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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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Structure of the pKID/KIX complex.(A) Domain structure of CREB, consisting of DNA-binding domain basic region/leucine zipper (bZIP), the cAMP activated domain KID, and the glutamine-rich domains Q1 and Q2. The sequence of the structured part of pKID is shown with residues in helices αA and αB underlined. (B) Folding and binding of pKID (red: helix αA; green: helix αB) to the KIX domain of CBP (blue).
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pcbi-1000060-g001: Structure of the pKID/KIX complex.(A) Domain structure of CREB, consisting of DNA-binding domain basic region/leucine zipper (bZIP), the cAMP activated domain KID, and the glutamine-rich domains Q1 and Q2. The sequence of the structured part of pKID is shown with residues in helices αA and αB underlined. (B) Folding and binding of pKID (red: helix αA; green: helix αB) to the KIX domain of CBP (blue).

Mentions: The transcription factor cAMP response-element binding protein (CREB) represents a well-characterized paradigm for an unstructured peptide that adopts a folded structure upon binding its co-activator CREB binding protein (CBP) [1],[8]. CREB participates in diverse cellular processes, ranging from glucose homeostasis, survival and proliferation to learning and memory [9],[10]. CREB is one of the best characterized transcription factors in terms of its structure and function [9]–[15]. Like many transcription factors, CREB consists of multiple domains (Figure 1A): (i) a C-terminal basic region/leucine zipper (bZIP) dimerization domain that binds DNA with high specificity for the conserved cAMP-responsive element (CRE) TGACGTCA [16],[17]; (ii) a 60-amino-acid kinase-inducible domain (KID) (amino acids 100–160); and (iii) two hydrophobic glutamine-rich domains, designated Q1 and Q2, that function as constitutive transcriptional activators [10]. CREB has both basal and inducible transcriptional activity [14], the latter being triggered by phosphorylation of the KID domain at Ser133 by the protein kinase A (PKA). Indeed, CREB was the first transcription factor whose activity was shown to be tightly regulated by phosphorylation/dephosphorylation [18]. The phosphorylated KID domain (pKID) promotes the recruitment of the transcriptional co-activator CBP (and the related molecule p300) by binding to its kinase-induced domain interacting domain (KIX) [12],[19]. Upon binding to KIX, pKID undergoes a transition from unstructured to structured [12].


Binding-induced folding of a natively unstructured transcription factor.

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

Structure of the pKID/KIX complex.(A) Domain structure of CREB, consisting of DNA-binding domain basic region/leucine zipper (bZIP), the cAMP activated domain KID, and the glutamine-rich domains Q1 and Q2. The sequence of the structured part of pKID is shown with residues in helices αA and αB underlined. (B) Folding and binding of pKID (red: helix αA; green: helix αB) to the KIX domain of CBP (blue).
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pcbi-1000060-g001: Structure of the pKID/KIX complex.(A) Domain structure of CREB, consisting of DNA-binding domain basic region/leucine zipper (bZIP), the cAMP activated domain KID, and the glutamine-rich domains Q1 and Q2. The sequence of the structured part of pKID is shown with residues in helices αA and αB underlined. (B) Folding and binding of pKID (red: helix αA; green: helix αB) to the KIX domain of CBP (blue).
Mentions: The transcription factor cAMP response-element binding protein (CREB) represents a well-characterized paradigm for an unstructured peptide that adopts a folded structure upon binding its co-activator CREB binding protein (CBP) [1],[8]. CREB participates in diverse cellular processes, ranging from glucose homeostasis, survival and proliferation to learning and memory [9],[10]. CREB is one of the best characterized transcription factors in terms of its structure and function [9]–[15]. Like many transcription factors, CREB consists of multiple domains (Figure 1A): (i) a C-terminal basic region/leucine zipper (bZIP) dimerization domain that binds DNA with high specificity for the conserved cAMP-responsive element (CRE) TGACGTCA [16],[17]; (ii) a 60-amino-acid kinase-inducible domain (KID) (amino acids 100–160); and (iii) two hydrophobic glutamine-rich domains, designated Q1 and Q2, that function as constitutive transcriptional activators [10]. CREB has both basal and inducible transcriptional activity [14], the latter being triggered by phosphorylation of the KID domain at Ser133 by the protein kinase A (PKA). Indeed, CREB was the first transcription factor whose activity was shown to be tightly regulated by phosphorylation/dephosphorylation [18]. The phosphorylated KID domain (pKID) promotes the recruitment of the transcriptional co-activator CBP (and the related molecule p300) by binding to its kinase-induced domain interacting domain (KIX) [12],[19]. Upon binding to KIX, pKID undergoes a transition from unstructured to structured [12].

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