Literature DB >> 19367865

Ultrahigh resolution characterization of domain motions and correlations by multialignment and multireference residual dipolar coupling NMR.

Charles K Fisher1, Qi Zhang, Andrew Stelzer, Hashim M Al-Hashimi.   

Abstract

Nuclear magnetic resonance (NMR) residual dipolar couplings (RDCs) provide a unique opportunity for spatially characterizing complex motions in biomolecules with time scale sensitivity extending up to milliseconds. Up to five motionally averaged Wigner rotation elements, (D(0k)2(alphaalpha)), can be determined experimentally using RDCs measured in five linearly independent alignment conditions and applied to define motions of axially symmetric bond vectors. Here, we show that up to 25 motionally averaged Wigner rotation elements, (D(mk)2(alphabetagamma)), can be determined experimentally from multialignment RDCs and used to characterize rigid-body motions of chiral domains. The 25 (D(mk)2(alphabetagamma)) elements form a basis set that allows one to measure motions of a domain relative to an isotropic distribution of reference frames anchored on a second domain (and vice versa), thus expanding the 3D spatial resolution with which motions can be characterized. The 25 (D(mk)2(alphabetagamma)) elements can also be used to fit an ensemble consisting of up to eight equally or six unequally populated states. For more than two domains, changing the identity of the domain governing alignment allows access to new information regarding the correlated nature of the domain fluctuations. Example simulations are provided that validate the theoretical derivation and illustrate the high spatial resolution with which rigid-body domain motions can be characterized using multialignment and multireference RDCs. Our results further motivate the development of experimental approaches for both modulating alignment and anchoring it on specifically targeted domains.

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Year:  2008        PMID: 19367865      PMCID: PMC3320164          DOI: 10.1021/jp806188j

Source DB:  PubMed          Journal:  J Phys Chem B        ISSN: 1520-5207            Impact factor:   2.991


  35 in total

1.  Domain orientation and dynamics in multidomain proteins from residual dipolar couplings.

Authors:  M W Fischer; J A Losonczi; J L Weaver; J H Prestegard
Journal:  Biochemistry       Date:  1999-07-13       Impact factor: 3.162

2.  Amplitudes of protein backbone dynamics and correlated motions in a small alpha/beta protein: correspondence of dipolar coupling and heteronuclear relaxation measurements.

Authors:  G Marius Clore; Charles D Schwieters
Journal:  Biochemistry       Date:  2004-08-24       Impact factor: 3.162

Review 3.  Weak alignment NMR: a hawk-eyed view of biomolecular structure.

Authors:  Ad Bax; Alexander Grishaev
Journal:  Curr Opin Struct Biol       Date:  2005-10       Impact factor: 6.809

Review 4.  New tools provide new insights in NMR studies of protein dynamics.

Authors:  Anthony Mittermaier; Lewis E Kay
Journal:  Science       Date:  2006-04-14       Impact factor: 47.728

5.  Resolving the motional modes that code for RNA adaptation.

Authors:  Qi Zhang; Xiaoyan Sun; Eric D Watt; Hashim M Al-Hashimi
Journal:  Science       Date:  2006-02-03       Impact factor: 47.728

6.  Characterizing complex dynamics in the transactivation response element apical loop and motional correlations with the bulge by NMR, molecular dynamics, and mutagenesis.

Authors:  Elizabeth A Dethoff; Alexandar L Hansen; Catherine Musselman; Eric D Watt; Ioan Andricioaei; Hashim M Al-Hashimi
Journal:  Biophys J       Date:  2008-07-11       Impact factor: 4.033

7.  NMR evidence for slow collective motions in cyanometmyoglobin.

Authors:  J R Tolman; J M Flanagan; M A Kennedy; J H Prestegard
Journal:  Nat Struct Biol       Date:  1997-04

8.  Order matrix analysis of residual dipolar couplings using singular value decomposition.

Authors:  J A Losonczi; M Andrec; M W Fischer; J H Prestegard
Journal:  J Magn Reson       Date:  1999-06       Impact factor: 2.229

9.  Direct measurement of distances and angles in biomolecules by NMR in a dilute liquid crystalline medium.

Authors:  N Tjandra; A Bax
Journal:  Science       Date:  1997-11-07       Impact factor: 47.728

10.  Nuclear magnetic dipole interactions in field-oriented proteins: information for structure determination in solution.

