of the human apoptosome using a crystal structure of full length Apaf-1 and a single particle, electron density map at ~9.5Å resolution. The apoptosome model includes N-terminal domains of Apaf-1, cognate β-propellers and cytochrome c. A direct comparison of Apaf-1 in the apoptosome and as a monomer reveals conformational changes that occur during the first
doi:10.1021/bi301721g
pmid:23521171
pmcid:PMC3645920
fatcat:ioiqgyerfveozogxo5wvblyfri
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... o steps of assembly. This includes an induced-fit mechanism for cytochrome c binding to regulatory β-propellers, which is dependent on shape and charge complimentarity, and a large rotation of the nucleotide binding module during nucleotide exchange. These linked conformational changes create an extended Apaf-1 monomer and drive apoptosome assembly. Moreover, the N-terminal CARD in the inactive Apaf-1 monomer is not shielded from other proteins by β-propellers. Hence, the Apaf-1 CARD may be free to interact with a procaspase-9 CARD either before or during apoptosome assembly. Irrespective of the timing, the end product of assembly is a holo-apoptosome with an acentric CARD-CARD disk and tethered pc-9 catalytic domains. Subsequent activation of pc-9 leads to a proteolytic cascade and cell death.
Structure of an Apoptosome-Procaspase-9 CARD Complex
2010
Structure
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Apaf-1 coassembles with cytochrome c to form the apoptosome, which then binds and activates procaspase-9 (pc-9). We removed pc-9 catalytic domains from the holoapoptosome by site-directed thrombinolysis. A structure of the resulting apoptosome-pc-9 CARD complex was then determined at 9.5 Å resolution. In our model, the central hub is constructed like other AAA+ protein rings but also contains novel features. At higher radius, the regulatory region of each Apaf-1 is comprised of tandem seven and
doi:10.1016/j.str.2010.04.001
pmid:20462491
pmcid:PMC2874686
fatcat:h2uf6wvdnbdnvit7dj66xmudbi
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... eight blade b-propellers with cytochrome c docked between them. Remarkably, Apaf-1 CARDs are disordered in the ground state. During activation, each Apaf-1 CARD interacts with a pc-9 CARD and these heterodimers form a flexibly tethered "disk" that sits above the central hub. When taken together, the data reveal conformational changes during Apaf-1 assembly that allow pc-9 activation. The model also provides a plausible explanation for the effects of NOD mutations that have been mapped onto the central hub.
Structural insight into the protein translocation channel
2004
Current Opinion in Structural Biology
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A comparison of the yeast and rabbit 80 S ribosome reveals the topology of the nascent chain exit tunnel, inter-subunit bridges and mammalian rRNA expansion segments 1 1Edited by W. Baumesiter
2000
Journal of Molecular Biology
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The tilted images corresponding to the largest class were processed to generate an initial low-resolution 3D volume using the random conical tilt procedure implemented in SPI-DER (Radermacher, 1988; Akey ...
The sample was then applied to a 10 %-30 % linear sucrose gradient (10 %-30 % (w/v) sucrose, 10 mM BisTris (pH 6.5), 2 mM magnesium acetate, 100 mM potassium acetate, 2 mM DTT, 1:500 Solution P) and spun ...
doi:10.1006/jmbi.2000.3947
pmid:10926511
fatcat:ag4ujgzb5ne7hfbv7wbxzgirpi
Structure of the Drosophila Apoptosome at 6.9 Å Resolution
2011
Structure
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The Yeast Spindle Pole Body Is Assembled around a Central Crystal of Spc42p
1997
Cell
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Conserved Vertical Architecture Supramolecular assemblies are generally well preserved in the frozen-hydrated state, as they are subjected to minimal changes in buffer composition, pH, and surface tension (Akey ...
array of a few proteins are anchored to the IL layers. by this organelle, because a precedent exists in the However, the pronounced hexagonal organization of the architecture of the nuclear pore complex (Akey ...
doi:10.1016/s0092-8674(00)80295-0
pmid:9215630
fatcat:sz7ned2qpja47mz5uw4jiccp4m
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