Structural insights into the degradation of Mcl-1induced by BH3 domainsPeter E. Czabotar*, Erinna F. Lee*†, Mark F. van Delft*†, Catherine L. Day‡, Brian J. Smith*, David C. S. Huang*,W. Douglas Fairlie*, Mark G. Hinds*, and Peter M. Colman*§

*The Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria 3050, Australia; †Department of Medical Biology, University of Melbourne,Parkville, Victoria 3050, Australia; and ‡Department of Biochemistry, University of Otago, Dunedin 9001, New Zealand

Communicated by Suzanne Cory, The Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria, Australia, February 12, 2007(received for review November 22, 2006)

Apoptosis is held in check by prosurvival proteins of the Bcl-2family. The distantly related BH3-only proteins bind to and an-tagonize them, thereby promoting apoptosis. Whereas binding ofthe BH3-only protein Noxa to prosurvival Mcl-1 induces Mcl-1degradation by the proteasome, binding of another BH3-onlyligand, Bim, elevates Mcl-1 protein levels. We compared the three-dimensional structures of the complexes formed between BH3peptides of both Bim and Noxa, and we show that a discreteC-terminal sequence of the Noxa BH3 is necessary to instigate Mcl-1degradation.

apoptosis � Bim � Noxa � crystallography

The mammalian Bcl-2-related antiapoptotic proteins (Bcl-2,Bcl-xL, Bcl-w, Mcl-1, and A1) are critical for maintaining cell

survival during development or in response to various stressstimuli (1). They share up to four Bcl-2 homology domains, BH1through BH4, and contain a putative membrane anchoringsequence at their C termini. Structural studies on proteinslacking only this C-terminal segment reveal that the Bcl-2 familyfold is that of an all-helical protein in which the BH1, BH2, andBH3 domains are spatially clustered around a depression on theprotein surface (2–5). In response to death signals, such ascytotoxic agents or radiation, a related protein family (theBH3-only proteins) antagonizes the function of the antiapoptoticproteins. The BH3 domains of these proapoptotic moleculesform an amphipathic �-helical fold when bound to a groove linedby the BH1, BH2, and BH3 domains of antiapoptotic proteinssuch as Bcl-xL (6–8), a step thought to be important for apoptosisinduction.

Mcl-1 (myeloid cell factor 1) (9) has features distinguishing itfrom the other prosurvival proteins. It has a central and non-redundant role in the maintenance of progenitor and stem cells(10–12). The levels of Mcl-1 are highly regulated. In some celltypes, signals for differentiation trigger its up-regulation (13),whereas basal levels are controlled, at least in part, by theubiquitin-proteasome machinery. The HECT domain-contain-ing E3 ligase Mule controls basal Mcl-1 protein abundance andinduces its degradation in response to DNA-damaging agentssuch as cisplatin (14). Mule harbors a BH3 domain that allowsit to bind Mcl-1. Noxa is a BH3-only protein that can bind andtrigger proteasome-mediated Mcl-1 degradation (15). WhetherMule and Noxa contribute to the proteasomal degradation ofMcl-1 in response to UV irradiation (16) or viral infection isunclear (17). Furthermore, the structural basis for Mcl-1 deg-radation induced by Noxa is unknown.

Recently we have shown that the five mammalian antiapopto-tic molecules cluster into two classes; one (containing Bcl-2,Bcl-xL, and Bcl-w) is neutralized by the BH3-only protein Bad,and the other (containing Mcl-1 and A1) is neutralized by theBH3-only protein Noxa (18). Inactivation of both subsets ofprosurvival proteins appears necessary for cell death to proceed.Interestingly, the recently described Bcl-2 antagonist ABT-737(19) is a Bad-like BH3 mimetic and does not bind Mcl-1. As

expected, ABT-737 is not a potent cytotoxic agent on its own,unless Mcl-1 is also inactivated (20). Thus, understanding thecontrol of Mcl-1 is critical for the discovery and development ofnovel therapeutic agents for the treatment of cancers, particu-larly those in which Mcl-1 appears to be critical for maintainingtheir survival, including B cell lymphoma (21), multiple myeloma(22), and chronic lymphocytic leukemia (23).

Here we show that, unlike Noxa, Bim stabilizes Mcl-1 againstdegradation. This observation prompted us to seek a structuralcorrelate of the differences in the regulation of Mcl-1 degrada-tion by these two BH3-only proteins: stabilization induced byBim and degradation induced by Noxa. The Mcl-1 proteinsequence contains a Bcl-2-like region (BLR) of some 150 aa and,unlike other antiapoptotic members of the Bcl-2 family, anadditional N-terminal domain of �170 residues. Here, we de-scribe crystal and NMR structures of the Bcl-2 homology regionof Mcl-1 in complex with a Bim BH3 peptide and with a mouseNoxaB BH3 peptide. These structures demonstrate that thereare no significant differences in the complexes Mcl-1 forms withBim or Noxa. Thus, the signal for degradation of Mcl-1 consistsof the complex of the two components rather than a Noxa-induced structural change in Mcl-1. We further map the se-quence signature on the Noxa BH3 required for triggering Mcl-1degradation to its C-terminal region.