Authors:  J R Tolman; J M Flanagan; M A Kennedy; J H Prestegard
Journal:  Proc Natl Acad Sci U S A       Date:  1995-09-26       Impact factor: 11.205

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  11 in total

Review 1.  NMR studies of dynamic biomolecular conformational ensembles.

Authors:  Dennis A Torchia
Journal:  Prog Nucl Magn Reson Spectrosc       Date:  2014-11-28       Impact factor: 9.795

Review 2.  Domain-elongation NMR spectroscopy yields new insights into RNA dynamics and adaptive recognition.

Authors:  Qi Zhang; Hashim M Al-Hashimi
Journal:  RNA       Date:  2009-09-23       Impact factor: 4.942

Review 3.  Characterizing RNA dynamics at atomic resolution using solution-state NMR spectroscopy.

Authors:  Jameson R Bothe; Evgenia N Nikolova; Catherine D Eichhorn; Jeetender Chugh; Alexandar L Hansen; Hashim M Al-Hashimi
Journal:  Nat Methods       Date:  2011-10-28       Impact factor: 28.547

4.  Unveiling Inherent Degeneracies in Determining Population-Weighted Ensembles of Interdomain Orientational Distributions Using NMR Residual Dipolar Couplings: Application to RNA Helix Junction Helix Motifs.

Authors:  Shan Yang; Hashim M Al-Hashimi
Journal:  J Phys Chem B       Date:  2015-07-17       Impact factor: 2.991

5.  Approximate reconstruction of continuous spatially complex domain motions by multialignment NMR residual dipolar couplings.

Authors:  Charles K Fisher; Hashim M Al-Hashimi
Journal:  J Phys Chem B       Date:  2009-05-07       Impact factor: 2.991

6.  The internal dynamics of mini c TAR DNA probed by electron paramagnetic resonance of nitroxide spin-labels at the lower stem, the loop, and the bulge.

Authors:  Yan Sun; Ziwei Zhang; Vladimir M Grigoryants; William K Myers; Fei Liu; Keith A Earle; Jack H Freed; Charles P Scholes
Journal:  Biochemistry       Date:  2012-10-18       Impact factor: 3.162

7.  Modulating RNA Alignment Using Directional Dynamic Kinks: Application in Determining an Atomic-Resolution Ensemble for a Hairpin using NMR Residual Dipolar Couplings.

Authors:  Loïc Salmon; George M Giambaşu; Evgenia N Nikolova; Katja Petzold; Akash Bhattacharya; David A Case; Hashim M Al-Hashimi
Journal:  J Am Chem Soc       Date:  2015-09-29       Impact factor: 15.419

8.  Enhanced Sampling of Interdomain Motion Using Map-Restrained Langevin Dynamics and NMR: Application to Pin1.

Authors:  Jill J Bouchard; Junchao Xia; David A Case; Jeffrey W Peng
Journal:  J Mol Biol       Date:  2018-05-16       Impact factor: 5.469

9.  NMR studies of nucleic acid dynamics.

Authors:  Hashim M Al-Hashimi
Journal:  J Magn Reson       Date:  2013-09-03       Impact factor: 2.229

10.  Constructing atomic-resolution RNA structural ensembles using MD and motionally decoupled NMR RDCs.

Authors:  Andrew C Stelzer; Aaron T Frank; Maximillian H Bailor; Ioan Andricioaei; Hashim M Al-Hashimi
Journal:  Methods       Date:  2009-08-21       Impact factor: 3.608

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