Literature DB >> 10070755

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

D Fushman1, D Cowburn.   

Abstract

Current approaches to 15N relaxation in proteins assume that the 15N-1H dipolar and 15N CSA tensors are collinear. We show theoretically that, when there is significant anisotropy of molecular rotation, different orientations of the two tensors, experimentally observed in proteins, nucleic acids, and small peptides, will result in differences in site-specific correlation functions and spectral densities. The standard treatments of the rates of longitudinal and transverse relaxation of amide 15N nuclei, of the 15N CSA/15N-1H dipolar cross correlation, and of the TROSY experiment are extended to account for the effect of noncollinearity of the 15N-1H dipolar and 15N CSA (chemical shift anisotropy) tensors. This effect, proportional to the degree of anisotropy of the overall motion, (D parallel/D perpendicular - 1), is sensitive to the relative orientation of the two tensors and to the orientation of the peptide plane with respect to the diffusion coordinate frame. The effect is negligible at small degrees of anisotropy, but is predicted to become significant for D parallel/D perpendicular > or = 1.5, and at high magnetic fields. The effect of noncollinearity of 15N CSA and 15N-1H dipolar interaction is sensitive to both gross (hydrodynamic) properties and atomic-level details of protein structure. Incorporation of this effect into relaxation data analysis is likely to improve both precision and accuracy of the derived characteristics of protein dynamics, especially at high magnetic fields and for molecules with a high degree of anisotropy of the overall motion. The effect will also make TROSY efficiency dependent on local orientation in moderately anisotropic systems.

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Year:  1999        PMID: 10070755     DOI: 10.1023/a:1008349331773

Source DB:  PubMed          Journal:  J Biomol NMR        ISSN: 0925-2738            Impact factor:   2.835


  9 in total

1.  Rotational diffusion anisotropy of proteins from simultaneous analysis of 15N and 13C alpha nuclear spin relaxation.

Authors:  L K Lee; M Rance; W J Chazin; A G Palmer
Journal:  J Biomol NMR       Date:  1997-04       Impact factor: 2.835

2.  Orientational constraints as three-dimensional structural constraints from chemical shift anisotropy: the polypeptide backbone of gramicidin A in a lipid bilayer.

Authors:  W Mai; W Hu; C Wang; T A Cross
Journal:  Protein Sci       Date:  1993-04       Impact factor: 6.725

Review 3.  The second decade--into the third millenium.

Authors:  K Wüthrich
Journal:  Nat Struct Biol       Date:  1998-07

4.  Contributions to conformational entropy arising from bond vector fluctuations measured from NMR-derived order parameters: application to protein folding.

Authors:  D Yang; L E Kay
Journal:  J Mol Biol       Date:  1996-10-25       Impact factor: 5.469

5.  Defining long range order in NMR structure determination from the dependence of heteronuclear relaxation times on rotational diffusion anisotropy.

Authors:  N Tjandra; D S Garrett; A M Gronenborn; A Bax; G M Clore
Journal:  Nat Struct Biol       Date:  1997-06

6.  New methods of structure refinement for macromolecular structure determination by NMR.

Authors:  G M Clore; A M Gronenborn
Journal:  Proc Natl Acad Sci U S A       Date:  1998-05-26       Impact factor: 11.205

7.  The solution structure and dynamics of the pleckstrin homology domain of G protein-coupled receptor kinase 2 (beta-adrenergic receptor kinase 1). A binding partner of Gbetagamma subunits.

Authors:  D Fushman; T Najmabadi-Haske; S Cahill; J Zheng; H LeVine; D Cowburn
Journal:  J Biol Chem       Date:  1998-01-30       Impact factor: 5.157

8.  Attenuated T2 relaxation by mutual cancellation of dipole-dipole coupling and chemical shift anisotropy indicates an avenue to NMR structures of very large biological macromolecules in solution.

Authors:  K Pervushin; R Riek; G Wider; K Wüthrich
Journal:  Proc Natl Acad Sci U S A       Date:  1997-11-11       Impact factor: 11.205

9.  Backbone dynamics of proteins as studied by 15N inverse detected heteronuclear NMR spectroscopy: application to staphylococcal nuclease.

Authors:  L E Kay; D A Torchia; A Bax
Journal:  Biochemistry       Date:  1989-11-14       Impact factor: 3.162

  9 in total
  18 in total

1.  Refinement of the protein backbone angle psi in NMR structure calculations.

Authors:  R Sprangers; M J Bottomley; J P Linge; J Schultz; M Nilges; M Sattler
Journal:  J Biomol NMR       Date:  2000-01       Impact factor: 2.835

2.  Efficient analysis of macromolecular rotational diffusion from heteronuclear relaxation data.

Authors:  P Dosset; J C Hus; M Blackledge; D Marion
Journal:  J Biomol NMR       Date:  2000-01       Impact factor: 2.835

3.  Determining protein dynamics from ¹⁵N relaxation data by using DYNAMICS.

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

4.  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

5.  Compensating increases in protein backbone flexibility occur when the Dead ringer AT-rich interaction domain (ARID) binds DNA: a nitrogen-15 relaxation study.

Authors:  Junji Iwahara; Robert D Peterson; Robert T Clubb
Journal:  Protein Sci       Date:  2005-03-31       Impact factor: 6.725

6.  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.

Authors:  Jennifer B Hall; David Fushman
Journal:  J Am Chem Soc       Date:  2006-06-21       Impact factor: 15.419

7.  NMR solution structure and backbone dynamics of domain III of the E protein of tick-borne Langat flavivirus suggests a potential site for molecular recognition.

Authors:  Munia Mukherjee; Kaushik Dutta; Mark A White; David Cowburn; Robert O Fox
Journal:  Protein Sci       Date:  2006-06       Impact factor: 6.725

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.  Transverse relaxation optimized triple-resonance NMR experiments for nucleic acids.

Authors:  R Fiala; J Czernek; V Sklenár
Journal:  J Biomol NMR       Date:  2000-04       Impact factor: 2.835

10.  Conformational dynamics and structural plasticity play critical roles in the ubiquitin recognition of a UIM domain.

Authors:  Nikolaos G Sgourakis; Mayank M Patel; Angel E Garcia; George I Makhatadze; Scott A McCallum
Journal:  J Mol Biol       Date:  2010-01-04       Impact factor: 5.469

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