ResultsNoxa Causes Mcl-1 Degradation, but Bim Causes Mcl-1 Stabilization.As previously shown (15), overexpression of human Noxa trig-gered the degradation of endogenous Mcl-1 in mouse embryonicfibroblasts (Fig. 1B). The BH3 region of Noxa alone seemedcritical because marked degradation of Mcl-1 was also seen whenthis was placed in the context of the BimS backbone. However,a Bim BH3 domain did not reduce Mcl-1 levels, either in itsnative form or when placed in the context of Noxa (Fig. 1C).Instead, Bim BH3 binding promoted Mcl-1 stabilization, akin tothat previously noted with Puma (24). Levels of another pro-survival protein, Bcl-2, remained constant regardless of whetherBims or Noxa were expressed.

Interestingly, mutating the unique lysine in the BH3 region ofNoxa to a glutamic acid (see Noxa mt3 in Fig. 1 A) did not affect

Author contributions: P.E.C., E.F.L., M.F.v.D., C.L.D., D.C.S.H., W.D.F., M.G.H., and P.M.C.designed research; P.E.C., E.F.L., M.F.v.D., C.L.D., W.D.F., and M.G.H. performed research;P.E.C., E.F.L., M.F.v.D., C.L.D., B.J.S., D.C.S.H., W.D.F., M.G.H., and P.M.C. analyzed data; andP.E.C., D.C.S.H., and P.M.C. wrote the paper.

The authors declare no conflict of interest.

Abbreviations: BLR, Bcl-2-like region; ITC, isothermal titration calorimetry; Mcl-1, myeloidcell factor 1.

Data deposition: The atomic coordinates and structure factors (x-ray structures) have beendeposited in the Protein Data Bank, www.pdb.org (PDB ID codes 2NL9, 2NLA, and 2JM6).

§To whom correspondence should be addressed. E-mail: pcolman@wehi.edu.au.

This article contains supporting information online at www.pnas.org/cgi/content/full/0701297104/DC1.

© 2007 by The National Academy of Sciences of the USA

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its capacity to trigger Mcl-1 degradation (Fig. 1C). Furthermore,an inactive form of hNoxa (3E), unable to bind Mcl-1 (18), didnot affect Mcl-1 levels. Likewise, expression of mBad, which isalso unable to bind Mcl-1 (18), does not affect Mcl-1 levels.Strikingly, a chimeric mBad containing the hNoxa BH3 did nottrigger Mcl-1 degradation, suggesting that regions outside of theBH3 may influence Noxa-induced degradation (Fig. 1C). UnlikehNoxa, mNoxa contains two BH3 domains. Both of thesesequences induced Mcl-1 degradation when expressed in thecontext of the human Noxa backbone, albeit not as efficiently asthe single human Noxa BH3 (Fig. 1D). This may reflect the lowerbinding affinities of the mouse Noxa BH3s, compared with thehuman one, for Mcl-1 (18).

Thus, Bim and Noxa BH3 domains may induce distinctconformational changes in Mcl-1, one stabilizing it and the otherprompting its destruction. To test this, we determined andanalyzed the three-dimensional structures of Mcl-1 bound toBim BH3 and to Noxa BH3.

A Mouse/Human Mcl-1 Chimera That Retains a Human BH3-BindingGroove. Previously, mouse Mcl-1 has been expressed in Esche-richia coli with an N-terminal truncation of 151 residues (�N151)and a C-terminal truncation of 23 residues (�C23) to remove thetransmembrane anchor (5). This leaves the BLR of the moleculein a form that can be expressed as a soluble protein (hereafterreferred to as mMcl-1BLR). However, the comparable humanMcl-1 construct (�N170 and �C21) did not produce solublerecombinant protein (data not shown). We have overcome thisby constructing a chimera of mouse and human Mcl-1BLR. Thisprotein is identical to the human sequence with the exceptionof nine N-terminal amino acids [hereafter referred to ashMcl-1BLR; see supporting information (SI) Fig. 5]. In particular,the region of the protein encompassing the BH3-binding grooveis of human origin. Additionally, this protein can be expressedand purified in similar yields to mMcl-1BLR. Isothermal titrationcalorimetry (ITC) confirms that hMcl-1BLR and mMcl-1BLR have

similar binding characteristics for peptides derived from the BH3regions of a variety of BH3-only proteins (SI Table 2 and datanot shown).

