Literature DB >> 20703963

Structural constraints from residual tensorial couplings in high resolution NMR without an explicit term for the alignment tensor.

S Moltke1, S Grzesiek.   

Abstract

Structural restraints from residual tensorial couplings in high resolution NMR are usually incorporated into molecular structure calculation programs by an energy penalty function which depends on the knowledge of the alignment tensor. Here, we show that the alignment tensor enters in linear form into such a function. Therefore, the explicit appearance of the alignment tensor can be eliminated from the penalty function. This avoids the necessity of a determination of magnitude and rhombicity of the alignment tensor in the absence of structural information. The price for this procedure is a slightly shallower energy landscape. Simulations in the vicinity of the energy minimum for the backbone of human ubiquitin show that the reduction in curvature is on the order of a few percent.

Entities:  

Year:  1999        PMID: 20703963     DOI: 10.1023/A:1008309630377

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.  A robust method for determining the magnitude of the fully asymmetric alignment tensor of oriented macromolecules in the absence of structural information.

Authors:  G M Clore; A M Gronenborn; A Bax
Journal:  J Magn Reson       Date:  1998-07       Impact factor: 2.229

3.  Direct structure refinement against residual dipolar couplings in the presence of rhombicity of unknown magnitude.

Authors:  G M Clore; A M Gronenborn; N Tjandra
Journal:  J Magn Reson       Date:  1998-03       Impact factor: 2.229

4.  Structure of ubiquitin refined at 1.8 A resolution.

Authors:  S Vijay-Kumar; C E Bugg; W J Cook
Journal:  J Mol Biol       Date:  1987-04-05       Impact factor: 5.469

5.  Use of dipolar 1H-15N and 1H-13C couplings in the structure determination of magnetically oriented macromolecules in solution.

Authors:  N Tjandra; J G Omichinski; A M Gronenborn; G M Clore; A Bax
Journal:  Nat Struct Biol       Date:  1997-09

6.  Torsion angle dynamics for NMR structure calculation with the new program DYANA.

Authors:  P Güntert; C Mumenthaler; K Wüthrich
Journal:  J Mol Biol       Date:  1997-10-17       Impact factor: 5.469

7.  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

8.  Long-range motional restrictions in a multidomain zinc-finger protein from anisotropic tumbling.

Authors:  R Brüschweiler; X Liao; P E Wright
Journal:  Science       Date:  1995-05-12       Impact factor: 47.728

9.  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

  9 in total
  12 in total

1.  Transverse relaxation optimised spin-state selective NMR experiments for measurement of residual dipolar couplings.

Authors:  P Permi; A Annila
Journal:  J Biomol NMR       Date:  2000-03       Impact factor: 2.835

2.  An easy way to include weak alignment constraints into NMR structure calculations.

Authors:  H J Sass; G Musco; S J Stahl; P T Wingfield; S Grzesiek
Journal:  J Biomol NMR       Date:  2001-11       Impact factor: 2.835

3.  Protein backbone structure determination using only residual dipolar couplings from one ordering medium.

Authors:  M Andrec; P Du; R M Levy
Journal:  J Biomol NMR       Date:  2001-12       Impact factor: 2.835

4.  Complete protein structure determination using backbone residual dipolar couplings and sidechain rotamer prediction.

Authors:  Michael Andrec; Yuichi Harano; Matthew P Jacobson; Richard A Friesner; Ronald M Levy
Journal:  J Struct Funct Genomics       Date:  2002

5.  Domain cooperativity in multidomain proteins: what can we learn from molecular alignment in anisotropic media?

Authors:  Tairan Yuwen; Carol Beth Post; Nikolai R Skrynnikov
Journal:  J Biomol NMR       Date:  2011-09-27       Impact factor: 2.835

Review 6.  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

7.  A unifying probabilistic framework for analyzing residual dipolar couplings.

Authors:  Michael Habeck; Michael Nilges; Wolfgang Rieping
Journal:  J Biomol NMR       Date:  2007-12-20       Impact factor: 2.835

8.  Fitting alignment tensor components to experimental RDCs, CSAs and RQCs.

Authors:  Lukas N Wirz; Jane R Allison
Journal:  J Biomol NMR       Date:  2015-02-05       Impact factor: 2.835

9.  A set of HNCO-based experiments for measurement of residual dipolar couplings in 15N, 13C, (2H)-labeled proteins.

Authors:  P Permi; P R Rosevear; A Annila
Journal:  J Biomol NMR       Date:  2000-05       Impact factor: 2.835

10.  16-fold degeneracy of peptide plane orientations from residual dipolar couplings: analytical treatment and implications for protein structure determination.

Authors:  Jean-Christophe Hus; Loïc Salmon; Guillaume Bouvignies; Johannes Lotze; Martin Blackledge; Rafael Brüschweiler
Journal:  J Am Chem Soc       Date:  2008-11-26       Impact factor: 15.419

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