Related ArticlesConformational variation of the central CG site in d(ATGACGTCAT)2 and d(GAAAACGTTTTC)2. An NMR, molecular modelling and 3D-homology investigation.
Eur J Biochem. 1999 May;261(3):722-33
Authors: Cordier C, Marcourt L, Petitjean M, Dodin G
The determination of the solution structure of two self-complementary oligomers d(ATGACGTCAT)2 (CG10) and d(GAAAACGTTTTC)2 (CG12), both containing the 5'-pur-ACGT-pyr-3' sequence, is reported. The impact of the base context on the conformation of the central CpG site has been examined by a combined approach of: (a) 2D 1H-NMR and 31P-NMR; (b) molecular mechanics under experimental constraints; (c) back-calculations of NOESY spectra and iterative refinements of distances; and (d) 3D-homology search of the central tetrad ACGT within the complete oligonucleotides. A full NMR study of each fragment is achieved by means of standard 2D experiments: NOESY, 2D homonuclear Hartmann-Hahn spectroscopy, double-quantum-filtered COSY and heteronuclear 1H-31P correlation. Sugar phase angle, epsilon-zeta difference angle and NOE-derived distances are input as experimental constraints to generate molecular models by energy minimization with the help of jumna. The morass program is used to iteratively refine the structures obtained. The similarity of the two ACGTs within the whole oligonucleotides is investigated. Both the decamer and the dodecamer adopt a B-like DNA conformation. However, the helical parameters within this conformational type are significantly different in CG12 and CG10. The central CpG step conformation is not locked by its nearest environment (5'A and 3'T) as seen from the structural analysis of ACGT in the two molecules. In CG12, despite the presence of runs of A-T pairs, CpG presents a high twist of 43 degrees and a sugar phase at the guanine of about 180 degrees, previously observed in other ACGT-containing-oligomers. Conversely, ACGT in CG10 exhibits strong inclinations, positive rolls, a flat profile of sugar phase, twist and glycosidic angles, as a result of the nucleotide sequence extending beyond the tetrad. The structural specificity of CG10 and its flexibility (as reflected by its energy) are tentatively related to the process of recognition of the cyclic AMP response element by its cognate protein.
Site-Specific Solid-State NMR Detection of Hydrogen-Deuterium Exchange Reveals Conformational Changes in a 7-Helical Transmembrane Protein.
Site-Specific Solid-State NMR Detection of Hydrogen-Deuterium Exchange Reveals Conformational Changes in a 7-Helical Transmembrane Protein.
Site-Specific Solid-State NMR Detection of Hydrogen-Deuterium Exchange Reveals Conformational Changes in a 7-Helical Transmembrane Protein.
Biophys J. 2011 Aug 3;101(3):L23-L25
Authors: Wang S, Shi L, Kawamura I, Brown LS, Ladizhansky V
Solid-state NMR spectroscopy is an efficient tool for following conformational dynamics of membrane proteins at atomic resolution. We used this technique for the site-specific...
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1H NMR-based metabolic profiling reveals inherent biological variation in yeast and nematode model systems
1H NMR-based metabolic profiling reveals inherent biological variation in yeast and nematode model systems
Abstract The application of metabolomics to human and animal model systems is poised to provide great insight into our understanding of disease etiology and the metabolic changes that are associated with these conditions. However, metabolomic studies have also revealed that there is significant, inherent biological variation in human samples and even in samples from animal model systems where the animals are housed under carefully controlled conditions. This inherent biological...
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Measurement of multiple torsional angles from one-dimensional solid-state NMR spectra: application to the conformational analysis of a ligand in its biological receptor site.
Measurement of multiple torsional angles from one-dimensional solid-state NMR spectra: application to the conformational analysis of a ligand in its biological receptor site.
Measurement of multiple torsional angles from one-dimensional solid-state NMR spectra: application to the conformational analysis of a ligand in its biological receptor site.
Phys Chem Chem Phys. 2010 Nov 14;12(42):13999-4008
Authors: Edwards R, Madine J, Fielding L, Middleton DA
Knowledge of the three-dimensional structure of a ligand in the binding site of its biological...
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[NMR paper] Probing site-specific conformational distributions in protein folding with solid-stat
Probing site-specific conformational distributions in protein folding with solid-state NMR.
Related Articles Probing site-specific conformational distributions in protein folding with solid-state NMR.
Proc Natl Acad Sci U S A. 2005 Mar 1;102(9):3284-9
Authors: Havlin RH, Tycko R
We demonstrate an experimental approach to structural studies of unfolded and partially folded proteins in which conformational distributions are probed at a site-specific level by 2D solid-state 13C NMR spectroscopy of glassy frozen solutions. Experiments on chemical...
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[NMR paper] Analysis of stress in the active site of myosin accompanied by conformational changes
Analysis of stress in the active site of myosin accompanied by conformational changes in transient state intermediate complexes using photoaffinity labeling and 19F-NMR spectroscopy.
Related Articles Analysis of stress in the active site of myosin accompanied by conformational changes in transient state intermediate complexes using photoaffinity labeling and 19F-NMR spectroscopy.
Eur J Biochem. 1998 Mar 15;252(3):520-9
Authors: Maruta S, Henry GD, Ohki T, Kambara T, Sykes BD, Ikebe M
Myosin forms stable ternary complexes with ADP and the...
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[NMR paper] Conformational preferences of synthetic peptides derived from the immunodominant site
Conformational preferences of synthetic peptides derived from the immunodominant site of the circumsporozoite protein of Plasmodium falciparum by 1H NMR.
Related Articles Conformational preferences of synthetic peptides derived from the immunodominant site of the circumsporozoite protein of Plasmodium falciparum by 1H NMR.
Biochemistry. 1990 Aug 28;29(34):7828-37
Authors: Dyson HJ, Satterthwait AC, Lerner RA, Wright PE
Proton nuclear magnetic resonance and ultraviolet circular dichroism spectroscopy have been used to probe the conformational...
CSA variation: how reliable model-free dynamics is
The following paper shows, in particular, how site-specific variations of 15N chemical shift anisotropy (CSA) can cause under- and overestimation of protein mobility that is inferred from the order parameter of model-free analysis.
Limited variations in 15N CSA magnitudes and orientations in ubiquitin are revealed by joint analysis of longitudinal and transverse NMR relaxation.
Damberg P, Jarvet J, Graslund A.
Department of Biochemistry and Biophysics, Stockholm University, Svante Arrheniusv.12, S-106 91 Stockholm, Sweden.
J Am Chem Soc. 2005 Feb 16;127(6):1995-2005.
Conformational variation of the central CG site in d(ATGACGTCAT)2 and d(GAAAACGTTTTC)
Linear Mode
