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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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The fraction of native contacts for pKID, KIX, and the complex.Fraction of native amino-acid contacts as a function of time for the intermolecular complex (QC; top), KIX (QKIX; center), and pKID (QKID; bottom). Data are shown for one out of thirteen simulations of the same length.
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pcbi-1000060-g002: The fraction of native contacts for pKID, KIX, and the complex.Fraction of native amino-acid contacts as a function of time for the intermolecular complex (QC; top), KIX (QKIX; center), and pKID (QKID; bottom). Data are shown for one out of thirteen simulations of the same length.

Mentions: Figure 1A shows a schematic representation of the distinct domains within CREB, including Q1, Q2, BZIP and pKID as described above. Long equilibrium simulations of the complex were initiated from the NMR structure of the complex (PDB code 1KDX [12]) as depicted in Figure 1B. Only residues 119–146 of phosphorylated KID, here referred to as pKID, undergo folding and binding (Figure 1C). To monitor folding and binding of pKID to KIX separately, we calculated the fraction of intramolecular native amino-acid contacts of KIX (QKIX) and pKID (QKID), and the fraction of intermolecular native contacts (QC) that are formed over the course of the simulation (Figure 2). During most of the simulation time the conformation of KIX remained folded and close to the native structure, held together by an extensive network of inter-residue interactions (as compared to the relatively few interactions between pKID and KIX, which makes it energetically much easier to dissociate the complex than to unfold KIX). However, a minor population of a partially unfolded state was found for the KIX domain (data not shown). This observation is qualitatively consistent with the existence of a partially unfolded high-energy state of KIX that is sparsely populated under native conditions [31]. The conformation of unbound pKID retains part of the intramolecular native contacts, as measured by QKID, mainly because helix αA remains partially folded, in agreement with previous experimental results [13]. The increased stability of helix αA in comparison to helix αB can be explained energetically, from αA having more and stronger intramolecular contacts than αB. The fraction of native intermolecular contacts between pKID and KIX, QC, allows us to monitor the exchange at equilibrium between the two most populated states of the system, the bound (QC∼0.9) and unbound conformations (QC∼0.0). The aggregate simulation data include a total of 889 binding and dissociation transitions, allowing us to characterize in detail the dynamic changes that occur during the folding/binding process.


Binding-induced folding of a natively unstructured transcription factor.

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

The fraction of native contacts for pKID, KIX, and the complex.Fraction of native amino-acid contacts as a function of time for the intermolecular complex (QC; top), KIX (QKIX; center), and pKID (QKID; bottom). Data are shown for one out of thirteen simulations of the same length.
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Related In: Results  -  Collection

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getmorefigures.php?uid=PMC2289845&req=5

pcbi-1000060-g002: The fraction of native contacts for pKID, KIX, and the complex.Fraction of native amino-acid contacts as a function of time for the intermolecular complex (QC; top), KIX (QKIX; center), and pKID (QKID; bottom). Data are shown for one out of thirteen simulations of the same length.
Mentions: Figure 1A shows a schematic representation of the distinct domains within CREB, including Q1, Q2, BZIP and pKID as described above. Long equilibrium simulations of the complex were initiated from the NMR structure of the complex (PDB code 1KDX [12]) as depicted in Figure 1B. Only residues 119–146 of phosphorylated KID, here referred to as pKID, undergo folding and binding (Figure 1C). To monitor folding and binding of pKID to KIX separately, we calculated the fraction of intramolecular native amino-acid contacts of KIX (QKIX) and pKID (QKID), and the fraction of intermolecular native contacts (QC) that are formed over the course of the simulation (Figure 2). During most of the simulation time the conformation of KIX remained folded and close to the native structure, held together by an extensive network of inter-residue interactions (as compared to the relatively few interactions between pKID and KIX, which makes it energetically much easier to dissociate the complex than to unfold KIX). However, a minor population of a partially unfolded state was found for the KIX domain (data not shown). This observation is qualitatively consistent with the existence of a partially unfolded high-energy state of KIX that is sparsely populated under native conditions [31]. The conformation of unbound pKID retains part of the intramolecular native contacts, as measured by QKID, mainly because helix αA remains partially folded, in agreement with previous experimental results [13]. The increased stability of helix αA in comparison to helix αB can be explained energetically, from αA having more and stronger intramolecular contacts than αB. The fraction of native intermolecular contacts between pKID and KIX, QC, allows us to monitor the exchange at equilibrium between the two most populated states of the system, the bound (QC∼0.9) and unbound conformations (QC∼0.0). The aggregate simulation data include a total of 889 binding and dissociation transitions, allowing us to characterize in detail the dynamic changes that occur during the folding/binding process.

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