Literature DB >> 18417394

On the measurement of 15N-{1H} nuclear Overhauser effects.

Fabien Ferrage1, Andrea Piserchio, David Cowburn, Ranajeet Ghose.   

Abstract

Accurate quantification of the 15N-{1H} steady-state NOE is central to current methods for the elucidation of protein backbone dynamics on the fast, sub-nanosecond time scale. This experiment is highly susceptible to systematic errors arising from multiple sources. The nature of these errors and their effects on the determined NOE ratio is evaluated by a detailed analysis of the spin dynamics during the pair of experiments used to measure this ratio and possible improvements suggested. The experiment that includes 1H irradiation, is analyzed in the framework of Average Liouvillian Theory and a modified saturation scheme that generates a stable steady-state and eliminates the need to completely saturate 1H nuclei is presented. The largest source of error, however, in 1H-dilute systems at ultra-high fields is found to be an overestimation of the steady-state NOE value as a consequence of the incomplete equilibration of the magnetization in the so-called "reference experiment". The use of very long relaxation delays is usually an effective, but time consuming, solution. Here, we introduce an alternative reference experiment, designed for larger, deuterated systems, that uses the fastest relaxing component of the longitudinal magnetization as a closer approximation to the equilibrium state for shorter relaxation delays. The utility of the modified approach is illustrated through simulations on realistic spin systems over a wide range of time scales and experimentally verified using a perdeuterated sample of human ubiquitin.

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Year:  2008        PMID: 18417394      PMCID: PMC3478131          DOI: 10.1016/j.jmr.2008.03.011

Source DB:  PubMed          Journal:  J Magn Reson        ISSN: 1090-7807            Impact factor:   2.229


  22 in total

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Authors:  K Pervushin
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2.  Determination of the rotational diffusion tensor of macromolecules in solution from nmr relaxation data with a combination of exact and approximate methods--application to the determination of interdomain orientation in multidomain proteins.

Authors:  R Ghose; D Fushman; D Cowburn
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Authors:  P M Hwang; N R Skrynnikov; L E Kay
Journal:  J Biomol NMR       Date:  2001-05       Impact factor: 2.835

7.  Single Transition-to-single Transition Polarization Transfer (ST2-PT) in [15N,1H]-TROSY.

Authors:  K V Pervushin; G Wider; K Wüthrich
Journal:  J Biomol NMR       Date:  1998-08       Impact factor: 2.835

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

Authors:  N A Farrow; O Zhang; A Szabo; D A Torchia; L E Kay
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9.  Mapping chemical exchange in proteins with MW > 50 kD.

Authors:  Chunyu Wang; Mark Rance; Arthur G Palmer
Journal:  J Am Chem Soc       Date:  2003-07-30       Impact factor: 15.419

10.  Practical aspects of the 2D 15N-[1h]-NOE experiment.

Authors:  Christian Renner; Michael Schleicher; Luis Moroder; Tad A Holak
Journal:  J Biomol NMR       Date:  2002-05       Impact factor: 2.835

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  18 in total

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Authors:  Jan Heering; Hendrik R A Jonker; Frank Löhr; Harald Schwalbe; Volker Dötsch
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2.  Accurate determination of rates from non-uniformly sampled relaxation data.

Authors:  Matthew A Stetz; A Joshua Wand
Journal:  J Biomol NMR       Date:  2016-07-08       Impact factor: 2.835

3.  The Anchored Flexibility Model in LC8 Motif Recognition: Insights from the Chica Complex.

Authors:  Sarah Clark; Afua Nyarko; Frank Löhr; P Andrew Karplus; Elisar Barbar
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4.  Characterization of molecular interactions between ACP and halogenase domains in the Curacin A polyketide synthase.

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Journal:  ACS Chem Biol       Date:  2011-12-15       Impact factor: 5.100

5.  A probe to monitor performance of ¹⁵N longitudinal relaxation experiments for proteins in solution.

Authors:  Rieko Ishima
Journal:  J Biomol NMR       Date:  2014-01-05       Impact factor: 2.835

6.  Measurement of ¹⁵N relaxation rates in perdeuterated proteins by TROSY-based methods.

Authors:  Nils-Alexander Lakomek; Jinfa Ying; Ad Bax
Journal:  J Biomol NMR       Date:  2012-06-12       Impact factor: 2.835

7.  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

8.  Accurate sampling of high-frequency motions in proteins by steady-state (15)N-{(1)H} nuclear Overhauser effect measurements in the presence of cross-correlated relaxation.

Authors:  Fabien Ferrage; David Cowburn; Ranajeet Ghose
Journal:  J Am Chem Soc       Date:  2009-05-06       Impact factor: 15.419

9.  Deuterium spin probes of backbone order in proteins: 2H NMR relaxation study of deuterated carbon alpha sites.

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Journal:  J Am Chem Soc       Date:  2009-11-04       Impact factor: 15.419

10.  Solution NMR studies of Chlorella virus DNA ligase-adenylate.

Authors:  Andrea Piserchio; Pravin A Nair; Stewart Shuman; Ranajeet Ghose
Journal:  J Mol Biol       Date:  2009-11-11       Impact factor: 5.469

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