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Binding-induced folding of a natively unstructured transcription factor.

Turjanski AG, Gutkind JS, Best RB, Hummer G - PLoS Comput. Biol. (2008)

Bottom Line: Interestingly, increasing the amount of structure in the unbound pKID reduces the rate of binding, suggesting a "fly-casting"-like process.We find that the inclusion of attractive non-native interactions results in the formation of non-specific encounter complexes that enhance the on-rate of binding, but do not significantly change the binding mechanism.The simulations are in general agreement with the results of a recently reported nuclear magnetic resonance study, and aid in the interpretation of the experimental binding kinetics.

View Article: PubMed Central - PubMed

Affiliation: Oral and Pharyngeal Cancer Branch, National Institute of Dental and Craniofacial Research, National Institutes of Health, Bethesda, Maryland, United States of America.

ABSTRACT
Transcription factors are central components of the intracellular regulatory networks that control gene expression. An increasingly recognized phenomenon among human transcription factors is the formation of structure upon target binding. Here, we study the folding and binding of the pKID domain of CREB to the KIX domain of the co-activator CBP. Our simulations of a topology-based Gō-type model predict a coupled folding and binding mechanism, and the existence of partially bound intermediates. From transition-path and Phi-value analyses, we find that the binding transition state resembles the unstructured state in solution, implying that CREB becomes structured only after committing to binding. A change of structure following binding is reminiscent of an induced-fit mechanism and contrasts with models in which binding occurs to pre-structured conformations that exist in the unbound state at equilibrium. Interestingly, increasing the amount of structure in the unbound pKID reduces the rate of binding, suggesting a "fly-casting"-like process. We find that the inclusion of attractive non-native interactions results in the formation of non-specific encounter complexes that enhance the on-rate of binding, but do not significantly change the binding mechanism. Our study helps explain how being unstructured can confer an advantage in protein target recognition. The simulations are in general agreement with the results of a recently reported nuclear magnetic resonance study, and aid in the interpretation of the experimental binding kinetics.

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2D free energy surface for the binding-induced folding of pKID.Potential of mean force for binding as a function of the fraction of intermolecular native contacts between helix αA (QCA) and helix αB (QCB) of pKID and KIX. The black line depicts one representative transition path from unbound to bound. Representative structures are shown for important regions of the free energy landscape.
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pcbi-1000060-g004: 2D free energy surface for the binding-induced folding of pKID.Potential of mean force for binding as a function of the fraction of intermolecular native contacts between helix αA (QCA) and helix αB (QCB) of pKID and KIX. The black line depicts one representative transition path from unbound to bound. Representative structures are shown for important regions of the free energy landscape.

Mentions: To characterize the binding mechanism of CREB to CBP, we calculated the free energy profile along QC (Figure 3), which shows a free energy barrier to binding of ∼4 kcal/mol. Notably, the free energy profile also suggests two major populated conformations in the bound state, one with the complex fully formed (QC∼0.9), and a second, “partially bound” intermediate conformation (QC∼0.75). We can gain further insight into the binding mechanism by separating the intermolecular contact fraction, QC, into contacts between KIX and helices αA and αB of pKID, QCA and QCB, respectively. The binding free energy surface as a function of these two coordinates (Figure 4; representative structures superimposed) shows a dominant L-shaped path from unbound (QCA∼QCB∼0) to fully bound (QCA∼QCB∼0.9), with the contacts to helix αB formed before those to αA. High values of QCB are observed at values of QCA as low as 0.0–0.2; in contrast, high values of QCA are not observed in the absence of high QCB. Two types of partially bound intermediates are evident in Figure 4: an intermediate IA with QCA<0.1 and QCB>0.4, and an intermediate IB with QCA>0.1 and QCB<0.1 (with a shallow free energy minimum at QCA∼0.2 and QCB∼0). In the high-population intermediate IA, αB is nearly completely bound while αA mostly detaches from KIX. In the low-population intermediate IB, αA is partially bound, while αB is detached. The local minimum at QCA∼0.2 and QCB∼0.9 corresponds to structures with transient native interactions formed between helix αA and KIX, with helix αB bound and folded.


Binding-induced folding of a natively unstructured transcription factor.

