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Long range recognition and selection in IDPs: the interactions of the C-terminus of p53.

Kannan S, Lane DP, Verma CS - Sci Rep (2016)

Bottom Line: The C-terminal domain of p53 is an extensively studied IDP, interacting with different partners through multiple distinct conformations.We find that the free peptide segment rapidly interconverts between ordered and disordered states with significant populations of the conformations that are seen in the complexed states.The underlying global folding-binding landscape points to a synergistic mechanism in which recognition is dictated via long range electrostatic recognition which results in the formation of reactive structures as far away as 10 Å, and binding proceeds with the steering of selected conformations followed by induced folding at the target surface or within a close range.

View Article: PubMed Central - PubMed

Affiliation: Bioinformatics Institute (A*STAR), 30 Biopolis Street, #07-01 Matrix, Singapore 138671.

ABSTRACT
The C-terminal domain of p53 is an extensively studied IDP, interacting with different partners through multiple distinct conformations. To explore the interplay between preformed structural elements and intrinsic fluctuations in its folding and binding we combine extensive atomistic equilibrium and non-equilibrium simulations. We find that the free peptide segment rapidly interconverts between ordered and disordered states with significant populations of the conformations that are seen in the complexed states. The underlying global folding-binding landscape points to a synergistic mechanism in which recognition is dictated via long range electrostatic recognition which results in the formation of reactive structures as far away as 10 Å, and binding proceeds with the steering of selected conformations followed by induced folding at the target surface or within a close range.

No MeSH data available.


Related in: MedlinePlus

2D free energy landscape as a function of fractions of native binding contacts (fnbc) formed between the receptor – p53CTD peptide fragment and rmsd of peptide (rmsd) from the peptide – receptor complex.SMD simulations were carried out for unbinding of p53CTD bound with five different receptors (A: S100B(ββ), B: Cyclin A, C: CBP, D: Sirtuin E: Set9). All the conformations sampled during SMD (5 independent for each system) are included in the 2D free energy calculations. The two paths describe the conformational selection (black) and induced fold (white) mechanisms.
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f3: 2D free energy landscape as a function of fractions of native binding contacts (fnbc) formed between the receptor – p53CTD peptide fragment and rmsd of peptide (rmsd) from the peptide – receptor complex.SMD simulations were carried out for unbinding of p53CTD bound with five different receptors (A: S100B(ββ), B: Cyclin A, C: CBP, D: Sirtuin E: Set9). All the conformations sampled during SMD (5 independent for each system) are included in the 2D free energy calculations. The two paths describe the conformational selection (black) and induced fold (white) mechanisms.

