Conformational Control of the Binding of the Transactivation Domain of the MLL Protein and c-Myb to the KIX Domain of CREB

Korkmaz, Elif Nihal; Nussinov, Ruth; Haliloğlu, Türkan

doi:10.1371/journal.pcbi.1002420

Cited by 34 publications

(45 citation statements)

References 42 publications

(69 reference statements)

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“…Overall, we found that binding of MLL and/or c-Myb resulted in an increase in stability (or a reduction in dynamics) of the α 3 C terminus and the L 12 -G 2 loop. This is consistent with observations made in previous NMR and computational studies, which have led to the suggestion that the increased structural stability of KIX may play a role in allosteric signaling (4,20,(28)(29)(30)(31)(32). For example, NMR backbone order parameter measurements of KIX have demonstrated that the L 12 -G 2 loop and the C-terminal residues of the α 3 helix are more rigid when MLL is bound to KIX (29).…”

Section: Discussionsupporting

confidence: 90%

“…Previous studies have observed changes in the KIX structure resulting from transcription factor binding, and both MLL and c-Myb have been shown to allosterically affect the affinity of KIX for the complementary peptide (4,20,(28)(29)(30)(31)(32). However, a connection between the changes in structural dynamics in KIX and how this directly leads to shifts in transcription factor binding affinities remain tenuous.…”

Section: Discussionmentioning

confidence: 99%

“…The binding of either MLL or c-Myb to one of these promiscuous sites can stabilize the C terminus of the α 3 helix of KIX and/or decrease the mobility of the L 12 -G 2 loop (4,20,(28)(29)(30)(31)(32), but the functional role of these changes remains to be delineated. Furthermore, in vitro, KIX alone demonstrates a ∼2-fold lower affinity for c-Myb and ∼1.6-fold lower affinity for MLL compared with KIX bound to MLL or c-Myb, respectively (13).…”

mentioning

confidence: 99%

“…Although numerous efforts have been put forth to clarify the molecular mechanism for cooperative binding in KIX, the current allosteric picture detailing the thermodynamic and structural effects of MLL and/or c-Myb binding remains incomplete. Although all-atom molecular dynamics (MD) simulations complement experiment and have provided valuable insight into the allosteric process (20,30,33), they are computationally too expensive to explore timescales where multiple binding events or protein folding/unfolding are necessary to understand the underlying mechanism of action. To address these limitations, we use a topology-based Go-like model (34,35) that has shown success in examining coupled protein folding and binding (36)(37)(38)(39)(40)(41)(42)(43)(44) as well as modeling ligand-induced structural transitions, and allosteric communication (45)(46)(47).…”

mentioning

confidence: 99%

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Prepaying the entropic cost for allosteric regulation in KIX

Law¹,

Gagnon²,

Mapp

et al. 2014

Proc. Natl. Acad. Sci. U.S.A.

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The kinase-inducible domain interacting (KIX) domain of the CREB binding protein (CBP) is capable of simultaneously binding two intrinsically disordered transcription factors, such as the mixedlineage leukemia (MLL) and c-Myb peptides, at isolated interaction sites. In vitro, the affinity for binding c-Myb is approximately doubled when KIX is in complex with MLL, which suggests a positive cooperative binding mechanism, and the affinity for MLL is also slightly increased when KIX is first bound by c-Myb. Expanding the scope of recent NMR and computational studies, we explore the allosteric mechanism at a detailed molecular level that directly connects the microscopic structural dynamics to the macroscopic shift in binding affinities. To this end, we have performed molecular dynamics simulations of free KIX, KIX-c-Myb, MLL-KIX, and MLL-KIX-c-Myb using a topology-based Go-like model. Our results capture an increase in affinity for the peptide in the allosteric site when KIX is prebound by a complementary effector and both peptides follow an effector-independent folding-and-binding mechanism. More importantly, we discover that MLL binding lowers the entropic cost for c-Myb binding, and vice versa, by stabilizing the L 12 -G 2 loop and the C-terminal region of the α 3 helix on KIX. This work demonstrates the importance of entropy in allosteric signaling between promiscuous molecular recognition sites and can inform the rational design of small molecule stabilizers to target important regions of conformationally dynamic proteins.

