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The Role of Electrostatic Interactions in Binding of Histone H3K4me2/3 to the Sgf29 Tandem Tudor Domain.

Pieters BJ, Meulenbroeks E, Belle R, Mecinović J - PLoS ONE (2015)

Bottom Line: Several reader domain proteins that specifically recognize methyllysine-containing histones contain the negatively-charged aspartate or glutamate residues as part of the aromatic cage.Small uncharged and large aromatic substitutions on the Asp266 site resulted in a significant decrease in binding affinities for both H3K4me3 and H3K4me2, demonstrating the role of the negative charge of Asp266 in the readout process by Sgf29.This study emphasizes the essential contribution of electrostatic interactions to the overall binding affinity, and reveals that the underlying mechanisms for the recognition of Kme2/3 depend on the composition and arrangement of the aromatic cage.

View Article: PubMed Central - PubMed

Affiliation: Institute of Molecules and Materials, Radboud University Nijmegen, Nijmegen, The Netherlands.

ABSTRACT
Several reader domain proteins that specifically recognize methyllysine-containing histones contain the negatively-charged aspartate or glutamate residues as part of the aromatic cage. Herein, we report thermodynamic analyses for the recognition of histone H3K4me3 and H3K4me2 by the tandem tudor domain of Sgf29 and its recognition site variants. Small uncharged and large aromatic substitutions on the Asp266 site resulted in a significant decrease in binding affinities for both H3K4me3 and H3K4me2, demonstrating the role of the negative charge of Asp266 in the readout process by Sgf29. This study emphasizes the essential contribution of electrostatic interactions to the overall binding affinity, and reveals that the underlying mechanisms for the recognition of Kme2/3 depend on the composition and arrangement of the aromatic cage.

No MeSH data available.


Thermodynamic analyses of Sgf29-H3K4me2 and Sgf29-H3K4me3 interactions.Representative ITC experiments showing the titration of H3K4me3 (top row, A-D) and H3K4me2 (bottom row, E-H) peptides to Sgf29 (first column, A,E), D266E (second column B, F), D266N (third column, C, G) and D266Y (fourth column, D, F).
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pone.0139205.g004: Thermodynamic analyses of Sgf29-H3K4me2 and Sgf29-H3K4me3 interactions.Representative ITC experiments showing the titration of H3K4me3 (top row, A-D) and H3K4me2 (bottom row, E-H) peptides to Sgf29 (first column, A,E), D266E (second column B, F), D266N (third column, C, G) and D266Y (fourth column, D, F).

Mentions: Recognition of 10-mer H3K4me3 and H3K4me2 histone peptides by WT Sgf29 and its D266 variants was examined by isothermal titration calorimetry (ITC). ITC provided full thermodynamic descriptions (i.e. dissociation constant Kd, free energy of binding ΔG°, enthalpy of binding ΔH°, and entropy of binding -TΔS°) for the association of reader-histone complexes (Table 2, Fig 4). Consistent with previous studies, thermodynamics of interactions between H3K4me3 and Sgf29 showed that the association is enthalpy-driven (ΔH° = -8.1 kcal mol-1), whereas the entropy of binding is slightly unfavorable (-TΔS° = 0.6 kcal mol-1)[12]. H3K4me2 histone peptide exhibits slightly lower binding affinity than H3K4me3 for binding to WT Sgf29 (Kd = 4.7 μM for H3K4me2 vs. 3.1 μM for H3K4me3). Thermodynamic analyses furthermore demonstrated that there is an enthalpy-entropy compensation for binding of H3K4me3 and H3K4me2 to WT Sgf29. ΔH° is more favorable for the formation of Sgf29-H3K4me3 complex relative to Sgf29-H3K4me2 by 0.9 kcal mol-1, while -TΔS° is less favorable by 0.7 kcal mol-1. Similar observations have been reported for other reader domain proteins, including BPTF and JARID1A, which specifically recognize H3K4me3 and H3K4me2 [13,14].


