Literature DB >> 11142514

Assessment of molecular structure using frame-independent orientational restraints derived from residual dipolar couplings.

N R Skrynnikov1, L E Kay.   

Abstract

Residual dipolar couplings measured in weakly aligning liquid-crystalline solvent contain valuable information on the structure of biomolecules in solution. Here we demonstrate that dipolar couplings (DCs) can be used to derive a comprehensive set of pairwise angular restraints that do not depend on the orientation of the alignment tensor principal axes. These restraints can be used to assess the agreement between a trial protein structure and a set of experimental dipolar couplings by means of a graphic representation termed a 'DC consistency map'. Importantly, these maps can be used to recognize structural elements consistent with the experimental DC data and to identify structural parameters that require further refinement, which could prove important for the success of DC-based structure calculations. This approach is illustrated for the 42 kDa maltodextrin-binding protein.

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Year:  2000        PMID: 11142514     DOI: 10.1023/a:1026501101716

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


  28 in total

1.  Refining the overall structure and subdomain orientation of ribosomal protein S4 delta41 with dipolar couplings measured by NMR in uniaxial liquid crystalline phases.

Authors:  M A Markus; R B Gerstner; D E Draper; D A Torchia
Journal:  J Mol Biol       Date:  1999-09-17       Impact factor: 5.469

2.  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

3.  Assessment of zinc finger orientations by residual dipolar coupling constants.

Authors:  V Tsui; L Zhu; T H Huang; P E Wright; D A Case
Journal:  J Biomol NMR       Date:  2000-01       Impact factor: 2.835

4.  A new approach for applying residual dipolar couplings as restraints in structure elucidation.

Authors:  J Meiler; N Blomberg; M Nilges; C Griesinger
Journal:  J Biomol NMR       Date:  2000-03       Impact factor: 2.835

5.  The use of dipolar couplings for determining the solution structure of rat apo-S100B(betabeta).

Authors:  A C Drohat; N Tjandra; D M Baldisseri; D J Weber
Journal:  Protein Sci       Date:  1999-04       Impact factor: 6.725

6.  Crystallographic evidence of a large ligand-induced hinge-twist motion between the two domains of the maltodextrin binding protein involved in active transport and chemotaxis.

Authors:  A J Sharff; L E Rodseth; J C Spurlino; F A Quiocho
Journal:  Biochemistry       Date:  1992-11-10       Impact factor: 3.162

7.  Crystallography & NMR system: A new software suite for macromolecular structure determination.

Authors:  A T Brünger; P D Adams; G M Clore; W L DeLano; P Gros; R W Grosse-Kunstleve; J S Jiang; J Kuszewski; M Nilges; N S Pannu; R J Read; L M Rice; T Simonson; G L Warren
Journal:  Acta Crystallogr D Biol Crystallogr       Date:  1998-09-01

8.  High-resolution heteronuclear NMR of human ubiquitin in an aqueous liquid crystalline medium.

Authors:  A Bax; N Tjandra
Journal:  J Biomol NMR       Date:  1997-10       Impact factor: 2.835

9.  NMR structure of tissue inhibitor of metalloproteinases-1 implicates localized induced fit in recognition of matrix metalloproteinases.

Authors:  B Wu; S Arumugam; G Gao; G I Lee; V Semenchenko; W Huang; K Brew; S R Van Doren
Journal:  J Mol Biol       Date:  2000-01-14       Impact factor: 5.469

10.  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

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  12 in total

1.  Exact solutions for chemical bond orientations from residual dipolar couplings.

Authors:  William J Wedemeyer; Carol A Rohl; Harold A Scherag
Journal:  J Biomol NMR       Date:  2002-02       Impact factor: 2.835

2.  Direct structure refinement of high molecular weight proteins against residual dipolar couplings and carbonyl chemical shift changes upon alignment: an application to maltose binding protein.

Authors:  W Y Choy; M Tollinger; G A Mueller; L E Kay
Journal:  J Biomol NMR       Date:  2001-09       Impact factor: 2.835

3.  Quaternary structure built from subunits combining NMR and small-angle x-ray scattering data.

Authors:  Maija-Liisa Mattinen; Kimmo Pääkkönen; Teemu Ikonen; Jeremy Craven; Torbjörn Drakenberg; Ritva Serimaa; Jonathan Waltho; Arto Annila
Journal:  Biophys J       Date:  2002-08       Impact factor: 4.033

4.  Backbone assignment of proteins with known structure using residual dipolar couplings.

Authors:  Young-Sang Jung; Markus Zweckstetter
Journal:  J Biomol NMR       Date:  2004-09       Impact factor: 2.835

5.  Statistical coil model of the unfolded state: resolving the reconciliation problem.

Authors:  Abhishek K Jha; Andrés Colubri; Karl F Freed; Tobin R Sosnick
Journal:  Proc Natl Acad Sci U S A       Date:  2005-08-30       Impact factor: 11.205

6.  Top-down approach in protein RDC data analysis: de novo estimation of the alignment tensor.

Authors:  Kang Chen; Nico Tjandra
Journal:  J Biomol NMR       Date:  2007-06-26       Impact factor: 2.835

7.  Measurement of (1)H-(15)N and (1)H-(13)C residual dipolar couplings in nucleic acids from TROSY intensities.

Authors:  Jinfa Ying; Jinbu Wang; Alex Grishaev; Ping Yu; Yun-Xing Wang; Ad Bax
Journal:  J Biomol NMR       Date:  2011-09-27       Impact factor: 2.835

8.  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

9.  High-resolution protein structure determination starting with a global fold calculated from exact solutions to the RDC equations.

Authors:  Jianyang Zeng; Jeffrey Boyles; Chittaranjan Tripathy; Lincong Wang; Anthony Yan; Pei Zhou; Bruce Randall Donald
Journal:  J Biomol NMR       Date:  2009-08-27       Impact factor: 2.835

10.  Improvement of hydrogen bond geometry in protein NMR structures by residual dipolar couplings--an assessment of the interrelation of NMR restraints.

Authors:  Pernille Rose Jensen; Jacob Bock Axelsen; Mathilde Hauge Lerche; Flemming M Poulsen
Journal:  J Biomol NMR       Date:  2004-01       Impact factor: 2.835

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