Novel dimerization mode of the human Bcl-2 family protein Bak, a mitochondrial apoptosis regulator

Systems and Structural Biology Center, Yokohama Institute, RIKEN, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama 230-0045, Japan.
Journal of Structural Biology (Impact Factor: 3.23). 04/2009; 166(1):32-7. DOI: 10.1016/j.jsb.2008.12.003
Source: PubMed


Interactions of Bcl-2 family proteins play a regulatory role in mitochondrial apoptosis. The pro-apoptotic protein Bak resides in the outer mitochondrial membrane, and the formation of Bak homo- or heterodimers is involved in the regulation of apoptosis. The previously reported structure of the human Bak protein (residues Glu16-Gly186) revealed that a zinc ion was coordinated with two pairs of Asp160 and His164 residues from the symmetry-related molecules. This zinc-dependent homodimer was regarded as an anti-apoptotic dimer. In the present study, we determined the crystal structure of the human Bak residues Ser23-Asn185 at 2.5A, and found a distinct type of homodimerization through Cys166 disulfide bridging between the symmetry-related molecules. In the two modes of homodimerization, the molecular interfaces are completely different. In the membrane-targeted model of the S-S bridged dimer, the BH3 motifs are too close to the membrane to interact directly with the anti-apoptotic relatives, such as Bcl-x(L). Therefore, the Bak dimer structure reported here may represent a pro-apoptotic mode under oxidized conditions.

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Available from: Zhi-Jie Liu, Mar 20, 2014
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    • "To be biologically relevant, the intermolecular interaction energy of Noxa with the Bak groove should intuitively be lower than that of polyalanine. To confirm this, we calculated intermolecular interaction energies of the Noxa·Bak complex and a reference complex of A1234567891011121314151617181920212223242526K27·Bak that was generated by mutating residues 19–45 of Noxa in the Noxa·Bak complex model to A1920212223242526272829303132333435363738394041424344K45. The mutation to A1920212223242526272829303132333435363738394041424344K45 rather than A192021222324252627282930313233343536373839404142434445 was to keep the net charge of the mutant peptide identical to that of Noxa. "
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    ABSTRACT: Recently we reported that the BH3-only proteins Bim and Noxa bind tightly but transiently to the BH3-binding groove of Bak to initiate Bak homo-oligomerization. However, it is unclear how such tight binding can induce Bak homo-oligomerization. Here we report the ligand-induced Bak conformational changes observed in 3D models of Noxa·Bak and Bim·Bak refined by molecular dynamics simulations. In particular, upon binding to the BH3-binding groove, Bim and Noxa induce a large conformational change of the loop between helices 1 and 2 and in turn partially expose a remote groove between helices 1 and 6 in Bak. These observations, coupled with the reported experimental data, suggest formation of a pore-forming Bak octamer, in which the BH3-binding groove is at the interface on one side of each monomer and the groove between helices 1 and 6 is at the interface on the opposite side, initiated by ligand binding to the BH3-binding groove.
    Full-text · Article · Feb 2012 · Scientific Reports
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    • "During the transition of Bak from 'inactive' to the 'primed' state an occluded N-terminal epitope is exposed in intact cells (Griffiths et al, 1999), the exposure of which is associated with the N-terminal conformational change. X-ray structures of the non-activated Bak conformer (Moldoveanu et al, 2006; Wang et al, 2009), show the protein fold in all three structures (2IMS, 2JCN and 2YV6) closely resembles the nonactivated cytosolic form of Bax (Suzuki et al, 2000). Therefore, they provide no clear insights regarding Bak activation. "
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    ABSTRACT: Activation of the cell-death mediator Bak commits a cell to mitochondrial apoptosis. The initial steps that govern Bak activation are poorly understood. To further clarify these pivotal events, we have investigated whether post-translational modifications of Bak impinge on its activation potential. In this study, we report that on apoptotic stimulation Bak undergoes dephosphorylation at tyrosine residue 108 (Y108), a critical event that is necessary but not sufficient for Bak activation, but is required both for early exposure of the occluded N-terminal domain and multimerisation. RNA interference (RNAi) screening identified non-receptor tyrosine phosphatases (PTPNs) required for Bak dephosphorylation and apoptotic induction through chemotherapeutic agents. Specifically, modulation of PTPN5 protein expression by siRNA and overexpression directly affected both Bak-Y108 phosphorylation and the initiation of Bak activation. We further show that MEK/ERK signalling directly affects Bak phosphorylation through inhibition of PTPN5 to promote cell survival. We propose a model of Bak activation in which the regulation of Bak dephosphorylation constitutes the initial step in the activation process, which reveals a previously unsuspected mechanism controlling the initiation of mitochondrial apoptosis.
    Full-text · Article · Oct 2010 · The EMBO Journal
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    • "In any case, the supraphysiological zinc levels required for inhibition in vitro, and the failure of binding-site mutagenesis to alter Bak function in cells (Figure 4), argue against a physiological role for zinc in directly regulating Bak function. Pertinently, the two other structures of truncated Bak (2JCN, 2YV6) (Graslund et al., 2008; Wang et al., 2009) do not exhibit the homodimeric zinc coordination site observed by Moldoveanu et al. (2006). "
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    ABSTRACT: A pivotal step toward apoptosis is oligomerization of the Bcl-2 relative Bak. We recently reported that its oligomerization initiates by insertion of an exposed BH3 domain into the groove of another Bak monomer. We now report that the resulting BH3:groove dimers can be converted to the larger oligomers that permeabilize mitochondria by an interface between alpha6 helices. Cysteine residues placed in alpha6 could be crosslinked only after apoptotic signaling. Cysteines placed at both interfaces established that the BH3:groove dimer is symmetric and that the alpha6:alpha6 interface can link these dimers into homo-oligomers containing at least 18 Bak molecules. A putative zinc-binding site in alpha6 was not required to form the alpha6:alpha6 interface, and its mutation in full-length Bak did not affect Bak conformation, oligomerization, or function. We conclude that alpha6:alpha6 interaction occurs during Bak oligomerization and proapoptotic function, but we find no evidence that zinc binding to that interface regulates apoptosis.
    Preview · Article · Nov 2009 · Molecular cell
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