Prevalence of Temperature-Dependent Heat Capacity Changes in Protein-DNA Interactions

Liu, Chin‐Chi; Richard, Allison J.; Datta, Kausiki; LiCata, Vince J.

doi:10.1529/biophysj.107.117697

Cited by 27 publications

(31 citation statements)

References 53 publications

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“…The stoichiometry obtained by ITC for this specific association is 1.1, consistent with a binding involving one palindromic DNA sequence per Mtb -HigA1 dimer present in the Mtb -SecB TA /HigA1 hetero-hexamer. Measuring the temperature dependence of the enthalpy gave a negative heat capacity of binding (−1.3 kJ mol −1 K −1 ) as typically reported for the majority of sequence-specific protein/DNA associations 43 . Together these results show that the highly unstable Mtb -HigA1 antitoxin can form a functional dimer following binding to its specific chaperone partner.…”

Section: Resultssupporting

confidence: 57%

Structural insights into chaperone addiction of toxin-antitoxin systems

et al. 2019

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SecB chaperones assist protein export by binding both unfolded proteins and the SecA motor. Certain SecB homologs can also control toxin-antitoxin (TA) systems known to modulate bacterial growth in response to stress. In such TA-chaperone (TAC) systems, SecB assists the folding and prevents degradation of the antitoxin, thus facilitating toxin inhibition. Chaperone dependency is conferred by a C-terminal extension in the antitoxin known as chaperone addiction (ChAD) sequence, which makes the antitoxin aggregation-prone and prevents toxin inhibition. Using TAC of Mycobacterium tuberculosis, we present the structure of a SecB-like chaperone bound to its ChAD peptide. We find differences in the binding interfaces when compared to SecB–SecA or SecB-preprotein complexes, and show that the antitoxin can reach a functional form while bound to the chaperone. This work reveals how chaperones can use discrete surface binding regions to accommodate different clients or partners and thereby expand their substrate repertoire and functions.

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Section: Resultssupporting

confidence: 57%

Structural insights into chaperone addiction of toxin-antitoxin systems

et al. 2019

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“…We and others have strongly suggested that these correlations may hold for some subset of protein-DNA interactions, but that neither correlation holds quantitatively for DNA-protein interactions in general (29,30). As a general indicator, DC p is definitely reflective of some DASA nonpolar in protein-DNA interactions, but exact quantitative correlation does not universally hold for any current model for this specific class of interactions (29,30).…”

Section: Enthalpies and Heat Capacities Of Binding Of Different Dna Smentioning

confidence: 85%

Thermodynamics of the DNA Structural Selectivity of the Pol I DNA Polymerases from Escherichia coli and Thermus aquaticus

Wowor

Datta

Brown

et al. 2010

Biophysical Journal

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Understanding the thermodynamics of substrate selection by DNA polymerase I is important for characterizing the balance between replication and repair for this enzyme in vivo. Due to their sequence and structural similarities, Klenow and Klentaq, the large fragments of the Pol I DNA polymerases from Escherichia coli and Thermus aquaticus, are considered functional homologs. Klentaq, however, does not have a functional proofreading site. Examination of the DNA binding thermodynamics of Klenow and Klentaq to different DNA structures: single-stranded DNA (ss-DNA), primer-template DNA (pt-DNA), and blunt-end double-stranded DNA (ds-DNA) show that the binding selectivity pattern is similar when examined across a wide range of salt concentration, but can significantly differ at any individual salt concentration. For both proteins, binding of single-stranded DNA shifts from weakest to tightest binding of the three structures as the salt concentration increases. Both Klenow and Klentaq release two to three more ions when binding to pt-DNA and ds-DNA than when binding to ss-DNA. Klenow exhibits significant differences in the Delta C(p) of binding to pt-DNA versus ds-DNA, and a difference in pI for these two complexes, whereas Klentaq does not, suggesting that Klenow and Klentaq discriminate between these two structures differently. Taken together, the data suggest that the two polymerases bind ds-DNA very differently, but that both bind pt-DNA and ss-DNA similarly, despite the absence of a proofreading site in Klentaq.

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“…Finally, over 40 % of E. coli's transcription factors are negatively autoregulated [55] and the formation of many protein-DNA complexes exhibits a non-linear temperature-dependence [56]. Negative autoregulation can thus play an important role in maintaining a linear response in the regulation of downstream genes [57] upon changes in environmental variables, such as temperature, affecting the activity of a DNA-binding protein.…”

Section: Autoregulation and The Temperature-dependence Of Dnaa-dna Inmentioning

confidence: 99%

Temperature-dependence of the DnaA–DNA interaction and its effect on the autoregulation of dnaA expression

Saggioro

Olliver

Sclavi

2012

Biochemical Journal

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The DnaA protein is a key factor for the regulation of the timing and synchrony of initiation of bacterial DNA replication. The transcription of the dnaA gene in Escherichia coli is regulated by two promoters, dnaAP1 and dnaAP2. The region between these two promoters contains several DnaA-binding sites that have been shown to play an important role in the negative auto-regulation of dnaA expression. The results obtained in the present study using an in vitro and in vivo quantitative analysis of the effect of mutations to the high-affinity DnaA sites reveal an additional effect of positive autoregulation. We investigated the role of transcription autoregulation in the change of dnaA expression as a function of temperature. While negative auto-regulation is lost at dnaAP1, the effects of both positive and negative autoregulation are maintained at the dnaAP2 promoter upon lowering the growth temperature. These observations can be explained by the results obtained in vitro showing a difference in the temperature-dependence of DnaA-ATP binding to its high- and low-affinity sites, resulting in a decrease in DnaA-ATP oligomerization at lower temperatures. The results of the present study underline the importance of the role for autoregulation of gene expression in the cellular adaptation to different growth temperatures.

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Prevalence of Temperature-Dependent Heat Capacity Changes in Protein-DNA Interactions

Cited by 27 publications

References 53 publications

Structural insights into chaperone addiction of toxin-antitoxin systems

Structural insights into chaperone addiction of toxin-antitoxin systems

Thermodynamics of the DNA Structural Selectivity of the Pol I DNA Polymerases from Escherichia coli and Thermus aquaticus

Temperature-dependence of the DnaA–DNA interaction and its effect on the autoregulation of dnaA expression

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