The Structure of the hMcl-1BLR:hBim BH3 Complex. The refined model(Table 1; and see SI Table 3) includes residues D172 to S193 andG203 to E322 on hMcl-1BLR and residues R53 to R75 on thehelical Bim BH3 peptide. The protein adopts the canonical Bcl-2family fold of eight �-helices. No interpretable electron densityis evident for residues 194–202 in the linker region betweenhelices �1 and �2, nor for residues 51, 52, and 76 at the end ofthe Bim peptide. The structure of the complex (Fig. 2 A andB) reveals the peptide bound to the homologous regions of Mcl-1as compared with the previously reported structure of a com-plex between mouse Bcl-xL and mouse Bim BH3 (Fig. 2C) (8).One strikingly conserved structural feature, not only with theBcl-xL:Bim complex but also with the CED-9:EGL-1 complex ofCaenorhabditis elegans proteins (25), is the hydrogen bondinginteraction between D67 on the peptide and a conserved arginylresidue in the BH1 domain of the antiapoptotic molecule (R263in hMcl-1BLR). This contact is displayed in SI Fig. 6, togetherwith the experimentally phased electron density.

The surface of hMcl-1BLR to which the peptide binds is agroove embellished by pockets of varying sizes and depth (Fig.2B). The deepest of these accommodates L62 of the BH3 peptideand includes two water molecules. It is contiguous with theshallower pockets for I58 and I65. A saddle point in the groovealigns with G66 of the peptide, separating the pockets accom-modating C-terminal residues in the peptide from the threepockets described above. Residues F69 and Y73 are both moresolvent-exposed than any of the three N-terminal pocket-bindingresidues.

The Bim BH3 peptide is completely located within the bindinggroove. Because of the proximity of M231 of Mcl-1 to Bimresidues I58 and L62, we measured the binding of the hBim BH3to hMcl-1BLR both in its native (methionyl) and derivatized(selenomethionyl) forms by ITC (SI Table 2). The dissociationconstants observed for both are indistinguishable.

The electrostatic potential at the solvent-exposed surface ofhMcl-1BLR, calculated with the Bim BH3 peptide removed, isdisplayed in Fig. 2B. The BH3-binding groove of hMcl-1 is morepositively charged than the corresponding region on mBcl-xL(Fig. 2C) as described earlier for the mouse protein (5). Thesurface profiles of Mcl-1 and Bcl-xL are also distinctly different,especially around the pockets for the first and fourth hydropho-bic residues of the BH3 ligand.

The Crystal Structure of the hMcl-1BLR:mNoxaB BH3 Complex. Thusfar, attempts to crystallize hMcl-1BLR with a mNoxaA or a hNoxaBH3 peptide have not been successful. Here we present thecrystal structure of hMcl-1BLR in complex with the mNoxaB BH3peptide. The model for this complex includes residues D172 toV321 of hMcl-1BLR and residues D73 to N93 of mNoxaB. Thecrystals and resulting model are of lesser quality than those of theBim complex (Table 1). The �1–�2 of hMcl-1BLR linker is visiblebecause of crystal contacts involving this segment. The mNoxaBBH3 peptide binds to hMcl-1BLR in a similar fashion to the Bim

Fig. 1. The Noxa BH3 is essential but not sufficient to induce Mcl-1 degra-dation. (A) Representative BH3 domain sequences. The four hydrophobicresidues that are accommodated within the four hydrophobic pockets ofpreviously described BH3 binding grooves (8) are indicated as h1 to h4. (B)Mcl-1 is degraded in cells overexpressing either hNoxa or hBims containinghNoxa BH3. In contrast, Mcl-1 levels are elevated in cells expressing hBims. Cellsexpressing an inactive mutant of hBims (Bims 4E) show no alteration in Mcl-1levels. Bcl-2 levels are unaffected by either Noxa or Bim expression. (C) Cellsexpressing hNoxa and hNoxa mt3 (18) show increased Mcl-1 degradation.However, Mcl-1 degradation is not increased in cells expressing an inactivevariant of hNoxa (hNoxa 3E) or hNoxa containing a BimBH3. Mcl-1 degrada-tion is not increased in cells expressing mBad, or mBad containing a hNoxaBH3, suggesting that sequences outside of the BH3 domain can also influencethe outcome. (D) Human Noxa variants containing either mNoxaA or mNoxaBBH3 induce modest Mcl-1 degradation.

