DNA Deformation Energy as an Indirect Recognition Mechanism in Protein-DNA Interactions

Aeling, Kimberly A.; Steffen, Nicholas R.; Johnson, Mark E.; Hatfield, G. Wesley; Lathrop, Richard H.; Senear, Donald F.

doi:10.1109/tcbb.2007.1000

Cited by 20 publications

(12 citation statements)

References 23 publications

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“…Deformation energy calculated in this manner was used to seed classifiers that could be trained to identify IHF-binding sites (22). Subsequently, this result was extended to four other DNA-binding proteins, which feature highly degenerate consensus DNA-binding sequences and substantial DNA deformation in the bound complexes, and for which high resolution structures are available (23).…”

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confidence: 94%

Indirect Recognition in Sequence-specific DNA Binding by Escherichia coli Integration Host Factor

Aeling

Opel

Steffen

et al. 2006

Journal of Biological Chemistry

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Integration host factor (IHF) is a bacterial histone-like protein whose primary biological role is to condense the bacterial nucleoid and to constrain DNA supercoils. It does so by binding in a sequence-independent manner throughout the genome. However, unlike other structurally related bacterial histone-like proteins, IHF has evolved a sequence-dependent, high affinity DNA-binding motif. The high affinity binding sites are important for the regulation of a wide range of cellular processes. A remarkable feature of IHF is that it employs an indirect readout mechanism to bind and wrap DNA at both the nonspecific and high affinity (sequence-dependent) DNA sites. In this study we assessed the contributions of pre-formed and protein-induced DNA conformations to the energetics of IHF binding. Binding energies determined experimentally were compared with energies predicted for the IHF-induced deformation of the DNA helix (DNA deformation energy) in the IHF-DNA complex. Combinatorial sets of de novo DNA sequences were designed to systematically evaluate the influence of sequence-dependent structural characteristics of the conserved IHF recognition elements of the consensus DNA sequence. We show that IHF recognizes pre-formed conformational characteristics of the consensus DNA sequence at high affinity sites, whereas at all other sites relative affinity is determined by the deformational energy required for nearest-neighbor base pairs to adopt the DNA structure of the bound DNA-IHF complex.Site-specific DNA binding by regulatory proteins is a feature of the regulatory processes that maintain, expand, and express genetic information such as replication, recombination, transposition, and transcription. The chemical and physical mechanisms that underlie sequence-specific recognition of regulatory elements by cognate DNA-binding proteins are typically classified as direct versus indirect readout. The former refers primarily to hydrogen bonds between proteins and the unique extra-cyclic substituents at C-4 of pyrimidines, C-6 of purines, and N-7 of purines. These groups provide a base pair-specific pattern of hydrogen bond donors and acceptors in the major groove of DNA that can be directly read by a complementary pattern of amino acid side chain donors and acceptors. Indirect readout refers to recognition of aspects of DNA structure such as intrinsic curvature, topology of major and minor grooves, ordered water structures, local geometry of backbone phosphates, and flexibility or deformability. Because both the local DNA structure and energy to deform DNA are themselves intrinsic sequence-dependent properties, the conserved sequences that distinguish binding sites necessarily include contributions from both direct and indirect mechanisms. Consequently, although the contribution from indirect mechanisms is expected to be significant in protein-DNA complexes that feature substantial DNA deformation, it has proven difficult to evaluate these contributions quantitatively. A protein that relies exclusively, or primarily, on indir...

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confidence: 94%

Indirect Recognition in Sequence-specific DNA Binding by Escherichia coli Integration Host Factor

Aeling

Opel

Steffen

et al. 2006

Journal of Biological Chemistry

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“…DNA structural changes momentously affect its interactions with proteins [ 5 ]. Recognition of DNA structural properties is referred to as indirect recognition or indirect readout [ 6 ]. Governed by the binding free energy of a protein-DNA interaction, some proteins bind more strongly to certain regions of the DNA than the other regions[ 7 ].…”

