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Cross Peaks (cross + peak)

Distribution by Scientific Domains

Chemistry	75%

Selected Abstracts

1H-NMR Studies of Duplex DNA Decamer Containing a Uracil Cyclobutane Dimer: Implications Regarding the High UV Mutagenecity of CC Photolesions,

PHOTOCHEMISTRY & PHOTOBIOLOGY, Issue 4 2002
Hyun Mee Lee
ABSTRACT To determine the origin of the UV-specific CC to TT tandem mutation at the CC site, we made a duplex DNA decamer containing a uracil cis,syn cyclobutane dimer (CBD) as the deaminated model of a cytosine dimer. Two-dimensional 1H-NMR spectroscopy studies were performed on this sequence where two adenines (Ade) were opposite to the uracil dimer. Two imino protons of the uracil dimer were found to retain Watson,Crick hydrogen bonding with the opposite Ade, although the 5,-U(NH) of the dimer site showed unusual upfield shift like that of the 5,-T(NH) of the TT dimer, which seemed to be associated with deshielding by the flanking base rather than with reduced hydrogen bonding. (McAteer et al. 1998, J. Mol. Biol. 282:1013,1032). Hydrogen bondings at the dimer site were also supported by detecting typical strong nuclear Overhauser effects (NOE) between two imino protons and the opposite Ade H2 or NH2. But sequential NOE interactions of base protons with sugar protons were absent at the two flanking nucleotides of the 5, side of the uracil dimer and at the intradimer site, contrasting with its thymine analog where sequential NOE was absent only at the A4,T5 step. In addition, NOE cross peak for U5(NH) , A4(H2) was detected, although the NOE interactions of U6(NH) with A7(H2) and A17(H2) were not observed in contrast to the thymine dimer duplex. This different local structural alteration may be affected by the induced right-hand twisted puckering mode of cis,syn cyclobutane ring of the uracil dimer in the B-DNA duplex, even though the isolated uracil dimer had left-hand twisted puckering rigidly. In parallel, these observations may be correlated with observed differences in mutagenic properties between cis,syn UU dimer and cis,syn TT dimer. [source]

Bacterial IscU is a well folded and functional single domain protein

FEBS JOURNAL, Issue 11 2004
Salvatore Adinolfi
Iron,sulfur clusters are widely represented in most organisms, but the mechanism of their formation is not fully understood. Of the two main proteins involved in cluster formation, NifS/IscS and NifU/IscU, only the former has been well studied from a structural point of view. Here we report an extensive structural characterization of Escherichia coli IscU. We show by a variety of physico-chemical techniques that E. coli IscU construct can be expressed to high purity as a monomeric protein, characterized by an ,, fold with high ,-helix content. The high melting temperature and the reversibility of the thermal unfolding curve (as measured by CD spectroscopy) hint at a well ordered stable fold. The excellent dispersion of cross peaks in the 1H- 15N correlation spectrum is consistent with these observations. Monomeric E. coli IscU is able to provide a scaffold for Iron,sulfur cluster assembly, but has no direct interaction with either Fe(II) or Fe(III) ions, suggesting the need of further partners to achieve a stable interaction. [source]

High resolution-HMBC (HR-HMBC), a new method for measuring heteronuclear long-range coupling constants

MAGNETIC RESONANCE IN CHEMISTRY, Issue 3 2010
Kazuo Furihata
Abstract A useful pulse sequence for measuring long-range CH coupling constants (JCH) named high resolution-HMBC (HR-HMBC) has been developed. In this pulse sequence, the J -scaling pulse [(nt1)/2180° (H/C) , (nt1)/2] is incorporated after the spin evolution period, and then followed by an 1H 180° pulse to reverse the magnetization of JCH couplings. As a result, splittings of the cross peaks due to the long-range JCH are realigned with separations of nJCH along the F1 dimension, and thus even the small long-range JCH values can easily be determined. The efficiency of measuring the long-range JCH using the proposed pulse sequences has been demonstrated in application to the complicated natural product, portmicin. Copyright © 2010 John Wiley & Sons, Ltd. [source]

A helix-turn motif in the C-terminal domain of histone H1

PROTEIN SCIENCE, Issue 4 2000
Roger Vila
Abstract The structural study of peptides belonging to the terminal domains of histone H1 can be considered as a step toward the understanding of the function of H1 in chromatin. The conformational properties of the peptide Ac-EPKRSVAFKKT KKEVKKVATPKK (CH-1), which belongs to the C-terminal domain of histone Hl° (residues 99,121) and is adjacent to the central globular domain of the protein, were examined by means of 1H-NMR and circular dichroism. In aqueous solution, CH-1 behaved as a mainly unstructured peptide, although turn-like conformations in rapid equilibrium with the unfolded state could be present. Addition of trifluoroethanol resulted in a substantial increase of the helical content. The helical limits, as indicated by (i, i + 3) nuclear Overhauser effect (NOE) cross correlations and significant up-field conformational shifts of the C, protons, span from Pro100 to Val 116, with Glu99 and Ala117 as N- and C-caps. A structure calculation performed on the basis of distance constraints derived from NOE cross peaks in 90% trifluoroethanol confirmed the helical structure of this region. The helical region has a marked amphipathic character, due to the location of all positively charged residues on one face of the helix and all the hydrophobic residues on the opposite face. The peptide has a TPKK motif at the C-terminus, following the ,-helical region. The observed NOE connectivities suggest that the TPKK sequence adopts a type (I) ,-turn conformation, a ,-turn conformation or a combination of both, in fast equilibrium with unfolded states. Sequences of the kind (S/T)P(K/R)(K/R) have been proposed as DNA binding motifs. The CH-1 peptide, thus, combines a positively charged amphipathic helix and a turn as potential DNA-binding motifs. [source]