Table 1. Crystallographic refinement statistics

StatistichMcl-1BLR:hBim

BH3hMcl-1BLR:mNoxaB

BH3

Resolution, Å 34.1–1.55 50–2.8Rwork/Rfree 0.173/0.203 0.207/0.291rmsd bond lengths, Å 0.015 0.012rmsd angles, ° 1.395 1.341

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BH3 peptide, but with one notable distinction. The N-terminalportion of the peptide, before Q77, is not helical (Fig. 3A) andis not intimately engaged with the binding groove of hMcl-1BLR.Sequence alignments of BH3 domains (see Fig. 1 A) indicate thatthe mNoxaB sequence is unique because it contains no hydro-phobic residue at position 74. No electron density is observed forthe N-terminal peptide sequence from residue 68 to residue 72,whereas the segment from 73 to 76 is neither helical norintimately bound to hMcl-1BLR. No ordered structure is evidentfor the carboxylate moieties of the peptide at residue D73 or E74or for the peptide side chains of L87 and R88. An overlay ofMcl-1 from the Bim BH3 and mNoxaB BH3 complexes isdisplayed in Fig. 3B (see Discussion).

During the refinement of this structure it became apparent thatcysteine residues on hMcl-1BLR (C286) and the peptide (C75) of acrystallographically (63) related complex were close enough to forma disulfide bond. SDS/PAGE analysis of dissolved crystals (data notshown) confirmed the presence of this covalent linkage.

Solution Structure of the mMcl-1BLR:mNoxaB BH3 Complex. The NMRstructure of the mMcl-1BLR:mNoxaB BH3 complex (SI Table 4)was solved to determine the state of the mNoxaB BH3 Nterminus in solution (Fig. 3C). Mouse Mcl-1BLR was used for thispurpose because the solution properties of the hMcl-1BLR pre-cluded a high-resolution structural study by NMR. The solutionstructure shows the mNoxaB peptide as helical from residue 72to residue 93 and demonstrates that the N-terminal region of thepeptide does indeed engage the Mcl-1 groove. This is the onlysignificant difference observed between the solution (Fig. 3C)and crystal (Fig. 3A) structures. Amino acid sequence differ-ences between human and mouse Mcl-1 (SI Fig. 5) reveal onlyone substitution in the binding groove, L246F, and that cannotaccount for this difference. Thus, the absence of helicityat the N terminus of the mNoxaB peptide described in thehMcl-1BLR:mNoxaB crystal structure is a crystallization artifact.Mouse NoxaB residue E74 is tolerated at the conserved hydro-phobic position because the charged carboxyl group is coordi-nated by K215 of mMcl-1 (K234 in the hMcl-1BLR protein) at thesolvent-exposed end of the peptide–protein interface (Fig. 3D).

Contribution of the N Terminus of mNoxaB to Mcl-1 Binding. ITC wasperformed to confirm the role of the N terminus of mNoxaB in

binding to the hMcl-1BLR chimera. Removal of seven amino acidsfrom the N terminus of the sequence together with the substi-tution C75A resulted in no reduction in the affinity (SI Table 2).However, removal of one more residue caused a 35-fold re-duction in the binding constant. A similar truncation of thehNoxa BH3 resulted in no detectable binding of the peptide tohMcl-1BLR.

These data suggest that the N-terminal region of mNoxaBBH3 may readily disengage from the hMcl-1BLR binding groove,providing a rationale for the crystallization artifact involving thedisulfide bond between neighboring protein–peptide complexes.

The Structural Determinant of BH3 Ligand-Induced Mcl-1 Degradation.BH3 chimeras (Fig. 4A), with regions of Noxa BH3 replaced withthose of Bim (which on its own did not cause Mcl-1 degradation)(Fig. 1C), point to a region toward the C terminus of the BH3region being required for Mcl-1 degradation (Fig. 4B). The NoxaBH3 sequence (-FRQKLL-) appears to be essential becausereplacing this with corresponding Bim sequences (-AYYARR-,hNoxa/Bim 3) abrogated the effect on Mcl-1 stability. Thischimeric BH3 peptide still binds Mcl-1 with low nanomolaraffinity (SI Table 2).

DiscussionComparison of Mcl-1 in Complex with the BH3 Domains of Bim or Noxa.The solution (Fig. 3C) and crystal structures (Fig. 3A) of themNoxaB BH3 complexes are not significantly different, apartfrom at the N terminus of the peptide as described above.Binding studies of N-terminally truncated mNoxaB BH3 pep-tides suggest that this region does not make a major contri-bution to the binding energy with the Mcl-1 groove and thatthe structure seen in the crystalline state has arisen throughcapture of an unbound form of the N-terminal segmentthrough a disulfide bond with a crystallographically neighbor-ing hMcl-1BLR:mNoxaB BH3 complex.