Mentions: To monitor the conformational flexibility of the p53CTD peptide during pulling, peptide rmsd was measured relative to its starting experimental bound structures. Changes in receptor–peptide interactions upon peptide unbinding were monitored by recording the fraction of native binding contacts (fnbc), together with the distance between the center of mass (COM) of the binding site and the peptide fragment. Although with increasing COM, an increase in peptide rmsd and a decrease in the fnbc was observed during SMD, interesting trends were observed. In the case of S100B(ββ)-p53CTD and CBP-p53CTD complexes, where the complex is stabilized mainly by hydrophobic interactions, rapid loss in fnbc was already observed (>60%) at COM of ~10 Å (Fig. S7). In other cases where the bound conformation of the peptide is stabilized by numerous h–bond interactions (Sir2, Cyclin A and Set9 complexed with p53CTD) a lag in reduction of fnbc was observed, with more than 50% of the native contacts existing even at COM of ~15 Å. Overall, the changes in peptide conformations appear to follow a common trend, with a rapid increase in rmsd (~3 Å) (Fig. S8) for all the peptides by ~10 Å from the binding site. However further changes in the peptide conformations appear to be less rapid, with the conformations of the bound states such as helix or sheet existing partially even at distances of ~20 Å from the receptor. The disordered bound conformations show rapid fluctuations and become partially ordered. The 2 D free-energy landscape (Fig. 3) revealed varied populations in several minima for the different complexes. A minima at the upper left corner of each graph corresponds to the complexed state (with the peptide in its folded/bound state with rmsd < 1.5 Å and fnbc >~60%) for the complexes of p53CTD with Cyclin A, Sirtuin and Set9, all of which are characterized by a number of hydrogen bonds mediating interactions between the proteins and the peptides. Such a native minima is less populated and slightly shifted (rmsd < 1.5 Å and fnbc ~40–60%) for the complexes between p53CTD with S100B(ββ) and p53CTD with CBP, where the protein-peptide interactions are governed mainly by hydrophobic interactions. The energy landscapes are also decorated with other minima that correspond to partially unfolded and unbound states, with rmsd >3.0 Å or fnbc <40%. There are several sparsely populated minima that are separated by low energy barriers that are rarely/transiently populated. Comparison of the landscape of all the five combined SMD simulations for each system shows that in all the simulated systems the bound/folded peptide follows two different pathways to reach its unfolded/unbound conformation. Along path1 (white arrow Fig. 3), the pc53CTD fragment rapidly loses its bound conformation (rmsd > 3 Å) but retains most of the native binding contacts (fnbc >60%), suggesting that the peptide becomes disordered upon exiting from the binding pocket. This suggests that order must be induced in the peptide by the receptor upon binding, and is seen for the p53CTD complexes with Sirtuin and Cyclin A - this is the induced folding mechanism131451. Along path2 (Black arrows Fig. 3), the bound conformation (alpha helix or beta sheet or disordered state) is retained (rmsd < 2.5 Å) or at least partially retained, with more than 70% of the fnbc lost already. This suggests that the peptide adopts the bound conformation even before it binds to its partner, and the native binding contacts play a role in selecting such a folded/bound conformation of the peptide, a scenario referred to as the conformational selection mechanism1617 and appears to characterize complex formation between p53CTD and S100B(ββ), CBP or Set9.


Long range recognition and selection in IDPs: the interactions of the C-terminus of p53.

Kannan S, Lane DP, Verma CS - Sci Rep (2016)

2D free energy landscape as a function of fractions of native binding contacts (fnbc) formed between the receptor – p53CTD peptide fragment and rmsd of peptide (rmsd) from the peptide – receptor complex.SMD simulations were carried out for unbinding of p53CTD bound with five different receptors (A: S100B(ββ), B: Cyclin A, C: CBP, D: Sirtuin E: Set9). All the conformations sampled during SMD (5 independent for each system) are included in the 2D free energy calculations. The two paths describe the conformational selection (black) and induced fold (white) mechanisms.
© Copyright Policy - open-access
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC4814905&req=5

