Literature DB >> 16771499

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.

Jennifer B Hall1, David Fushman.   

Abstract

We applied a combination of 15N relaxation and CSA/dipolar cross-correlation measurements at five magnetic fields (9.4, 11.7, 14.1, 16.4, and 18.8 T) to determine the 15N chemical shielding tensors for backbone amides in protein G in solution. The data were analyzed using various model-independent approaches and those based on Lipari-Szabo approximation, all of them yielding similar results. The results indicate a range of site-specific values of the anisotropy (CSA) and orientation of the 15N chemical shielding tensor, similar to those in ubiquitin (Fushman, et al. J. Am. Chem. Soc. 1998, 120, 10947; J. Am. Chem. Soc. 1999, 121, 8577). Assuming a Gaussian distribution of the 15N CSA values, the mean anisotropy is -173.9 to -177.2 ppm (for 1.02 A NH bond length) and the site-to-site CSA variability is +/-17.6 to +/-21.4 ppm, depending on the method used. This CSA variability is significantly larger than derived previously for ribonuclease H (Kroenke, et al. J. Am. Chem. Soc. 1999, 121, 10119) or recently, using "meta-analysis" for ubiquitin (Damberg, et al. J. Am. Chem. Soc. 2005, 127, 1995). Standard interpretation of 15N relaxation studies of backbone dynamics in proteins involves an a priori assumption of a uniform 15N CSA. We show that this assumption leads to a significant discrepancy between the order parameters obtained at different fields. Using the site-specific CSAs obtained from our study removes this discrepancy and allows simultaneous fit of relaxation data at all five fields to Lipari-Szabo spectral densities. These findings emphasize the necessity of taking into account the variability of 15N CSA for accurate analysis of protein dynamics from 15N relaxation measurements.

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Year:  2006        PMID: 16771499      PMCID: PMC2519110          DOI: 10.1021/ja060406x

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


  31 in total

1.  Assessing potential bias in the determination of rotational correlation times of proteins by NMR relaxation.

Authors:  A L Lee; A J Wand
Journal:  J Biomol NMR       Date:  1999-02       Impact factor: 2.835

2.  Direct measurement of the 15N CSA/dipolar relaxation interference from coupled HSQC spectra.

Authors:  Jennifer B Hall; Kwaku T Dayie; David Fushman
Journal:  J Biomol NMR       Date:  2003-06       Impact factor: 2.835

3.  15N chemical shift anisotropy in protein structure refinement and comparison with NH residual dipolar couplings.

Authors:  Rebecca S Lipsitz; Nico Tjandra
Journal:  J Magn Reson       Date:  2003-09       Impact factor: 2.229

4.  Site-specific variations of carbonyl chemical shift anisotropies in proteins.

Authors:  Phineus R L Markwick; Michael Sattler
Journal:  J Am Chem Soc       Date:  2004-09-22       Impact factor: 15.419

5.  Quantitative estimation of magnitude and orientation of the CSA tensor from field dependence of longitudinal NMR relaxation rates.

Authors:  P Damberg; J Jarvet; P Allard; A Gräslund
Journal:  J Biomol NMR       Date:  1999-09       Impact factor: 2.835

6.  Protein backbone angle restraints from searching a database for chemical shift and sequence homology.

Authors:  G Cornilescu; F Delaglio; A Bax
Journal:  J Biomol NMR       Date:  1999-03       Impact factor: 2.835

7.  The effect of noncollinearity of 15N-1H dipolar and 15N CSA tensors and rotational anisotropy on 15N relaxation, CSA/dipolar cross correlation, and TROSY.

Authors:  D Fushman; D Cowburn
Journal:  J Biomol NMR       Date:  1999-02       Impact factor: 2.835

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

Authors:  Peter Damberg; Jüri Jarvet; Astrid Gräslund
Journal:  J Am Chem Soc       Date:  2005-02-16       Impact factor: 15.419

9.  Spectral density function mapping using 15N relaxation data exclusively.

Authors:  N A Farrow; O Zhang; A Szabo; D A Torchia; L E Kay
Journal:  J Biomol NMR       Date:  1995-09       Impact factor: 2.835

Review 10.  Chemical shifts and three-dimensional protein structures.

Authors:  E Oldfield
Journal:  J Biomol NMR       Date:  1995-04       Impact factor: 2.835

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  44 in total

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Authors:  David Fushman
Journal:  Methods Mol Biol       Date:  2012

2.  Ultrahigh resolution protein structures using NMR chemical shift tensors.

Authors:  Benjamin J Wylie; Lindsay J Sperling; Andrew J Nieuwkoop; W Trent Franks; Eric Oldfield; Chad M Rienstra
Journal:  Proc Natl Acad Sci U S A       Date:  2011-10-03       Impact factor: 11.205

Review 3.  Chemical shift tensor - the heart of NMR: Insights into biological aspects of proteins.

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Journal:  Prog Nucl Magn Reson Spectrosc       Date:  2010-05-07       Impact factor: 9.795

4.  Structural analysis of protein dynamics by MD simulations and NMR spin-relaxation.

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Journal:  Proteins       Date:  2008-05-01

5.  Protein conformational flexibility prediction using machine learning.

Authors:  Oleg Trott; Keri Siggers; Burkhard Rost; Arthur G Palmer
Journal:  J Magn Reson       Date:  2008-02-01       Impact factor: 2.229

6.  NMR structure note: alkaline proteinase inhibitor APRin from Pseudomonas aeruginosa.

Authors:  Sengodagounder Arumugam; Robert D Gray; Andrew N Lane
Journal:  J Biomol NMR       Date:  2008-01-24       Impact factor: 2.835

7.  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

8.  Deriving quantitative dynamics information for proteins and RNAs using ROTDIF with a graphical user interface.

Authors:  Konstantin Berlin; Andrew Longhini; T Kwaku Dayie; David Fushman
Journal:  J Biomol NMR       Date:  2013-10-30       Impact factor: 2.835

9.  Internal protein dynamics on ps to μs timescales as studied by multi-frequency (15)N solid-state NMR relaxation.

Authors:  Tatiana Zinkevich; Veniamin Chevelkov; Bernd Reif; Kay Saalwächter; Alexey Krushelnitsky
Journal:  J Biomol NMR       Date:  2013-09-19       Impact factor: 2.835

10.  Structure and dynamics of the second CARD of human RIG-I provide mechanistic insights into regulation of RIG-I activation.

Authors:  Fabien Ferrage; Kaushik Dutta; Estanislao Nistal-Villán; Jenish R Patel; María T Sánchez-Aparicio; Pablo De Ioannes; Angeliki Buku; Gloria González Aseguinolaza; Adolfo García-Sastre; Aneel K Aggarwal
Journal:  Structure       Date:  2012-10-11       Impact factor: 5.006

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