An overlay of the x-ray structures of Mcl-1 from the complexeswith both Bim and mNoxaB is illustrated in Fig. 3B. Differentcrystal contacts are the likely explanation for minor differences inthe two Mcl-1 structures at the �2–�3, �3–�4, and �5–�6 corners.Bearing in mind the medium resolution of the mNoxaB complex, noevidence is found of significant structural differences in the bindinggroove of hMcl-1BLR reflecting adaptation to the different peptide

Fig. 2. X-ray structure of the hMcl-1BLR:hBim complex. (A) Ribbon diagram showing the Bim BH3 peptide in green and the BH1, BH2, and BH3 regions of Mcl-1in blue, yellow, and red, respectively. (B and C) Electrostatic potential over the solvent-exposed surface of Mcl-1 (B) and Bcl-xL (C) (8) complexed with Bim BH3.The electrostatic potential over the solvent-exposed surface of the protein in the absence of ligand was calculated with the program MEAD (48) by using Parseatomic charges and radii (49). Ionizable residues were charged according to their standard state at neutral pH. The surface is color-coded as follows: blue, positivepotential (14 kT); red, negative potential (�14 kT); white, zero potential. Residues of the peptide discussed in the text are indicated and numbered accordingto either hBim (B) or mBim (C). This figure was prepared by using DINO (www.dino3d.org).

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ligands. However, the side chain orientations of Mcl-1 residuesL235 and I237 are different in the two complexes, presumablybecause of the failure of the bound mNoxaB peptide to extend ina canonical helical conformation back toward its N terminus.

Because no significant differences are observed in the structuresof Mcl-1 in the two peptide complexes, we conclude that it is thestructure of the Mcl-1:Noxa complex itself that triggers its elimi-nation rather than a Noxa-induced conformational change in Mcl-1.

The Structural Correlate of Degradation. Steady-state levels ofMcl-1 in healthy cells are regulated in part by the E3 ubiquitinligase Mule (14). Mule contains a BH3 sequence that binds toMcl-1, but not to Bcl-xL or Bcl-2, resulting in Mule-mediatedMcl-1 degradation. Here, we show that the Bim BH3 sequencestabilizes Mcl-1 levels. In a recent study, it was shown that theBH3-only protein Puma also stabilized Mcl-1 levels (24). Onemodel by which Bim and Puma may stabilize Mcl-1 holds thattheir binding to Mcl-1 precludes that of Mule. Conversely, theNoxa BH3 region causes proteasomal-dependent Mcl-1 degra-dation (15), suggesting that this interaction may promote bindingof an E3 ligase or some other adapter molecule, which is requiredfor degradation to occur. Alternatively, the complex may bedirectly recognized by the proteasome itself. The structures ofthe Bim and Noxa BH3 peptides with Mcl-1 may reveal distinc-tive features that delineate the recognition epitope.

The sequences of BH3 domains of Bim and hNoxa differmarkedly at both the N and C termini (Fig. 1 A) but are similarthroughout the central region of the domain. The properties ofhNoxa mutant 3 (Fig. 1C) eliminate a role for K35 in degrada-tion, although that lysine is a unique feature of Noxa among allof the mammalian BH3-only proteins. Mouse Noxa also causesMcl-1 degradation (data not shown), but it has two BH3 motifs,

and, at least in the context of human Noxa, both harbor thisactivity, although not as strongly as the hNoxa BH3. Within thehNoxa BH3, the sequence -FRQKLL- is important for degra-dation because its substitution by the sequence -AYYARR-from Bim leads to Mcl-1 stabilization, as seen for Bim itself. Inthe structure we report for the mNoxaB complex, the sequenceis -LRQKLL-, and the glutaminyl residue projects toward theMcl-1 surface with other amino acids in the sequence remaininghighly solvent-accessible. One similarity among hNoxa,mNoxaB, and mNoxaA within this region is the presence of twohydrophobic residues, either -LL- or -AP-, at the end of thesequence. In contrast, the two BH3 domains that have beenshown to stabilize Mcl-1 levels, Bim and Puma, have argininylresidues at both of these positions. Further experiments areneeded to clarify the precise role of these residues.

Interestingly, unlike hNoxa BH3 in the context of the BH3-onlyprotein Bim, hNoxa BH3 in the context of the BH3-only proteinBad does not promote destruction of Mcl-1. This result suggests thatsequences outside of the BH3 domain of the protein Bad inhibitMcl-1 degradation. Formally identifying such sequences may provedifficult because Bad (like Bim) is an intrinsically unstructuredprotein that assumes some structure in its BH3 domain only onengagement with Bcl-2 family proteins (26).

Collectively, these results support a model whereby the com-plex formed between Noxa and Mcl-1 is recognized for destruc-tion, potentially by an E3 ligase or some other adapter molecule.Furthermore, the region of the complex recognized includes theC-terminal residues of the Noxa BH3 domain. Whether it alsoincludes regions of the N-terminal PEST domain of Mcl-1, whichis predicted to be unstructured, awaits clarification.

