Literature DB >> 15504678

A phase cycle scheme that significantly suppresses offset-dependent artifacts in the R2-CPMG 15N relaxation experiment.

Grover N B Yip1, Erik R P Zuiderweg.   

Abstract

R2-CPMG 15N relaxation experiments form the basis of NMR dynamics measurements, both for analysis of nano-pico second dynamics and milli-micro second dynamics (kinetics). It has been known for some time that in the practical limit of finite pulse widths, which becomes acute when using cryogenic probes, systematic errors in the apparent R2 relaxation behavior occur for spins far off-resonance from the RF carrier. Inaccurate measurement of R2 rates propagates into quantitative models such as model-free relaxation analysis, rotational diffusion tensor analysis, and relaxation dispersion. The root of the problem stems from evolution of the magnetization vectors out of the XY-plane, both during the pulses as well as between the pulses. These deviations vary as a function of pulse length, number of applied CPMG pulses, and CPMG inter-pulse delay. Herein, we analyze these effects in detail with experimentation, numerical simulations, and analytical equations. Our work suggests a surprisingly simple change in the phase progression of the CPMG pulses, which leads to a remarkable improvement in performance. First, the applicability range of the CPMG experiment is increased by a factor of two in spectral width; second, the dynamical/kinetic processes that can be assessed are significantly extended towards the slower time scale; finally, the robustness of the relaxation dispersion experiments is greatly improved.

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Year:  2004        PMID: 15504678     DOI: 10.1016/j.jmr.2004.06.021

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


  37 in total

1.  Conformational selection and substrate binding regulate the monomer/dimer equilibrium of the C-terminal domain of Escherichia coli enzyme I.

Authors:  Vincenzo Venditti; G Marius Clore
Journal:  J Biol Chem       Date:  2012-06-21       Impact factor: 5.157

2.  Structural plasticity and Mg2+ binding properties of RNase P P4 from combined analysis of NMR residual dipolar couplings and motionally decoupled spin relaxation.

Authors:  Melissa M Getz; Andy J Andrews; Carol A Fierke; Hashim M Al-Hashimi
Journal:  RNA       Date:  2006-12-28       Impact factor: 4.942

3.  Dynamically driven ligand selectivity in cyclic nucleotide binding domains.

Authors:  Rahul Das; Somenath Chowdhury; Mohammad T Mazhab-Jafari; Soumita Sildas; Rajeevan Selvaratnam; Giuseppe Melacini
Journal:  J Biol Chem       Date:  2009-04-29       Impact factor: 5.157

4.  Probing the transient dark state of substrate binding to GroEL by relaxation-based solution NMR.

Authors:  David S Libich; Nicolas L Fawzi; Jinfa Ying; G Marius Clore
Journal:  Proc Natl Acad Sci U S A       Date:  2013-06-24       Impact factor: 11.205

5.  Enhanced accuracy of kinetic information from CT-CPMG experiments by transverse rotating-frame spectroscopy.

Authors:  David Ban; Adam Mazur; Marta G Carneiro; T Michael Sabo; Karin Giller; Leonardus M I Koharudin; Stefan Becker; Angela M Gronenborn; Christian Griesinger; Donghan Lee
Journal:  J Biomol NMR       Date:  2013-08-15       Impact factor: 2.835

6.  Simple tests for the validation of multiple field spin relaxation data.

Authors:  Sébastien Morin; Stéphane M Gagné
Journal:  J Biomol NMR       Date:  2009-10-20       Impact factor: 2.835

7.  Chemical exchange effects during refocusing pulses in constant-time CPMG relaxation dispersion experiments.

Authors:  Wazo Myint; Rieko Ishima
Journal:  J Biomol NMR       Date:  2009-07-19       Impact factor: 2.835

8.  Conformational dynamics are a key factor in signaling mediated by the receiver domain of a sensor histidine kinase from Arabidopsis thaliana.

Authors:  Olga Otrusinová; Gabriel Demo; Petr Padrta; Zuzana Jaseňáková; Blanka Pekárová; Zuzana Gelová; Agnieszka Szmitkowska; Pavel Kadeřávek; Séverine Jansen; Milan Zachrdla; Tomáš Klumpler; Jaromír Marek; Jozef Hritz; Lubomír Janda; Hideo Iwaï; Michaela Wimmerová; Jan Hejátko; Lukáš Žídek
Journal:  J Biol Chem       Date:  2017-08-31       Impact factor: 5.157

9.  A methyl 1H double quantum CPMG experiment to study protein conformational exchange.

Authors:  Anusha B Gopalan; Tairan Yuwen; Lewis E Kay; Pramodh Vallurupalli
Journal:  J Biomol NMR       Date:  2018-10-01       Impact factor: 2.835

10.  Active Site Breathing of Human Alkbh5 Revealed by Solution NMR and Accelerated Molecular Dynamics.

Authors:  Jeffrey A Purslow; Trang T Nguyen; Timothy K Egner; Rochelle R Dotas; Balabhadra Khatiwada; Vincenzo Venditti
Journal:  Biophys J       Date:  2018-10-11       Impact factor: 4.033

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