The role of DNA bending in Cro protein-DNA interactions

Gromiha, M. Michael; Munteanu, Mircea; Simon, István; Pongor, Sándor

doi:10.1016/s0301-4622(97)00088-4

Cited by 18 publications

(13 citation statements)

References 26 publications

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“…Integration host factor (IHF) is one such protein; indeed the structure of the IHF -DNA complex 31 (PDB code, 1IHF) shows the DNA to be severely bent (overall bending angle , 1608), and it has been suggested that the conformation of the DNA is crucial to the protein-DNA interactions in this case. 10,32 Consistent with that idea, the calculated Z-score for the intramolecular readout was 2 2.3, twice that of the intermolecular readout ðZ ¼ 21:2Þ:…”

Section: Proteins Causing Severe Dna Bendingsupporting

confidence: 60%

Intermolecular and Intramolecular Readout Mechanisms in Protein–DNA Recognition

Gromiha

Siebers

Selvaraj

et al. 2004

Journal of Molecular Biology

112

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Section: Proteins Causing Severe Dna Bendingsupporting

confidence: 60%

Intermolecular and Intramolecular Readout Mechanisms in Protein–DNA Recognition

Gromiha

Siebers

Selvaraj

et al. 2004

Journal of Molecular Biology

112

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“…The importance of direct and indirect readout and protein–DNA binding affinities have been addressed computationally by sequence-structure threading. The elastic models considered range from a combination of fixed coarse-grained protein structure with DNA rigid rod ( 8 , 9 ), rigid base pair ( 10 , 11 ) and rigid base ( 12 ) models, to all-atom force fields with sequence-independent partial protein structure relaxation ( 13 , 14 ) and more recently, with sequence-dependent protein side chain relaxation ( 15 , 16 ), leading to high computational requirements.…”

Section: Introductionmentioning

confidence: 99%

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

Becker

Wolff

Everaers

2006

Nucleic Acids Research

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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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“…such as ETS proteins, 434, λ, Mnt and trp repressors, cro protein, EcoRV endonuclease V and zinc finger proteins. In most of the complexes, we observed a strong relationship between DNA stiffness and protein-DNA binding specificity and the correlation coefficient varies in the range of 0.65-0.97 (Gromiha et al, 1997;Gromiha, 2005b). This result indicates that the elastic properties of DNA are also important for understanding the mechanism of protein-DNA recognition, which may be included in the contribution of intramolecular interactions.…”

Section: Influence Of Dna Stiffness In Protein-dna Binding Specificitymentioning

confidence: 69%