Comparison of Bound and Free Mcl-1. The structures reported hereinvite comparisons with Bcl-xL, with respect to the unliganded-to-liganded transition and to the liganded states with a commonpeptide ligand Bim BH3. Compared with the solution structureof mMcl-1BLR with no peptide ligand (5), both of the complexesreported here have a more open binding groove (SI Fig. 7). Thestructural change that accompanies peptide binding is largest inthe region of the central two hydrophobic pockets, h2 and h3.The C� atoms of hMcl-1BLR residues N223 and D256 are 6 Åfurther apart in the Bim BH3 complex than in the solutionstructure of the unliganded mouse molecule. The binding sitesfor the C terminus (beyond the conserved -GD- sequence) ofboth the Bim and mNoxaB BH3 peptides are preformed in the

Fig. 3. X-ray and NMR structures of the Mcl-1BLR:mNoxaB complex. (A)Ribbon diagram showing the mNoxaB BH3 peptide in purple and the BH1,BH2, and BH3 regions of hMcl-1 in blue, yellow, and red, respectively.(B) Overlay of hMcl-1BLR from the hMcl-1BLR:hBim BH3 complex (gray) andhMcl-1BLR:mNoxaB BH3 complex (pink). (C) Overlay of 20 minimum-energyNMR structures of the mMclBLR:mNoxaB BH3 complex. Mcl-1 is in blue, and themNoxaB BH3 is in gray. (D) Close-up of the N terminus of the mNoxaB BH3peptide from the NMR-derived structure illustrates that Glu-74 in the peptideengages Lys-215 of mMcl-1 (mMcl-1 numbering).

Fig. 4. Mapping the region of the Noxa BH3 that induces Mcl-1 degradation.(A) BH3 domain chimeras of hBim and hNoxa. The signature sequence of fourhydrophobic residues is indicated. The Bim BH3 sequence is underlined. (B)Human Noxa variants containing chimeric Noxa/Bim BH3 domains demon-strate that the C terminus of the BH3 is required for Noxa-induced Mcl-1degradation.

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unliganded mMcl-1 structure. As predicted (5), unligandedMcl-1 undergoes a smaller conformational change in binding aBH3 peptide than do Bcl-xL (8) and CED-9 (25, 27).

Unique Features of the Mcl-1 Binding Groove. The binding affinitiesof Mcl-1 and Bcl-xL for certain BH3 domains vary over four ormore orders of magnitude (18). In particular, the BH3 domainof Bad has no measurable binding to Mcl-1 whereas it bindstightly (nanomolar) to Bcl-xL, Bcl-2, and Bcl-w. Interestingly, therecently described Bcl-xL antagonist ABT-737 (19) mimics thisbinding profile. The high-resolution structure we describe herefor hMcl-1 complexed with the Bim BH3 peptide reveals signif-icant differences from the complex formed by Bcl-xL (8).

The BH3-binding grooves of Mcl-1 and Bcl-xL share manyfeatures that derive from common sequences within their BH1,BH2, and BH3 domains. However, three points of difference arenoteworthy. (i) A single amino acid inserted into the BH1domain of Mcl-1 is located in the �4–�5 corner. Two Mcl-1residues (G257 and V258) occupy the space of a single residue(glycine) in Bcl-xL (SI Fig. 8). As a consequence, R263 issomewhat less solvent-exposed in the Mcl-1:Bim BH3 complexthan its homolog in the Bcl-xL complex. It is this arginyl residuethat participates in a conserved hydrogen-bonding interactionwith an aspartyl residue of the peptide (D67 in this case) in allcrystal structures of complexes reported to date. (ii) Comparedwith Bcl-xL (and with Bcl-2 and Bcl-w), the BH3 domainsequence of Mcl-1 has distinctive differences adjacent to theconserved glycine and aspartic acid residues where the Mcl-1sequence reads -VGDGVXXN- compared with -AGDEFXXR-.The consequence of these substitutions is to radically remodelthe binding site for the C terminus of the peptide ligand,especially for the fourth hydrophobic residue (h4 in Fig. 1 A), F69in the case of Bim. The pocket accommodating this residue is lesswell defined and more solvent-exposed than its counterpart inBcl-xL (see Fig. 2). (iii) Helix �3 is well formed in the Mcl-1complex but poorly so in the Bcl-xL complex (SI Fig. 9). Oneresult of this difference in the paths of the protein backbones(Q229 to K234 of Mcl-1 compared with S106 to Q111 of mouseBcl-xL) is that the binding pockets for the first two hydrophobicresidues of the Bim BH3 sequence (h1-I58 and h2-L62) are moreconstricted and less contiguous in the Mcl-1 complex.