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Section: Discussionsupporting

confidence: 90%

Section: Discussionmentioning

confidence: 99%

mentioning

confidence: 99%

mentioning

confidence: 99%

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Prepaying the entropic cost for allosteric regulation in KIX

Law¹,

Gagnon²,

Mapp

et al. 2014

Proc. Natl. Acad. Sci. U.S.A.

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“…Not surprisingly, 1-10 bound to either mutant affects the residues within and proximal to the pKID binding site. However, 1-10 has a larger overall effect on KIX L664C residues (blue and green), with perturbations distributed not only at both MLL (between helices α 2 and α 3 ) and pKID (between helices α 1 and α 3 ) binding interfaces but also at the loop region, which has been implicated to play an important role in the conformational dynamics of KIX during binding events (12,33,34). The perturbations exhibited at the N terminus of α 3 and the two termini of α 1 are consistent with those observed upon MLL binding to KIX (12).…”

Section: Identification Of Kix Residues Affected In Positive and Negamentioning

confidence: 99%

Dissecting allosteric effects of activator–coactivator complexes using a covalent small molecule ligand

Wang

Lodge

Fierke³

et al. 2014

Proc. Natl. Acad. Sci. U.S.A.

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Allosteric binding events play a critical role in the formation and stability of transcriptional activator-coactivator complexes, perhaps in part due to the often intrinsically disordered nature of one or more of the constituent partners. The kinase-inducible domain interacting (KIX) domain of the master coactivator CREB binding protein/ p300 is a conformationally dynamic domain that complexes with transcriptional activators at two discrete binding sites in allosteric communication. The complexation of KIX with the transcriptional activation domain of mixed-lineage leukemia protein leads to an enhancement of binding by the activation domain of CREB (phosphorylated kinase-inducible domain of CREB) to the second site. A transient kinetic analysis of the ternary complex formation aided by small molecule ligands that induce positive or negative cooperative binding reveals that positive cooperativity is largely governed by stabilization of the bound complex as indicated by a decrease in k off . Thus, this suggests the increased binding affinity for the second ligand is not due to an allosteric creation of a more favorable binding interface by the first ligand. This is consistent with data from us and from others indicating that the on rates of conformationally dynamic proteins approach the limits of diffusion. In contrast, negative cooperativity is manifested by alterations in both k on and k off , suggesting stabilization of the binary complex.IDP | protein-protein interaction P rotein-protein interactions (PPIs) underscore all cellular processes, and the mechanistic dissection of PPI networks is thus a high priority (1-4). A particular challenge is defining the mechanism of PPI formation between intrinsically disordered proteins (IDPs) where allosteric changes play a substantive role (5-7). Allosteric communication between binding sites is vital for the proper function of feedback and regulatory circuits in the cell (8, 9). For example, the conformationally dynamic kinase-inducible domain interacting (KIX) domain of the master transcriptional coactivator CREB binding protein (CBP) undergoes a structural shift and stabilization upon binding to a cognate ligand such as the intrinsically disordered transcriptional activation domain (TAD) of mixed-lineage leukemia protein (MLL) (Fig. 1A) (10). The interaction of a second ligand, phosphorylated kinase-inducible domain (pKID) of CREB, is enhanced (up to twofold) by the presence of MLL and several elegant studies have documented allosteric communication between the two binding sites (11-15). However, the relatively modest affinities (micromolar) of the native complexes and the aggregation propensities and the promiscuous binding profiles of the transcriptional activation domains have hampered kinetic dissection of this and other complexes (16,17).The coactivator CBP exists across metazoans (18)(19)(20) and is a transcription hub that interacts with numerous transcriptional activators, using several discrete domains (21,22). The KIX domain within CBP is a 90-residue motif ...

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