Major groove width variations in RNA structures determined by NMR and impact of 13C r
Abstract Ribonucleic acid structure determination by NMR spectroscopy relies primarily on local structural restraints provided by 1Hâ?? 1H NOEs and J-couplings. When employed loosely, these restraints are broadly compatible with A- and B-like helical geometries and give rise to calculated structures that are highly sensitive to the force fields employed during refinement. A survey of recently reported NMR structures reveals significant variations in helical parameters, particularly the major groove width. Although helical parameters observed in high-resolution X-ray crystal structures of isolated A-form RNA helices are sensitive to crystal packing effects, variations among the published X-ray structures are significantly smaller than those observed in NMR structures. Here we show that restraints derived from aromatic 1Hâ?? 13C residual dipolar couplings (RDCs) and residual chemical shift anisotropies (RCSAs) can overcome NMR restraint and force field deficiencies and afford structures with helical properties similar to those observed in high-resolution X-ray structures.
Content Type Journal Article
DOI 10.1007/s10858-010-9424-x
Authors
Blanton S. Tolbert, University of Maryland Baltimore County Howard Hughes Medical Institute and Department of Chemistry and Biochemistry 1000 Hilltop Circle Baltimore MD 21250 USA
Yasuyuki Miyazaki, University of Maryland Baltimore County Howard Hughes Medical Institute and Department of Chemistry and Biochemistry 1000 Hilltop Circle Baltimore MD 21250 USA
Shawn Barton, University of Maryland Baltimore County Howard Hughes Medical Institute and Department of Chemistry and Biochemistry 1000 Hilltop Circle Baltimore MD 21250 USA
Benyam Kinde, University of Maryland Baltimore County Howard Hughes Medical Institute and Department of Chemistry and Biochemistry 1000 Hilltop Circle Baltimore MD 21250 USA
Patrice Starck, University of Maryland Baltimore County Howard Hughes Medical Institute and Department of Chemistry and Biochemistry 1000 Hilltop Circle Baltimore MD 21250 USA
Rashmi Singh, University of Maryland Baltimore County Howard Hughes Medical Institute and Department of Chemistry and Biochemistry 1000 Hilltop Circle Baltimore MD 21250 USA
Ad Bax, NIDDK, National Institutes of Health Laboratory of Chemical Physics Bethesda MD 208992 USA
David A. Case, Rutgers University Department of Chemistry & Chemical Biology and BioMaPS Institute 610 Taylor Road Piscataway NJ 08854-8087 USA
Michael F. Summers, University of Maryland Baltimore County Howard Hughes Medical Institute and Department of Chemistry and Biochemistry 1000 Hilltop Circle Baltimore MD 21250 USA
Influence of common preanalytical variations on the metabolic profile of serum samples in biobanks
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Abstract A blood pre-centrifugation delay of 24 h at room temperature influenced the proton NMR spectroscopic profiles of human serum. A blood pre-centrifugation delay of 24 h at 4°C did not influence the spectroscopic profile as compared with 4 h delays at either room temperature or 4°C. Five or ten serum freezeâ??thaw cycles also influenced the proton NMR spectroscopic profiles. Certain common in vitro preanalytical variations occurring in biobanks may impact the metabolic profile of...
[KPWU blog] statistics of NMR/X-ray determined protein structures in PDB (up to May 10, 2011)
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Two brief plots of protein structures (protein-DNA/RNA/ligand complexes are excluded) determined by either X-ray or NMR. Structures determined by hybrid method are not counted in the two plots. The dataset was obtain from PDB based on its released statistics by May 10th, 2011. Molecules with sequence length longer than 1200 residues are also excluded. There http://stats.wordpress.com/b.gif?host=kpwu.wordpress.com&blog=76132&post=380&subd=kpwu&ref=&feed=1
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Major groove width variations in RNA structures determined by NMR and impact of 13C r
Linear Mode
