Indirect Readout of DNA Sequence by P22 Repressor: Roles of DNA and Protein Functional Groups in Modulating DNA Conformation

Harris, Lydia-Ann; Watkins, Davita L.; Williams, Loren Dean; Koudelka, Gerald B.

doi:10.1016/j.jmb.2012.10.008

Cited by 8 publications

(18 citation statements)

References 48 publications

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“…Here, we observe a cation density of roughly 15 M with a corresponding probability of 75% for finding a K + ion in this zone (see Figure 7). As shown in figure, these ions undoubtedly help to offset the repulsion between the P22 glutamic acid groups and the DNA phosphates (39,40). …”

Section: Resultsmentioning

confidence: 99%

Protein–DNA interfaces: a molecular dynamics analysis of time-dependent recognition processes for three transcription factors

Éthève¹,

Martin²,

Lavery³

2016

Nucleic Acids Res

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We have studied the dynamics of three transcription factor–DNA complexes using all-atom, microsecond-scale MD simulations. In each case, the salt bridges and hydrogen bond interactions formed at the protein–DNA interface are found to be dynamic, with lifetimes typically in the range of tens to hundreds of picoseconds, although some interactions, notably those involving specific binding to DNA bases, can be a hundred times longer lived. Depending on the complex studied, this dynamics may or may not lead to the existence of distinct conformational substates. Using a sequence threading technique, it has been possible to determine whether DNA sequence recognition is sensitive or not to such conformational changes, and, in one case, to show that recognition appears to be locally dependent on protein-mediated cation distributions.

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Section: Resultsmentioning

confidence: 99%

Protein–DNA interfaces: a molecular dynamics analysis of time-dependent recognition processes for three transcription factors

Éthève¹,

Martin²,

Lavery³

2016

Nucleic Acids Res

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“…Hence, DNA A-tracts embedded in AT-rich sequences may not have a narrow minor groove and may not preferentially interact with monovalent cations in the surrounding medium. Such sequence-dependent variations in minor groove width are likely to contribute to indirect readout mechanisms (5,(64)(65)(66)(67)(68) and nucleosome positioning (69).…”

Section: Discussionmentioning

confidence: 99%

Flanking A·T Basepairs Destabilize the B∗ Conformation of DNA A-Tracts

Stellwagen

2015

Biophysical Journal

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Capillary electrophoresis has been used to characterize the interaction of monovalent cations with 26-basepair DNA oligomers containing A-tracts embedded in flanking sequences with different basepair compositions. A 26-basepair random-sequence oligomer was used as the reference; lithium and tetrabutylammonium (TBA(+)) ions were used as the probe ions. The free solution mobilities of the A-tract and random-sequence oligomers were identical in solutions containing <∼ 100 mM cation. At higher cation concentrations, the A-tract oligomers migrated faster than the reference oligomer in TBA(+) and slower than the reference in Li(+). Hence, cations of different sizes can interact very differently with DNA A-tracts. The increased mobilities observed in TBA(+) suggest that the large hydrophobic TBA(+) ions are preferentially excluded from the vicinity of the A-tract minor groove, increasing the effective net charge of the A-tract oligomers and increasing the mobility. By contrast, Li(+) ions decrease the mobility of A-tract oligomers because of the preferential localization of Li(+) ions in the narrow A-tract minor groove. Embedding the A-tracts in AT-rich flanking sequences markedly alters preferential interactions of monovalent cations with the B(∗) conformation. Hence, A-tracts embedded in genomic DNA may or may not interact preferentially with monovalent cations, depending on the relative number of A · T basepairs in the flanking sequences.

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“…Thus proteins evidently utilise the additional information from DNA structure and DNA deformability. In the example mentioned above, the bHLH TFs recognise the specific bases of the conserved E-box in the major groove, whereas local DNA shape recognition in the flanking regions appears to enable distinct DNA binding preferences among paralogous TFs [16,90]. …”

Section: Base Readout Pre-shaped Dna and Protein Recognitionmentioning

confidence: 99%

Making the Bend: DNA Tertiary Structure and Protein-DNA Interactions

Harteis

Schneider

2014

IJMS

105

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DNA structure functions as an overlapping code to the DNA sequence. Rapid progress in understanding the role of DNA structure in gene regulation, DNA damage recognition and genome stability has been made. The three dimensional structure of both proteins and DNA plays a crucial role for their specific interaction, and proteins can recognise the chemical signature of DNA sequence (“base readout”) as well as the intrinsic DNA structure (“shape recognition”). These recognition mechanisms do not exist in isolation but, depending on the individual interaction partners, are combined to various extents. Driving force for the interaction between protein and DNA remain the unique thermodynamics of each individual DNA-protein pair. In this review we focus on the structures and conformations adopted by DNA, both influenced by and influencing the specific interaction with the corresponding protein binding partner, as well as their underlying thermodynamics.

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Indirect Readout of DNA Sequence by P22 Repressor: Roles of DNA and Protein Functional Groups in Modulating DNA Conformation

Cited by 8 publications

References 48 publications

Protein–DNA interfaces: a molecular dynamics analysis of time-dependent recognition processes for three transcription factors

Protein–DNA interfaces: a molecular dynamics analysis of time-dependent recognition processes for three transcription factors

Flanking A·T Basepairs Destabilize the B∗ Conformation of DNA A-Tracts

Making the Bend: DNA Tertiary Structure and Protein-DNA Interactions

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