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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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Related in: MedlinePlus

Representation of 434 repressor–OR3 complex structure (4). The outer 5 + 5 and the inner 4 bp are shaded differently. Together they form the 14 bp binding site. The OR sequences are indicated.
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fig1: Representation of 434 repressor–OR3 complex structure (4). The outer 5 + 5 and the inner 4 bp are shaded differently. Together they form the 14 bp binding site. The OR sequences are indicated.

Mentions: The bacteriophage 434 repressor, Figure 1, is a well-studied example. It was shown that mutations in the non-contacted region affect binding affinities 50-fold (4), and a correlation of affinity to the twisting rigidity and intrinsic twist of these mutations was found (5–7).


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)

Representation of 434 repressor–OR3 complex structure (4). The outer 5 + 5 and the inner 4 bp are shaded differently. Together they form the 14 bp binding site. The OR sequences are indicated.
© Copyright Policy
Related In: Results  -  Collection

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

fig1: Representation of 434 repressor–OR3 complex structure (4). The outer 5 + 5 and the inner 4 bp are shaded differently. Together they form the 14 bp binding site. The OR sequences are indicated.
Mentions: The bacteriophage 434 repressor, Figure 1, is a well-studied example. It was shown that mutations in the non-contacted region affect binding affinities 50-fold (4), and a correlation of affinity to the twisting rigidity and intrinsic twist of these mutations was found (5–7).

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