The Bcl-xL complex is of mouse proteins (Protein Data Bank IDcode 1PQ1), so the Bim peptide sequences are not identical. Theonly significant differences occur in the side chain conformations ofthe first and third of the four canonical hydrophobic residues of theBH3 motif, I58 and I65 (SI Fig. 9). These differences appear tocompensate for corresponding structural differences betweenhMcl-1BLR and Bcl-xL described above. It is interesting to note thatthe sequence of Bad BH3, which is selective for Bcl-xL over Mcl-1,has Tyr and Met, respectively, at these two positions.

Do any of these structural differences correlate with thefailure of the BH3 domain of Bad to bind to Mcl-1? An earlierstudy (5) of selected point mutants of Mcl-1 failed to rescuebinding to the Bad BH3, but a substitution in that BH3 domainof Y105I did recover some binding to wild-type Mcl-1. Thedifferences between Mcl-1 and Bcl-xL in �3 described above maybear on this result and suggest that binding to Bad BH3 might beenabled, at least partially, by relieving crowding around the h1pocket. Note, however, that this crowding is largely due to adifference in the main chain conformations of Mcl-1 and Bcl-xLin this region, a difference unlikely to be fully remedied by asingle amino acid sequence change.

No structure has yet been reported for ABT-737 bound to Bcl-xL,so one cannot directly attribute the differences described above tothe selectivity of ABT-737 for Bcl-xL. Nevertheless, the mere sizeof ABT-737 (�800 Da) suggests that it engages a significant portionof the binding groove, whereon any or all of these differences maycome into play to prevent binding to Mcl-1.

Experimental ProceduresRetroviral Expression of BH3-Only Proteins. Retroviral expressionconstructs were made by using the pMIG vector (MSCV-IRES-GFP; GFP sequence is that of EGFP) as described previously(18, 28). These plasmids were transiently transfected, by usingLipofectamine (Invitrogen, Carlsbad, CA), into Phoenix Eco-tropic packaging cells (29). Filtered virus-containing superna-tants were used to infect Bax�/�Bak�/� mouse embryonic fibro-blasts by spin inoculation as described previously (15). Stable celllines expressing vector alone, BimS, or Noxa variants weregenerated by selection of GFP� mouse embryonic fibroblastsafter retrovirus spin inoculation. After lysis of 1.5 � 106 cells inbuffer containing 1% (vol/vol) Triton X-100, proteins wereresolved by SDS/PAGE and immunoblotted by using antibodiesagainst Mcl-1, Bcl-2, and HSP 70 [N6; gift of W. Welch (Uni-versity of California, San Francisco, CA) and R. Anderson(Peter MacCallum Cancer Centre, Melbourne, Australia)] asdescribed (15). Fig. 1 A describes the regions of sequence thatwere shuttled to construct hybrid BH3-only proteins. In the caseof mBad, the chimeric BH3 domain replaced residues 97–122.

Protein Expression and Purification. The hMcl-1BLR chimera con-sists of residues 152–189 from mouse Mcl-1 and 209–327 fromhuman Mcl-1 and was constructed by using the conserved SphIsite. Mouse Mcl-1BLR (amino acids 152–308) and hMcl-1BLR

(171–327) were expressed in E. coli BL21 (DE3) as GST fusionproteins as previously described (5). Cells were grown in super-broth at 37°C and induced with 1 mM isopropyl �-D-thiogalactoside (IPTG) at an OD600 of 0.3. After 3 h, cells wereharvested and lysed in buffer 1 (50 mM Tris, pH 8.0/150 mMNaCl/1 mM EDTA). Supernatant was applied to a glutathioneSepharose column (GE Healthcare, Piscataway, NJ) and thenwashed with buffer 1. On-column cleavage was performed withPrescission Protease (GE Healthcare). Mcl-1 was eluted withbuffer 1 and further purified on a Superdex 200 column (GEHealthcare) in 50 mM Tris (pH 8.0)/150 mM NaCl. Selenome-thionine-labeled protein was expressed as described (30) andpurified as per native protein.

Mouse NoxaB BH3 peptide for use in NMR was prepared aspreviously outlined (26). Mass spectrometry was used to confirmpeptide homogeneity. Isotopically labeled proteins were grownin minimal media by using 15NH4Cl and D-[U-13C]glucose as thesole nitrogen and carbon sources, respectively, as described (31).Mouse Mcl-1/NoxaB complex was prepared by titration by usingNMR to detect the end point. Two samples were prepared,13C,15N-labeled Mcl-1/unlabeled NoxaB-BH3 and unlabeledMcl-1/13C,15N-labeled NoxaB-BH3. NMR samples contained�0.5 mM protein in 50 mM sodium phosphate (pH 6.7), 70 mMNaCl, and 0.04% sodium azide in H2O:2H2O (95:5). Syntheticpeptides were purchased from Mimotopes (Victoria, Australia).

