Dataset Information

The Study of the Aggregated Pattern of TX100 Micelle by Using Solvent Paramagnetic Relaxation Enhancements.

ABSTRACT: TX100 (Triton X-100) is a typical nonionic surfactant that is widely used in biology. However, the detailed aggregated conformation of TX100, such as the boundary between the polar region and the nonpolar region, and the arrangement of hydrophobic chains in micelles, are still controversial. In the manuscript, the aggregation pattern of TX100 has been studied using sPREs (solvent Paramagnetic Relaxation Enhancements)-based NMR (Nuclear Magnetic Resonance spectroscopy). It was found that the average positions of the protons in the TX100 micelle are consistent with those in the multilayer staggered spherical micelle model with the p-tertoctylphenyl groups dispersing in the different layers.

SUBMITTER: Zhang L

PROVIDER: S-EPMC6539090 | biostudies-literature | 2019 Apr

REPOSITORIES: biostudies-literature

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The Study of the Aggregated Pattern of TX100 Micelle by Using Solvent Paramagnetic Relaxation Enhancements.

Zhang Liang L Chai Xin X Sun Peng P Yuan Bin B Jiang Bin B Zhang Xu X Liu Maili M

Molecules (Basel, Switzerland) 20190426 9

TX100 (Triton X-100) is a typical nonionic surfactant that is widely used in biology. However, the detailed aggregated conformation of TX100, such as the boundary between the polar region and the nonpolar region, and the arrangement of hydrophobic chains in micelles, are still controversial. In the manuscript, the aggregation pattern of TX100 has been studied using sPREs (solvent Paramagnetic Relaxation Enhancements)-based NMR (Nuclear Magnetic Resonance spectroscopy). It was found that the aver ...[more]

PMID: 31027389

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Project description:The human DNA repair enzyme uracil DNA glycosylase (hUNG) locates and excises rare uracil bases that arise in DNA from cytosine deamination or through dUTP incorporation by DNA polymerases. Previous NMR studies of hUNG have revealed millisecond time scale dynamic transitions in the enzyme-nonspecific DNA complex, but not the free enzyme, that were ascribed to a reversible clamping motion of the enzyme as it scans along short regions of duplex DNA in its search for uracil. Here we further probe the properties of the nonspecific DNA binding surface of {(2)H(12)C}{(15)N}-labeled hUNG using a neutral chelate of a paramagnetic Gd(3+) cosolute (Gd(HP-DO3A)). Overall, the measured paramagnetic relaxation enhancements (PREs) on R(2) of the backbone amide protons for free hUNG and its DNA complex were in good agreement with those calculated based on their relative exposure observed in the crystal structures of both enzyme forms. However, the calculated PREs systematically underestimated the experimental PREs by large amounts in discrete regions implicated in DNA recognition and catalysis: active site loops involved in DNA recognition (268-274, 246-250), the uracil binding pocket (143-148, 169-170), a transient extrahelical base binding site (214-216), and a remote hinge region (129-132) implicated in dynamic clamping. These reactive hot spots were not correlated with structural, hydrophobic, or solvent exchange properties that might be common to these regions, leaving the possibility that the effects arise from dynamic sampling of exposed conformations that are distinct from the static structures. Consistent with this suggestion, the above regions have been previously shown to be flexible based on relaxation dispersion measurements and course-grained normal-mode analysis. A model is suggested where the intrinsic dynamic properties of these regions allows sampling of transient conformations where the backbone amide groups have greater average exposure to the cosolute as compared to the static structures. We conclude that PREs derived from the paramagnetic cosolute reveal dynamic hot spots in hUNG and that these regions are highly correlated with substrate binding and recognition.

Dataset Information

The Study of the Aggregated Pattern of TX100 Micelle by Using Solvent Paramagnetic Relaxation Enhancements.

Publications

The Study of the Aggregated Pattern of TX100 Micelle by Using Solvent Paramagnetic Relaxation Enhancements.

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