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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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Non-specific encounter complexes.Potential of mean force as function of the number of native and non-native contacts between pKID and KIX. Free energy surfaces are shown as a function of all non-native contacts (NNC) and native contacts (NC) (A–B) at equilibrium and (C–D) in transition paths. (E–F) The probability p(TP/NC,NNC) of being in the transition path as a function of NC and NNC. (A), (C), and (E) correspond to a potential with only native attractive interactions and (B), (D), and (F) correspond to the same potential with added non-native interactions at a strength of 40% of the native contacts.
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pcbi-1000060-g007: Non-specific encounter complexes.Potential of mean force as function of the number of native and non-native contacts between pKID and KIX. Free energy surfaces are shown as a function of all non-native contacts (NNC) and native contacts (NC) (A–B) at equilibrium and (C–D) in transition paths. (E–F) The probability p(TP/NC,NNC) of being in the transition path as a function of NC and NNC. (A), (C), and (E) correspond to a potential with only native attractive interactions and (B), (D), and (F) correspond to the same potential with added non-native interactions at a strength of 40% of the native contacts.

Mentions: To clarify the role of non-native binding, as stated above, we performed additional simulations using non-Gō potentials. As discussed, the inclusion of non-native contacts at reasonable strengths does not substantially affect the binding mechanism (Figure S1). However, the additional non-native interactions result in the formation of non-specific encounter complexes. To quantify their population, we determined the binding free energy surface as functions of NNC and NC, the numbers of non-native and native contacts between pKID and KIX, respectively. The results are shown in Figure 7A and 7B for non-native interaction strengths of 0% and 40%, respectively, and in Figure S2 for other interaction strengths.


Binding-induced folding of a natively unstructured transcription factor.

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

Non-specific encounter complexes.Potential of mean force as function of the number of native and non-native contacts between pKID and KIX. Free energy surfaces are shown as a function of all non-native contacts (NNC) and native contacts (NC) (A–B) at equilibrium and (C–D) in transition paths. (E–F) The probability p(TP/NC,NNC) of being in the transition path as a function of NC and NNC. (A), (C), and (E) correspond to a potential with only native attractive interactions and (B), (D), and (F) correspond to the same potential with added non-native interactions at a strength of 40% of the native contacts.
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Related In: Results  -  Collection

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getmorefigures.php?uid=PMC2289845&req=5

pcbi-1000060-g007: Non-specific encounter complexes.Potential of mean force as function of the number of native and non-native contacts between pKID and KIX. Free energy surfaces are shown as a function of all non-native contacts (NNC) and native contacts (NC) (A–B) at equilibrium and (C–D) in transition paths. (E–F) The probability p(TP/NC,NNC) of being in the transition path as a function of NC and NNC. (A), (C), and (E) correspond to a potential with only native attractive interactions and (B), (D), and (F) correspond to the same potential with added non-native interactions at a strength of 40% of the native contacts.
Mentions: To clarify the role of non-native binding, as stated above, we performed additional simulations using non-Gō potentials. As discussed, the inclusion of non-native contacts at reasonable strengths does not substantially affect the binding mechanism (Figure S1). However, the additional non-native interactions result in the formation of non-specific encounter complexes. To quantify their population, we determined the binding free energy surface as functions of NNC and NC, the numbers of non-native and native contacts between pKID and KIX, respectively. The results are shown in Figure 7A and 7B for non-native interaction strengths of 0% and 40%, respectively, and in Figure S2 for other interaction strengths.

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