Crystallography, Data Collection, and Structure Determination. Forthe hMcl-1BLR:hBim BH3 complex, selenomethionine-labeled pro-tein was mixed with an equimolar amount of peptide and concen-trated to 12 mg/ml. Crystals of the complex were grown in hangingdrops at 22°C [reservoir solution: 0.2 M ZnCl2/0.2 M imidazole, pH5.75/2 mM tris(2-carboxyethyl)phosphine (TCEP)]. Before flash-freezing in liquid N2, crystals were equilibrated into cryoprotectantconsisting of reservoir solution and increasing concentrations oftrehalose (final trehalose concentration, 30%). X-ray data werecollected at three wavelengths on beamline X29A at the NationalSynchrotron Light Source (Brookhaven National Laboratory).Data were integrated and scaled with HKL2000 (32). Two Se siteswere found by using data from all three wavelengths usingHKL2MAP (33). An initial model was built from the resulting mapusing COOT (34). Several rounds of building and refinement inREFMAC5 (35) led to the final model shown in Table 1.

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For the hMcl-1BLR:mNoxaB BH3 complex, native protein wasmixed with an equimolar amount of peptide and concentrated to 15mg/ml. Crystals were grown in hanging drops at 22°C (reservoirsolution: 12% PEG 4000/4% isopropanol/5% dioxane/0.1 M Tris,pH 8.0). Crystals were equilibrated into cryoprotectant consistingof reservoir solution and increasing concentrations of ethyleneglycol (final concentration, 25%) before flash-freezing. A nativex-ray data set was collected on beamline X-29A at the NationalSynchrotron Light Source. Data were integrated and scaled withHKL2000 (32) (Table 1). The structure was determined by molec-ular replacement with PHASER (36–38) using the coordinates ofhMcl-1BLR from the hMcl-1BLR:hBim BH3 complex as a searchmodel. Several rounds of building in COOT and refinement withREFMAC5 led to the model described in Table 1.

NMR Spectroscopy. Spectra were recorded at 25°C on a BrukerDRX 600 600-MHz spectrometer equipped with triple-resonance probes and pulsed-field gradients or AV-500 andAV-800 spectrometers equipped with a cryogenically cooledprobes, operating at 500 and 800 MHz, respectively. A series ofheteronuclear 3D NMR experiments were recorded by usingeither 15N or 13C,15N double-labeled mMcl-1BLR (39). Spectrawere processed by using TOPSPIN (Bruker, Billerica, MA) andanalyzed by using XEASY (40).

Distance restraints were measured from the 120-ms mixing time3D 15N-edited NOESY, 13C-edited NOESY, and 2D NOESYspectra. Hydrogen bond constraints were applied within �-helicesat a late stage of the structure calculation (4). � and � backbonetorsion angles were derived by using TALOS (41). Dihedral angle

restraints for � and � angles were used as summarized in SI Table4. 3JHNH� were derived from a 3D HNHA spectrum (42).

Initial structures were calculated by using CYANA 2.1 (43) andoptimized to obtain low target functions and refined with X-PLOR-NIH 2.14 (44) by using the OPLSX nonbonded parameters inexplicit water (45). Structural statistics for the final set of 20structures, chosen on the basis of their stereochemical energies, arepresented in SI Table 4. PROCHECK�NMR (46) and MOLMOL(47) were used for the analysis of structure quality. The finalstructures had no experimental distance violations �0.3 Å ordihedral angle violations �5°. Structural figures were generated inMOLMOL.

ITC. ITC was performed by using a VP-ITC microcalorimeter(Microcal, Amherst, MA). Experiments were performed in 20mM Tris (pH 8.0)/150 mM NaCl at 25°C. Titrations consisted of42 7-�l injections of peptide at 40 �M into 1.34 ml of protein at5 �M. Data were analyzed by using Origin software (OriginLab,Northampton, MA).

We thank M. Evangelista, H. Ierino, and J. Blyth for technical assistance;M. Kvansakul, T. Huyton, M. Gorman, J. Gulbis, and T. Garrett forhelpful discussions; and the staff at National Synchrotron Light Sourcebeamlines X-12B and X-29A for assistance with data collection andprocessing. Our work is supported by the Australian National Health andMedical Research Council (Program Grant 257502 and fellowships toW.D.F., P.M.C., and D.C.S.H.), the U.S. National Cancer Institute(Grant CA80188), the Leukemia and Lymphoma Society (SCOR 7015-02), a Melbourne International Research Scholarship (to M.F.v.D.), theCancer Council of Victoria (a scholarship to E.F.L. and a FraserFellowship to P.M.C.), the Australian Cancer Research Foundation, theWellcome Trust, and the Marsden Fund (C.L.D.).

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