The Role of Electrostatic Interactions in Binding of Histone H3K4me2/3 to the Sgf29 Tandem Tudor Domain.

Pieters BJ, Meulenbroeks E, Belle R, Mecinović J - PLoS ONE (2015)

Thermodynamic analyses of Sgf29-H3K4me2 and Sgf29-H3K4me3 interactions.Representative ITC experiments showing the titration of H3K4me3 (top row, A-D) and H3K4me2 (bottom row, E-H) peptides to Sgf29 (first column, A,E), D266E (second column B, F), D266N (third column, C, G) and D266Y (fourth column, D, F).
© Copyright Policy
Related In: Results  -  Collection

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Show All Figures
getmorefigures.php?uid=PMC4589357&req=5

pone.0139205.g004: Thermodynamic analyses of Sgf29-H3K4me2 and Sgf29-H3K4me3 interactions.Representative ITC experiments showing the titration of H3K4me3 (top row, A-D) and H3K4me2 (bottom row, E-H) peptides to Sgf29 (first column, A,E), D266E (second column B, F), D266N (third column, C, G) and D266Y (fourth column, D, F).
Mentions: Recognition of 10-mer H3K4me3 and H3K4me2 histone peptides by WT Sgf29 and its D266 variants was examined by isothermal titration calorimetry (ITC). ITC provided full thermodynamic descriptions (i.e. dissociation constant Kd, free energy of binding ΔG°, enthalpy of binding ΔH°, and entropy of binding -TΔS°) for the association of reader-histone complexes (Table 2, Fig 4). Consistent with previous studies, thermodynamics of interactions between H3K4me3 and Sgf29 showed that the association is enthalpy-driven (ΔH° = -8.1 kcal mol-1), whereas the entropy of binding is slightly unfavorable (-TΔS° = 0.6 kcal mol-1)[12]. H3K4me2 histone peptide exhibits slightly lower binding affinity than H3K4me3 for binding to WT Sgf29 (Kd = 4.7 μM for H3K4me2 vs. 3.1 μM for H3K4me3). Thermodynamic analyses furthermore demonstrated that there is an enthalpy-entropy compensation for binding of H3K4me3 and H3K4me2 to WT Sgf29. ΔH° is more favorable for the formation of Sgf29-H3K4me3 complex relative to Sgf29-H3K4me2 by 0.9 kcal mol-1, while -TΔS° is less favorable by 0.7 kcal mol-1. Similar observations have been reported for other reader domain proteins, including BPTF and JARID1A, which specifically recognize H3K4me3 and H3K4me2 [13,14].

Bottom Line: Several reader domain proteins that specifically recognize methyllysine-containing histones contain the negatively-charged aspartate or glutamate residues as part of the aromatic cage.Small uncharged and large aromatic substitutions on the Asp266 site resulted in a significant decrease in binding affinities for both H3K4me3 and H3K4me2, demonstrating the role of the negative charge of Asp266 in the readout process by Sgf29.This study emphasizes the essential contribution of electrostatic interactions to the overall binding affinity, and reveals that the underlying mechanisms for the recognition of Kme2/3 depend on the composition and arrangement of the aromatic cage.

View Article: PubMed Central - PubMed

Affiliation: Institute of Molecules and Materials, Radboud University Nijmegen, Nijmegen, The Netherlands.

ABSTRACT
Several reader domain proteins that specifically recognize methyllysine-containing histones contain the negatively-charged aspartate or glutamate residues as part of the aromatic cage. Herein, we report thermodynamic analyses for the recognition of histone H3K4me3 and H3K4me2 by the tandem tudor domain of Sgf29 and its recognition site variants. Small uncharged and large aromatic substitutions on the Asp266 site resulted in a significant decrease in binding affinities for both H3K4me3 and H3K4me2, demonstrating the role of the negative charge of Asp266 in the readout process by Sgf29. This study emphasizes the essential contribution of electrostatic interactions to the overall binding affinity, and reveals that the underlying mechanisms for the recognition of Kme2/3 depend on the composition and arrangement of the aromatic cage.

No MeSH data available.