The Energetics of Specific Binding of AT-hooks from HMGA1 to Target DNA

Dragan, Anatoly I.; Liggins, John R.; Crane‐Robinson, Colyn; Privalov, Peter L.

doi:10.1016/s0022-2836(03)00050-0

Cited by 57 publications

(70 citation statements)

References 65 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…S10). These AT-hook motifs also confer the highest affinity to AT-rich DNA (12,46). The flanking AT-hook motifs of HMGAs are similar to the type 2 AT-hook motif of AHLs.…”

Section: Discussionmentioning

confidence: 83%

Arabidopsis thaliana AHL family modulates hypocotyl growth redundantly by interacting with each other via the PPC/DUF296 domain

Zhao

Favero

Peng

et al. 2013

Proc. Natl. Acad. Sci. U.S.A.

113

256

View full text Add to dashboard Cite

The Arabidopsis thaliana genome encodes 29 AT-HOOK MOTIF CONTAINING NUCLEAR LOCALIZED (AHL) genes, which evolved into two phylogenic clades. The AHL proteins contain one or two AT-hook motif(s) and one plant and prokaryote conserved (PPC)/domain of unknown function #296 (DUF296) domain. Seedlings lacking both SOB3/AHL29 and ESC/AHL27 confer a subtle long-hypocotyl phenotype compared with the WT or either single-null mutant. In contrast, the missense allele sob3-6 confers a dramatic long-hypocotyl phenotype in the light. In this study, we examined the dominant-negative feature of sob3-6 and found that it encodes a protein with a disrupted AT-hook motif that abolishes binding to AT-rich DNA. A loss-of-function approach demonstrated different, yet redundant, contributions of additional AHL genes in suppressing hypocotyl elongation in the light. We showed that AHL proteins interact with each other and themselves via the PPC/DUF296 domain. AHLs also share interactions with other nuclear proteins, such as transcription factors, suggesting that these interactions also contribute to the functional redundancy within this gene family. The coordinated action of AHLs requires an AT-hook motif capable of binding AT-rich DNA, as well as a PPC/DUF296 domain containing a conserved Gly-Arg-Phe-Glu-Ile-Leu region. Alteration of this region abolished SOB3/AHL29's physical interaction with transcription factors and resulted in a dominant-negative allele in planta that was phenotypically similar to sob3-6. We propose a molecular model where AHLs interact with each other and themselves, as well as other nuclear proteins, to form complexes which modulate plant growth and development.enhanceosome | seedling establishment

show abstract

“…S10). These AT-hook motifs also confer the highest affinity to AT-rich DNA (12,46). The flanking AT-hook motifs of HMGAs are similar to the type 2 AT-hook motif of AHLs.…”

Section: Discussionmentioning

confidence: 83%

Arabidopsis thaliana AHL family modulates hypocotyl growth redundantly by interacting with each other via the PPC/DUF296 domain

Zhao

Favero

Peng

et al. 2013

Proc. Natl. Acad. Sci. U.S.A.

113

256

View full text Add to dashboard Cite

show abstract

“…Effective enthalpyentropy compensation, which maintains the free energy constant, is quite common for DNA binding agents and proteins, especially in the case of minor-groove binders [24][25][26]. Furthermore, it also suggests that the cationic amino-group probably does not electrostatically interact with DNA phosphates, because this interaction has an entropic nature (enthalpic contribution is close to zero), and should invariably increase the Gibbs energy [25,[27][28][29].…”

