Literature DB >> 22621977

Heteronuclear Adiabatic Relaxation Dispersion (HARD) for quantitative analysis of conformational dynamics in proteins.

Nathaniel J Traaseth1, Fa-An Chao, Larry R Masterson, Silvia Mangia, Michael Garwood, Shalom Michaeli, Burckhard Seelig, Gianluigi Veglia.   

Abstract

NMR relaxation methods probe biomolecular motions over a wide range of timescales. In particular, the rotating frame spin-lock R(1ρ) and Carr-Purcell-Meiboom-Gill (CPMG) R(2) experiments are commonly used to characterize μs to ms dynamics, which play a critical role in enzyme folding and catalysis. In an effort to complement these approaches, we introduced the Heteronuclear Adiabatic Relaxation Dispersion (HARD) method, where dispersion in rotating frame relaxation rate constants (longitudinal R(1ρ) and transverse R(2ρ)) is created by modulating the shape and duration of adiabatic full passage (AFP) pulses. Previously, we showed the ability of the HARD method to detect chemical exchange dynamics in the fast exchange regime (k(ex)∼10(4)-10(5) s(-1)). In this article, we show the sensitivity of the HARD method to slower exchange processes by measuring R(1ρ) and R(2ρ) relaxation rates for two soluble proteins (ubiquitin and 10C RNA ligase). One advantage of the HARD method is its nominal dependence on the applied radio frequency field, which can be leveraged to modulate the dispersion in the relaxation rate constants. In addition, we also include product operator simulations to define the dynamic range of adiabatic R(1ρ) and R(2ρ) that is valid under all exchange regimes. We conclude from both experimental observations and simulations that this method is complementary to CPMG-based and rotating frame spin-lock R(1ρ) experiments to probe conformational exchange dynamics for biomolecules. Finally, this approach is germane to several NMR-active nuclei, where relaxation rates are frequency-offset independent.
Copyright © 2012 Elsevier Inc. All rights reserved.

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Year:  2012        PMID: 22621977      PMCID: PMC3568944          DOI: 10.1016/j.jmr.2012.03.024

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


  51 in total

1.  Transverse relaxation in the rotating frame induced by chemical exchange.

Authors:  Shalom Michaeli; Dennis J Sorce; Djaudat Idiyatullin; Kamil Ugurbil; Michael Garwood
Journal:  J Magn Reson       Date:  2004-08       Impact factor: 2.229

2.  Storage of nuclear magnetization as long-lived singlet order in low magnetic field.

Authors:  Giuseppe Pileio; Marina Carravetta; Malcolm H Levitt
Journal:  Proc Natl Acad Sci U S A       Date:  2010-09-20       Impact factor: 11.205

3.  Heteronuclear relaxation in time-dependent spin systems: (15)N-T1 (rho) dispersion during adiabatic fast passage.

Authors:  R Konrat; M Tollinger
Journal:  J Biomol NMR       Date:  1999-03       Impact factor: 2.835

Review 4.  NMR studies of protein structure and dynamics.

Authors:  Lewis E Kay
Journal:  J Magn Reson       Date:  2005-04       Impact factor: 2.229

5.  Lipid-mediated folding/unfolding of phospholamban as a regulatory mechanism for the sarcoplasmic reticulum Ca2+-ATPase.

Authors:  Martin Gustavsson; Nathaniel J Traaseth; Christine B Karim; Elizabeth L Lockamy; David D Thomas; Gianluigi Veglia
Journal:  J Mol Biol       Date:  2011-03-17       Impact factor: 5.469

6.  A dynamic knockout reveals that conformational fluctuations influence the chemical step of enzyme catalysis.

Authors:  Gira Bhabha; Jeeyeon Lee; Damian C Ekiert; Jongsik Gam; Ian A Wilson; H Jane Dyson; Stephen J Benkovic; Peter E Wright
Journal:  Science       Date:  2011-04-08       Impact factor: 47.728

7.  Fast broadband inversion by adiabatic pulses.

Authors:  T L Hwang; P C van Zijl; M Garwood
Journal:  J Magn Reson       Date:  1998-07       Impact factor: 2.229

8.  Selection and evolution of enzymes from a partially randomized non-catalytic scaffold.

Authors:  Burckhard Seelig; Jack W Szostak
Journal:  Nature       Date:  2007-08-16       Impact factor: 49.962

9.  The role of conformational entropy in molecular recognition by calmodulin.

Authors:  Michael S Marlow; Jakob Dogan; Kendra K Frederick; Kathleen G Valentine; A Joshua Wand
Journal:  Nat Chem Biol       Date:  2010-04-11       Impact factor: 15.040

10.  Evidence for dynamics in proteins as a mechanism for ligand dissociation.

Authors:  Mary J Carroll; Randall V Mauldin; Anna V Gromova; Scott F Singleton; Edward J Collins; Andrew L Lee
Journal:  Nat Chem Biol       Date:  2012-01-15       Impact factor: 15.040

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  7 in total

Review 1.  Chemical exchange in biomacromolecules: past, present, and future.

Authors:  Arthur G Palmer
Journal:  J Magn Reson       Date:  2014-04       Impact factor: 2.229

2.  Multiple frequency saturation pulses reduce CEST acquisition time for quantifying conformational exchange in biomolecules.

Authors:  Maureen Leninger; William M Marsiglia; Alexej Jerschow; Nathaniel J Traaseth
Journal:  J Biomol NMR       Date:  2018-05-23       Impact factor: 2.835

3.  Evaluating the influence of initial magnetization conditions on extracted exchange parameters in NMR relaxation experiments: applications to CPMG and CEST.

Authors:  Tairan Yuwen; Ashok Sekhar; Lewis E Kay
Journal:  J Biomol NMR       Date:  2016-07-29       Impact factor: 2.835

4.  General expressions for R1ρ relaxation for N-site chemical exchange and the special case of linear chains.

Authors:  Hans Koss; Mark Rance; Arthur G Palmer
Journal:  J Magn Reson       Date:  2016-10-27       Impact factor: 2.229

5.  Inherent conformational plasticity in dsRBDs enables interaction with topologically distinct RNAs.

Authors:  Harshad Paithankar; Guneet Singh Tarang; Firdousi Parvez; Aniket Marathe; Manali Joshi; Jeetender Chugh
Journal:  Biophys J       Date:  2022-02-05       Impact factor: 4.033

6.  Geometric Approximation: A New Computational Approach To Characterize Protein Dynamics from NMR Adiabatic Relaxation Dispersion Experiments.

Authors:  Fa-An Chao; R Andrew Byrd
Journal:  J Am Chem Soc       Date:  2016-06-07       Impact factor: 15.419

7.  Protein Dynamics revealed by NMR Relaxation Methods.

Authors:  Fa-An Chao; R Andrew Byrd
Journal:  Emerg Top Life Sci       Date:  2020-04-18
  7 in total

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