f3: 2D free energy landscape as a function of fractions of native binding contacts (fnbc) formed between the receptor – p53CTD peptide fragment and rmsd of peptide (rmsd) from the peptide – receptor complex.SMD simulations were carried out for unbinding of p53CTD bound with five different receptors (A: S100B(ββ), B: Cyclin A, C: CBP, D: Sirtuin E: Set9). All the conformations sampled during SMD (5 independent for each system) are included in the 2D free energy calculations. The two paths describe the conformational selection (black) and induced fold (white) mechanisms.
Mentions: To monitor the conformational flexibility of the p53CTD peptide during pulling, peptide rmsd was measured relative to its starting experimental bound structures. Changes in receptor–peptide interactions upon peptide unbinding were monitored by recording the fraction of native binding contacts (fnbc), together with the distance between the center of mass (COM) of the binding site and the peptide fragment. Although with increasing COM, an increase in peptide rmsd and a decrease in the fnbc was observed during SMD, interesting trends were observed. In the case of S100B(ββ)-p53CTD and CBP-p53CTD complexes, where the complex is stabilized mainly by hydrophobic interactions, rapid loss in fnbc was already observed (>60%) at COM of ~10 Å (Fig. S7). In other cases where the bound conformation of the peptide is stabilized by numerous h–bond interactions (Sir2, Cyclin A and Set9 complexed with p53CTD) a lag in reduction of fnbc was observed, with more than 50% of the native contacts existing even at COM of ~15 Å. Overall, the changes in peptide conformations appear to follow a common trend, with a rapid increase in rmsd (~3 Å) (Fig. S8) for all the peptides by ~10 Å from the binding site. However further changes in the peptide conformations appear to be less rapid, with the conformations of the bound states such as helix or sheet existing partially even at distances of ~20 Å from the receptor. The disordered bound conformations show rapid fluctuations and become partially ordered. The 2 D free-energy landscape (Fig. 3) revealed varied populations in several minima for the different complexes. A minima at the upper left corner of each graph corresponds to the complexed state (with the peptide in its folded/bound state with rmsd < 1.5 Å and fnbc >~60%) for the complexes of p53CTD with Cyclin A, Sirtuin and Set9, all of which are characterized by a number of hydrogen bonds mediating interactions between the proteins and the peptides. Such a native minima is less populated and slightly shifted (rmsd < 1.5 Å and fnbc ~40–60%) for the complexes between p53CTD with S100B(ββ) and p53CTD with CBP, where the protein-peptide interactions are governed mainly by hydrophobic interactions. The energy landscapes are also decorated with other minima that correspond to partially unfolded and unbound states, with rmsd >3.0 Å or fnbc <40%. There are several sparsely populated minima that are separated by low energy barriers that are rarely/transiently populated. Comparison of the landscape of all the five combined SMD simulations for each system shows that in all the simulated systems the bound/folded peptide follows two different pathways to reach its unfolded/unbound conformation. Along path1 (white arrow Fig. 3), the pc53CTD fragment rapidly loses its bound conformation (rmsd > 3 Å) but retains most of the native binding contacts (fnbc >60%), suggesting that the peptide becomes disordered upon exiting from the binding pocket. This suggests that order must be induced in the peptide by the receptor upon binding, and is seen for the p53CTD complexes with Sirtuin and Cyclin A - this is the induced folding mechanism131451. Along path2 (Black arrows Fig. 3), the bound conformation (alpha helix or beta sheet or disordered state) is retained (rmsd < 2.5 Å) or at least partially retained, with more than 70% of the fnbc lost already. This suggests that the peptide adopts the bound conformation even before it binds to its partner, and the native binding contacts play a role in selecting such a folded/bound conformation of the peptide, a scenario referred to as the conformational selection mechanism1617 and appears to characterize complex formation between p53CTD and S100B(ββ), CBP or Set9.

Bottom Line: The C-terminal domain of p53 is an extensively studied IDP, interacting with different partners through multiple distinct conformations.We find that the free peptide segment rapidly interconverts between ordered and disordered states with significant populations of the conformations that are seen in the complexed states.The underlying global folding-binding landscape points to a synergistic mechanism in which recognition is dictated via long range electrostatic recognition which results in the formation of reactive structures as far away as 10 Å, and binding proceeds with the steering of selected conformations followed by induced folding at the target surface or within a close range.

View Article: PubMed Central - PubMed

Affiliation: Bioinformatics Institute (A*STAR), 30 Biopolis Street, #07-01 Matrix, Singapore 138671.

ABSTRACT
The C-terminal domain of p53 is an extensively studied IDP, interacting with different partners through multiple distinct conformations. To explore the interplay between preformed structural elements and intrinsic fluctuations in its folding and binding we combine extensive atomistic equilibrium and non-equilibrium simulations. We find that the free peptide segment rapidly interconverts between ordered and disordered states with significant populations of the conformations that are seen in the complexed states. The underlying global folding-binding landscape points to a synergistic mechanism in which recognition is dictated via long range electrostatic recognition which results in the formation of reactive structures as far away as 10 Å, and binding proceeds with the steering of selected conformations followed by induced folding at the target surface or within a close range.

No MeSH data available.


Related in: MedlinePlus