Section: Interactions Of Sg With Dsdnamentioning

confidence: 99%

SYBR Green I: Fluorescence Properties and Interaction with DNA

Dragan

Pavlović

McGivney³

et al. 2012

J Fluoresc

267

164

View full text Add to dashboard Cite

In this study, we have investigated the fluorescence properties of SYBR Green I (SG) dye and its interaction with double-stranded DNA (dsDNA). SG/dsDNA complexes were studied using various spectroscopic techniques, including fluorescence resonance energy transfer and time-resolved fluorescence techniques. It is shown that SG quenching in the free state has an intrinsic intramolecular origin; thus, the observed >1,000-fold SG fluorescence enhancement in complex with DNA can be explained by a dampening of its intra-molecular motions. Analysis of the obtained SG/DNA binding isotherms in solutions of different ionic strength and of SG/DNA association in the presence of a DNA minor groove binder, Hoechst 33258, revealed multiple modes of interaction of SG inner groups with DNA. In addition to interaction within the DNA minor groove, both intercalation between base pairs and stabilization of the electrostatic SG/DNA complex contributed to increased SG affinity to double-stranded DNA. We show that both fluorescence and the excited state lifetime of SG dramatically increase in viscous solvents, demonstrating an approximate 200-fold enhancement in 100 % glycerol, compared to water, which also makes SG a prospective fluorescent viscosity probe. A proposed structural model of the SG/DNA complex is compared and discussed with results recently reported for the closely related PicoGreen chromophore.

show abstract

“…[2][3][4][5][6][15][16][17][18][19][20][21][22][23][24][25][26][27][28][29][30] For the present analysis, we have selected data obtained under similar conditions (20°C, near neutral pH, 100 mM NaCl) and analyzed by the same approach, namely correcting for refolding effects and resolving the electrostatic and non-electrostatic components of the binding characteristics, as outlined in Figures 1 and 2. All these data are illustrated in Figure 3 and summarized in Table 1 in Supplementary Materials.…”

Section: Thermodynamic Parameters Of Protein-dna Interactionsmentioning

confidence: 99%

What Drives Proteins into the Major or Minor Grooves of DNA?

Privalov

Dragan

Crane‐Robinson

et al. 2007

Journal of Molecular Biology

Self Cite

172

158

View full text Add to dashboard Cite

The energetic profiles of a significant number of protein-DNA systems at 20°C reveal that, despite comparable Gibbs free energies, association with the major groove is primarily an enthalpy driven process, whereas binding to the minor groove is characterized by an unfavorable enthalpy that is compensated by favorable entropic contributions. These distinct energetic signatures for major versus minor groove binding are irrespective of the magnitude of DNA bending and/or the extent of binding-induced protein refolding. The primary determinants of their different energetic profiles appear to be the distinct hydration properties of the major and minor grooves, namely that the water in the AT-rich minor groove is in a highly ordered state and its removal results in a substantial positive contribution to the binding entropy. Since the entropic forces driving protein binding into the minor groove are a consequence of displacing water ordered by the regular arrangement of polar contacts, they cannot be regarded as hydrophobic. KeywordsDNA binding; DNA grooves; hydration; thermodynamics; electrostatics Structural and energetic characterizations of protein-nucleic acid complexes are important for a better understanding of the molecular interactions that govern transcriptional regulation. Of particular importance are the energetic profiles of DNA binding domains (DBDs) interacting with their target recognition sites. DBDs are known to interact specifically with either the major or minor grooves of DNA, with binding-induced structural effects ranging from negligible perturbation of the B-DNA conformation to substantial distortions, such as bending and kinking. One can then ask if there are qualitative differences in the forces driving protein binding to the different grooves of DNA. Comparing the association constants of these two types of DBDs does not furnish a satisfactory answer, since both categories contain examples of stronger and weaker binding interactions. An answer to this question therefore requires a detailed analysis of the forces involved in the formation of the specific protein-DNA complexes. This assumes not only measurement of the association constant but also determination of the Gibbs energy and its enthalpic and entropic components over a broad range of conditions, particularly temperature and ionic strength. In this review, we analyze the thermodynamic characteristics of protein binding to DNA published over the last several years. This overall consideration has revealed qualitative differences in the energetic signatures of

show abstract

The Energetics of Specific Binding of AT-hooks from HMGA1 to Target DNA

Cited by 57 publications

References 65 publications

Arabidopsis thaliana AHL family modulates hypocotyl growth redundantly by interacting with each other via the PPC/DUF296 domain

Arabidopsis thaliana AHL family modulates hypocotyl growth redundantly by interacting with each other via the PPC/DUF296 domain

SYBR Green I: Fluorescence Properties and Interaction with DNA

What Drives Proteins into the Major or Minor Grooves of DNA?

Contact Info

Product

Resources

About