Femtosecond Studies of Protein–DNA Binding and Dynamics: Histone I

Zhong, Dongping; Pal, Samir Kumar; Zewail, Ahmed H.

doi:10.1002/1439-7641(20010417)2:4<219::aid-cphc219>3.3.co;2-b

Cited by 16 publications

(28 citation statements)

References 4 publications

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“…A detail molecular mechanism of fluorescence of a similar TICT probe, TNS, has been reported previously. 40 In nonpolar solvents the steady-state emission is strong and is mostly from the locally excited state, i.e., before charge separation. In polar solvents, the fluorescence decreases and is dominated by emission from the TICT state.…”

Section: Resultsmentioning

confidence: 99%

Validation and Divergence of the Activation Energy Barrier Crossing Transition at the AOT/Lecithin Reverse Micellar Interface

et al. 2008

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In this report, the validity and divergence of the activation energy barrier crossing model for the bound to free type water transition at the interface of the AOT/lecithin mixed reverse micelle (RM) has been investigated for the first time in a wide range of temperatures by time-resolved solvation of fluorophores. Here, picosecondresolved solvation dynamics of two fluorescent probes, ANS (1-anilino-8-naphthalenesulfonic acid, ammonium salt) and Coumarin 500 (C-500), in the mixed RM have been carefully examined at 293, 313, 328, and 343 K. Using the dynamic light scattering (DLS) technique, the size of the mixed RMs at different temperatures was found to have an insignificant change. The solvation process at the reverse micellar interface has been found to be the activation energy barrier crossing type, in which interface-bound type water molecules get converted into free type water molecules. The activation energies, E a , calculated for ANS and C-500 are 7.4 and 3.9 kcal mol -1 , respectively, which are in good agreement with that obtained by molecular dynamics simulation studies. However, deviation from the regular Arrhenius type behavior was observed for ANS around 343 K, which has been attributed to the spatial heterogeneity of the probe environments. Time-resolved fluorescence anisotropy decay of the probes has indicated the existence of the dyes in a range of locations in RM. With the increase in temperature, the overall anisotropy decay becomes faster revealing the lability of the microenvironment at elevated temperatures.

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Section: Resultsmentioning

confidence: 99%

Validation and Divergence of the Activation Energy Barrier Crossing Transition at the AOT/Lecithin Reverse Micellar Interface

et al. 2008

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“…Steady-state absorption and emission spectrophotometers were used to measure the sample concentration and steady-state fluorescence emission. More sophisticated time-resolved fluorescence techniques were used to monitor dynamical aspects in the femtosecond to picosecond time domain (17,22). Details of the time-resolved techniques are available in the published literature (27,28).…”

Section: Methodsmentioning

confidence: 99%

“…In another study, Zewail et al explored the nature of binding interactions and dynamics of protein histone I (H1) with ligands in solution and as a complex with DNA in femotosecond time resolution (17). Both covalent and noncovalent labeling on the protein was carried out using 2-(p-toluidino)naphthalene-6-sulfonate (TNS) and 5-(dimethylamino)naphthalene-1-sulfonyl chloride (DC), respectively.…”

Section: Femtosecond Revolved Solvation and Charge Transfer Dynamics mentioning

confidence: 99%

“…Many factors may contribute in this process of complex recognition process. Recent works on specific and nonspecific protein-DNA interactions have demonstrated effects of binding rigidity, local solvation and micropolarity on the biological function of the complexes (11)(12)(13)(14)(15)(16)(17). In the recent past, there has been some advancement in the exploration of the dynamical perspective of protein-DNA interaction.…”

Section: Introductionmentioning

confidence: 99%

“…In order to reassess protein-DNA interaction, we have divided this review into two main sections. For the nonspecific protein-DNA interaction, the interaction of histone protein with DNA is elaborated in great detail (17,22). The studies of the nature of binding interactions and dynamics of protein histone I (H1) with ligands in solution and as a complex with DNA, an important biological process for the higher-order structure in chromatin are discussed.…”

Section: Introductionmentioning

confidence: 99%

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Dynamical perspective of protein-DNA interaction

Batabyal

Choudhury

Sao

et al. 2014

BioMolecular Concepts

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Abstract:The interactions between protein-DNA are essential for various biological activities. In this review, we provide an overview of protein-DNA interactions that emphasizes the importance of dynamical aspects. We divide protein-DNA interactions into two categories: nonspecific and specific and both the categories would be discussed highlighting some of our relevant work. In the case of nonspecific protein-DNA interaction, solvation studies (picosecond and femtosecond-resolved) explore the role environmental dynamics and change in the micropolarity around DNA molecules upon complexation with histone protein (H1). While exploring the specific protein-DNA interaction at λ-repressor-operator sites interaction, particularly O R 1 and O R 2, it was observed that the interfacial water dynamics is minimally perturbed upon interaction with DNA, suggesting the labile interface in the protein-DNA complex. Förster resonance energy transfer (FRET) study revealed that the structure of the protein is more compact in repressor-O R 2 complex than in the repressor-O R 1 complex. Fluorescence anisotropy studies indicated enhanced flexibility of the C-terminal domain of the repressor at fast timescales after complex formation with O R 1. The enhanced flexibility and different conformation of the C-terminal domain of the repressor upon complexation with O R 1 DNA compared to O R 2 DNA were found to have pronounced effect on the rate of photoinduced electron transfer.

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Interfacial characterization of epoxy/silica nanocomposites measured by fluorescence

Antonelli

Serrano

Baselga

et al. 2015

European Polymer Journal

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Fluorescence labeling was used as a tool for the interfacial characterization of nanocom-posites. The solvatochromic probe dansyl chloride was employed as interfacial reporter in epoxy/silica nanocomposites. Molecular spacers (organosiloxanes and polyetheramines) of different lengths were used to vary the location of the chromophore at the interface. The steady state and time resolved fluorescent responses reflect a rigid polar interface. Fluores-cence changes during heating at a constant rate were analyzed for determining the local glass transition (T g ) at the interface region. The fluorescence results were then compared to the T g obtained from differential scanning calorimetry and the results showed the existence of a gradient interface of a few nanometers thick having different properties than the bulk matrix. The thickness of this interface is small but its altered dynamics due to strong interactions with the nanofiller spreads its influence throughout the whole matrix.

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Femtosecond Studies of Protein–DNA Binding and Dynamics: Histone I

Cited by 16 publications

References 4 publications

Validation and Divergence of the Activation Energy Barrier Crossing Transition at the AOT/Lecithin Reverse Micellar Interface

Validation and Divergence of the Activation Energy Barrier Crossing Transition at the AOT/Lecithin Reverse Micellar Interface

Dynamical perspective of protein-DNA interaction

Interfacial characterization of epoxy/silica nanocomposites measured by fluorescence

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