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Indirect readout: detection of optimized subsequences and calculation of relative binding affinities using different DNA elastic potentials.

Becker NB, Wolff L, Everaers R - Nucleic Acids Res. (2006)

Bottom Line: In agreement with known results we find that indirect readout dominates at the central, non-contacted bases of the binding site.Their quantitative comparison with experimental data allows for a critical evaluation of DNA elastic potentials and of the correspondence between crystal and solution structures.The software written for the presented analysis is included as Supplementary Data.

View Article: PubMed Central - PubMed

Affiliation: Max-Planck-Institut für Physik komplexer Systeme, Nöthnitzer Strasse 38, 01187 Dresden, Germany. nbecker@pks.mpg.de

ABSTRACT
Essential biological processes require that proteins bind to a set of specific DNA sites with tuned relative affinities. We focus on the indirect readout mechanism and discuss its theoretical description in relation to the present understanding of DNA elasticity on the rigid base pair level. Combining existing parametrizations of elastic potentials for DNA, we derive elastic free energies directly related to competitive binding experiments, and propose a computationally inexpensive local marker for elastically optimized subsequences in protein-DNA co-crystals. We test our approach in an application to the bacteriophage 434 repressor. In agreement with known results we find that indirect readout dominates at the central, non-contacted bases of the binding site. Elastic optimization involves all deformation modes and is mainly due to the adapted equilibrium structure of the operator, while sequence-dependent elasticity plays a minor role. These qualitative observations are robust with respect to current parametrization uncertainties. Predictions for relative affinities mediated by indirect readout depend sensitively on the chosen parametrization. Their quantitative comparison with experimental data allows for a critical evaluation of DNA elastic potentials and of the correspondence between crystal and solution structures. The software written for the presented analysis is included as Supplementary Data.

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Computed deformation free energy differences versus measured log affinity differences, for all combinations of crystal structure and employed parametrization, see also Figure 10. Linear correlation coefficients (upper number) and the RMSD from the line  (lower number) are inset.
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fig11: Computed deformation free energy differences versus measured log affinity differences, for all combinations of crystal structure and employed parametrization, see also Figure 10. Linear correlation coefficients (upper number) and the RMSD from the line (lower number) are inset.

Mentions: A posteriori, we can check whether one combination of parametrization and crystal structure stands out as the best model for the measured solution affinities. Figure 11 gives an overview of affinity-free energy plots for all such combinations. They show widely varying RMS deviation, ranging from 1.5 kBT to 26 kBT depending on the parametrization and structure used. Note that the global energy scales agree for all potentials except B′. Only for the rescaled ensembles B′ and P′ is it higher, increasing the spread of computed affinities.


Indirect readout: detection of optimized subsequences and calculation of relative binding affinities using different DNA elastic potentials.

Becker NB, Wolff L, Everaers R - Nucleic Acids Res. (2006)

Computed deformation free energy differences versus measured log affinity differences, for all combinations of crystal structure and employed parametrization, see also Figure 10. Linear correlation coefficients (upper number) and the RMSD from the line  (lower number) are inset.
© Copyright Policy
Related In: Results  -  Collection

Show All Figures
getmorefigures.php?uid=PMC1636474&req=5

fig11: Computed deformation free energy differences versus measured log affinity differences, for all combinations of crystal structure and employed parametrization, see also Figure 10. Linear correlation coefficients (upper number) and the RMSD from the line (lower number) are inset.
Mentions: A posteriori, we can check whether one combination of parametrization and crystal structure stands out as the best model for the measured solution affinities. Figure 11 gives an overview of affinity-free energy plots for all such combinations. They show widely varying RMS deviation, ranging from 1.5 kBT to 26 kBT depending on the parametrization and structure used. Note that the global energy scales agree for all potentials except B′. Only for the rescaled ensembles B′ and P′ is it higher, increasing the spread of computed affinities.

Bottom Line: In agreement with known results we find that indirect readout dominates at the central, non-contacted bases of the binding site.Their quantitative comparison with experimental data allows for a critical evaluation of DNA elastic potentials and of the correspondence between crystal and solution structures.The software written for the presented analysis is included as Supplementary Data.

View Article: PubMed Central - PubMed

Affiliation: Max-Planck-Institut für Physik komplexer Systeme, Nöthnitzer Strasse 38, 01187 Dresden, Germany. nbecker@pks.mpg.de

ABSTRACT
Essential biological processes require that proteins bind to a set of specific DNA sites with tuned relative affinities. We focus on the indirect readout mechanism and discuss its theoretical description in relation to the present understanding of DNA elasticity on the rigid base pair level. Combining existing parametrizations of elastic potentials for DNA, we derive elastic free energies directly related to competitive binding experiments, and propose a computationally inexpensive local marker for elastically optimized subsequences in protein-DNA co-crystals. We test our approach in an application to the bacteriophage 434 repressor. In agreement with known results we find that indirect readout dominates at the central, non-contacted bases of the binding site. Elastic optimization involves all deformation modes and is mainly due to the adapted equilibrium structure of the operator, while sequence-dependent elasticity plays a minor role. These qualitative observations are robust with respect to current parametrization uncertainties. Predictions for relative affinities mediated by indirect readout depend sensitively on the chosen parametrization. Their quantitative comparison with experimental data allows for a critical evaluation of DNA elastic potentials and of the correspondence between crystal and solution structures. The software written for the presented analysis is included as Supplementary Data.

Show MeSH
Related in: MedlinePlus