Turjanski AG, Gutkind JS, Best RB, Hummer G - PLoS Comput. Biol. (2008)

2D free energy surface for the binding-induced folding of pKID.Potential of mean force for binding as a function of the fraction of intermolecular native contacts between helix αA (QCA) and helix αB (QCB) of pKID and KIX. The black line depicts one representative transition path from unbound to bound. Representative structures are shown for important regions of the free energy landscape.
© Copyright Policy
Related In: Results  -  Collection

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getmorefigures.php?uid=PMC2289845&req=5

pcbi-1000060-g004: 2D free energy surface for the binding-induced folding of pKID.Potential of mean force for binding as a function of the fraction of intermolecular native contacts between helix αA (QCA) and helix αB (QCB) of pKID and KIX. The black line depicts one representative transition path from unbound to bound. Representative structures are shown for important regions of the free energy landscape.
Mentions: To characterize the binding mechanism of CREB to CBP, we calculated the free energy profile along QC (Figure 3), which shows a free energy barrier to binding of ∼4 kcal/mol. Notably, the free energy profile also suggests two major populated conformations in the bound state, one with the complex fully formed (QC∼0.9), and a second, “partially bound” intermediate conformation (QC∼0.75). We can gain further insight into the binding mechanism by separating the intermolecular contact fraction, QC, into contacts between KIX and helices αA and αB of pKID, QCA and QCB, respectively. The binding free energy surface as a function of these two coordinates (Figure 4; representative structures superimposed) shows a dominant L-shaped path from unbound (QCA∼QCB∼0) to fully bound (QCA∼QCB∼0.9), with the contacts to helix αB formed before those to αA. High values of QCB are observed at values of QCA as low as 0.0–0.2; in contrast, high values of QCA are not observed in the absence of high QCB. Two types of partially bound intermediates are evident in Figure 4: an intermediate IA with QCA<0.1 and QCB>0.4, and an intermediate IB with QCA>0.1 and QCB<0.1 (with a shallow free energy minimum at QCA∼0.2 and QCB∼0). In the high-population intermediate IA, αB is nearly completely bound while αA mostly detaches from KIX. In the low-population intermediate IB, αA is partially bound, while αB is detached. The local minimum at QCA∼0.2 and QCB∼0.9 corresponds to structures with transient native interactions formed between helix αA and KIX, with helix αB bound and folded.

Bottom Line: Interestingly, increasing the amount of structure in the unbound pKID reduces the rate of binding, suggesting a "fly-casting"-like process.We find that the inclusion of attractive non-native interactions results in the formation of non-specific encounter complexes that enhance the on-rate of binding, but do not significantly change the binding mechanism.The simulations are in general agreement with the results of a recently reported nuclear magnetic resonance study, and aid in the interpretation of the experimental binding kinetics.

View Article: PubMed Central - PubMed

Affiliation: Oral and Pharyngeal Cancer Branch, National Institute of Dental and Craniofacial Research, National Institutes of Health, Bethesda, Maryland, United States of America.

ABSTRACT
Transcription factors are central components of the intracellular regulatory networks that control gene expression. An increasingly recognized phenomenon among human transcription factors is the formation of structure upon target binding. Here, we study the folding and binding of the pKID domain of CREB to the KIX domain of the co-activator CBP. Our simulations of a topology-based Gō-type model predict a coupled folding and binding mechanism, and the existence of partially bound intermediates. From transition-path and Phi-value analyses, we find that the binding transition state resembles the unstructured state in solution, implying that CREB becomes structured only after committing to binding. A change of structure following binding is reminiscent of an induced-fit mechanism and contrasts with models in which binding occurs to pre-structured conformations that exist in the unbound state at equilibrium. Interestingly, increasing the amount of structure in the unbound pKID reduces the rate of binding, suggesting a "fly-casting"-like process. We find that the inclusion of attractive non-native interactions results in the formation of non-specific encounter complexes that enhance the on-rate of binding, but do not significantly change the binding mechanism. Our study helps explain how being unstructured can confer an advantage in protein target recognition. The simulations are in general agreement with the results of a recently reported nuclear magnetic resonance study, and aid in the interpretation of the experimental binding kinetics.

Show MeSH