Literature DB >> 15701036

Limited variations in 15N CSA magnitudes and orientations in ubiquitin are revealed by joint analysis of longitudinal and transverse NMR relaxation.

Peter Damberg1, Jüri Jarvet, Astrid Gräslund.   

Abstract

The site-specific magnitudes and orientations of the chemical shift tensors have been estimated for 70 backbone (15)N-nuclei in human ubiquitin from the field dependence of dynamic independent ratios between relaxation rates, both longitudinal and transverse, measured at 9.4, 11.7, 14.1, and 18.8 T. The results were jointly analyzed with previously published relaxation data [Fushman; Tjandra; Cowburn. J.Am. Chem. Soc. 1998, 120, 10947-10952] [Kover; Batta. J. Mag. Reson. 2001, 150, 137-146]. The effective magnitudes of the anisotropies distribute around 169 ppm with a variability of 5 ppm. The orientation factors, reflecting the orientation of the CSA relative to the NH bond, distribute around -0.80 with a variability of 0.04, which corresponds to an angle between the symmetry axis of an assumed axially symmetric shielding tensor and the NH bond of 21.4 degrees, and a variability of 2.3 degrees. Correlations with the isotropic (15)N-chemical shifts are observed. Variations in the shielding anisotropies add uncertainty to the obtained order parameters proportional to the square of the magnetic field, when data are analyzed using an assumed invariant CSA tensor for all sites. Around 3% additional uncertainty in the order parameters for 800 MHz data is expected. The optimal TROSY field for amide nitrogen TROSY is estimated, with only marginal variations due to site-to-site variations. Variations in the shielding tensors add uncertainty to the exchange terms calculated from cross-correlation rates. An approach for estimating the exchange terms is suggested, where the uncertainty due to CSA-variations is minimized.

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Year:  2005        PMID: 15701036     DOI: 10.1021/ja045956e

Source DB:  PubMed          Journal:  J Am Chem Soc        ISSN: 0002-7863            Impact factor:   15.419


  22 in total

Review 1.  Structural dynamics of bio-macromolecules by NMR: the slowly relaxing local structure approach.

Authors:  Eva Meirovitch; Yury E Shapiro; Antonino Polimeno; Jack H Freed
Journal:  Prog Nucl Magn Reson Spectrosc       Date:  2010-05       Impact factor: 9.795

2.  Protein dynamics from NMR: the slowly relaxing local structure analysis compared with model-free analysis.

Authors:  Eva Meirovitch; Yury E Shapiro; Antonino Polimeno; Jack H Freed
Journal:  J Phys Chem A       Date:  2006-07-13       Impact factor: 2.781

3.  Variability of the 15N chemical shielding tensors in the B3 domain of protein G from 15N relaxation measurements at several fields. Implications for backbone order parameters.

Authors:  Jennifer B Hall; David Fushman
Journal:  J Am Chem Soc       Date:  2006-06-21       Impact factor: 15.419

4.  Maximum entropy reconstruction of joint phi, psi-distribution with a coil-library prior: the backbone conformation of the peptide hormone motilin in aqueous solution from phi and psi-dependent J-couplings.

Authors:  Tariq Massad; Jüri Jarvet; Risto Tanner; Katrin Tomson; Julia Smirnova; Peep Palumaa; Mariko Sugai; Toshiyuki Kohno; Kalju Vanatalu; Peter Damberg
Journal:  J Biomol NMR       Date:  2007-04-26       Impact factor: 2.835

5.  Vibrational averaging of chemical shift anisotropies in model peptides.

Authors:  Sishi Tang; David A Case
Journal:  J Biomol NMR       Date:  2007-06-12       Impact factor: 2.835

6.  Quantifying protein dynamics in the ps-ns time regime by NMR relaxation.

Authors:  Griselda Hernández; David M LeMaster
Journal:  J Biomol NMR       Date:  2016-10-12       Impact factor: 2.835

7.  Determination of 15N chemical shift anisotropy from a membrane-bound protein by NMR spectroscopy.

Authors:  Manoj Kumar Pandey; Subramanian Vivekanandan; Shivani Ahuja; Kumar Pichumani; Sang-Choul Im; Lucy Waskell; Ayyalusamy Ramamoorthy
Journal:  J Phys Chem B       Date:  2012-06-04       Impact factor: 2.991

8.  Structure and Dynamics of Ribosomal Protein L12: An Ensemble Model Based on SAXS and NMR Relaxation.

Authors:  Pau Bernadó; Kristofer Modig; Przemysław Grela; Dmitri I Svergun; Marek Tchorzewski; Miquel Pons; Mikael Akke
Journal:  Biophys J       Date:  2010-05-19       Impact factor: 4.033

9.  Application of the random coil index to studying protein flexibility.

Authors:  Mark V Berjanskii; David S Wishart
Journal:  J Biomol NMR       Date:  2007-11-06       Impact factor: 2.835

10.  Influence of the O-phosphorylation of serine, threonine and tyrosine in proteins on the amidic ¹⁵N chemical shielding anisotropy tensors.

Authors:  Jiří Emmer; Andrea Vavrinská; Vladimír Sychrovský; Ladislav Benda; Zdeněk Kříž; Jaroslav Koča; Rolf Boelens; Vladimír Sklenář; Lukáš Trantírek
Journal:  J Biomol NMR       Date:  2012-12-01       Impact factor: 2.835

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