Section: Introductionmentioning

confidence: 99%

A theoretical investigation of DNA dynamics and desolvation kinetics for zinc finger proteinZif268

et al. 2015

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BackgroundTranscription factors, regulating the expression inventory of a cell, interact with its respective DNA subjugated by a specific recognition pattern, which if well exploited may ensure targeted genome engineering. The mostly widely studied transcription factors are zinc finger proteins that bind to its target DNA via direct and indirect recognition levels at the interaction interface. Exploiting the binding specificity and affinity of the interaction between the zinc fingers and the respective DNA can help in generating engineered zinc fingers for therapeutic applications. Experimental evidences lucidly substantiate the effect of indirect interaction like DNA deformation and desolvation kinetics, in empowering ZFPs to accomplish partial sequence specificity functioning around structural properties of DNA. Exploring the structure-function relationships of the existing zinc finger-DNA complexes at the indirect recognition level can aid in predicting the probable zinc fingers that could bind to any target DNA. Deformation energy, which defines the energy required to bend DNA from its native shape to its shape when bound to the ZFP, is an effect of indirect recognition mechanism. Water is treated as a co-reactant for unfurling the affinity studies in ZFP-DNA binding equilibria that takes into account the unavoidable change in hydration that occurs when these two solvated surfaces come into contact.ResultsAspects like desolvation and DNA deformation have been theoretically investigated based on simulations and free energy perturbation data revealing a consensus in correlating affinity and specificity as well as stability for ZFP-DNA interactions. Greater loss of water at the interaction interface of the DNA calls for binding with higher affinity, eventually distorting the DNA to a greater extent accounted by the change in major groove width and DNA tilt, stretch and rise.ConclusionMost prediction algorithms for ZFPs do not account for water loss at the interface. The above findings may significantly affect these algorithms. Further the sequence dependent deformation in the DNA upon complexation with our prototype as well as preference of bases at the 2nd and 3rd position of the repeating triplet provide an absolutely new insight about the indirect interactions undergoing a change that have not been probed yet.

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“…83 Remarkably, IHF accomplishes this feat with almost no direct interactions between the protein residues and specific bases, and has thus become an excellent model system for studies of sequence-dependent DNA shape and deformability that underpins binding site recognition by indirect readout. 71,[84][85][86] The sharp DNA bends induced by IHF allow for FRET measurements to be sensitive reporters of the extent of DNA bending. Previous studies took advantage of time-resolved FRET to investigate DNA-bending kinetics in IHF-DNA complexes, 60, 68 which demonstrated the stepwise binding-then-bending mechanism for site recognition by IHF.…”

Section: Discussionmentioning

confidence: 99%

Static Kinks or Flexible Hinges: Conformational Distributions of Bent DNA Bound to Integration Host Factor Mapped by Fluorescence Lifetime Measurements

Connolly

Arra

Zvoda

et al. 2018

Preprint

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Gene regulation depends on proteins that bind to specific DNA sites. Such specific recognition often involves severe DNA deformations including sharp kinks. It has been unclear how rigid or flexible these protein-induced kinks are. Here, we investigated the dynamic nature of DNA in complex with integration host factor (IHF), a nucleoid-associated architectural protein known to bend one of its cognate sites (35 base pair H') into a U-turn by kinking DNA at two sites. We utilized fluorescence lifetime based FRET spectroscopy to map the distribution of bent conformations in various IHF-DNA complexes. Our results reveal a surprisingly dynamic specific complex: while 80% of the IHF-H' population exhibited FRET efficiency consistent with the crystal structure, 20% exhibited FRET efficiency indicative of unbent or partially bent DNA. This conformational flexibility is modulated by sequence variations in the cognate site. In another site (H1) that lacks an A-tract of H' on one side of the binding site, the population in the fully U-bent conformation decreased to 36%, as did the extent of bending. A similar decrease in the U-bent population was observed with a single base mutation in H' in a consensus region on the other side. Taken together, these results provide important insights into the finely tuned interactions between IHF and its cognate sites that keep the DNA bent (or not), and yield quantitative data on the dynamic equilibrium between different DNA conformations (kinked or not kinked) that depend sensitively on DNA sequence and deformability. Notably, the difference in dynamics between IHF-H' and IHF-H1 reflects the different roles of these complexes in their natural context, in the phage lambda "intasome" (the complex that integrates phage lambda into the E. coli chromosome).

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DNA Deformation Energy as an Indirect Recognition Mechanism in Protein-DNA Interactions

Cited by 20 publications

References 23 publications

Indirect Recognition in Sequence-specific DNA Binding by Escherichia coli Integration Host Factor

Indirect Recognition in Sequence-specific DNA Binding by Escherichia coli Integration Host Factor

A theoretical investigation of DNA dynamics and desolvation kinetics for zinc finger proteinZif268

Static Kinks or Flexible Hinges: Conformational Distributions of Bent DNA Bound to Integration Host Factor Mapped by Fluorescence Lifetime Measurements

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