Literature DB >> 10805131

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

J Meiler1, N Blomberg, M Nilges, C Griesinger.   

Abstract

Residual dipolar couplings are useful global structural restraints. The dipolar couplings define the orientation of a vector with respect to the alignment tensor. Although the size of the alignment tensor can be derived from the distribution of the experimental dipolar couplings, its orientation with respect to the coordinate system of the molecule is unknown at the beginning of structure determination. This causes convergence problems in the simulated annealing process. We therefore propose a protocol that translates dipolar couplings into intervector projection angles, which are independent of the orientation of the alignment tensor with respect to the molecule. These restraints can be used during the whole simulated annealing protocol.

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Year:  2000        PMID: 10805131     DOI: 10.1023/a:1008378624590

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


  14 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.  A doublet-separated sensitivity-enhanced HSQC for the determination of scalar and dipolar one-bond J-couplings.

Authors:  F Cordier; A J Dingley; S Grzesiek
Journal:  J Biomol NMR       Date:  1999-02       Impact factor: 2.835

3.  Induced alignment and measurement of dipolar couplings of an SH2 domain through direct binding with filamentous phage.

Authors:  D Dahlke Ojennus; R M Mitton-Fry; D S Wuttke
Journal:  J Biomol NMR       Date:  1999-06       Impact factor: 2.835

4.  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

5.  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

6.  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

7.  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

8.  Conformational constraints on the headgroup and sn-2 chain of bilayer DMPC from NMR dipolar couplings.

Authors:  M Hong; K Schmidt-Rohr; H Zimmermann
Journal:  Biochemistry       Date:  1996-06-25       Impact factor: 3.162

9.  Measurement of dipolar couplings for methylene and methyl sites in weakly oriented macromolecules and their use in structure determination.

Authors:  M Ottiger; F Delaglio; J L Marquardt; N Tjandra; A Bax
Journal:  J Magn Reson       Date:  1998-10       Impact factor: 2.229

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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  29 in total

1.  Efficiency of paramagnetism-based constraints to determine the spatial arrangement of alpha-helical secondary structure elements.

Authors:  Ivano Bertini; Marco Longinetti; Claudio Luchinat; Giacomo Parigi; Luca Sgheri
Journal:  J Biomol NMR       Date:  2002-02       Impact factor: 2.835

2.  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

3.  DipoCoup: A versatile program for 3D-structure homology comparison based on residual dipolar couplings and pseudocontact shifts.

Authors:  J Meiler; W Peti; C Griesinger
Journal:  J Biomol NMR       Date:  2000-08       Impact factor: 2.835

4.  Rapid protein fold determination using unassigned NMR data.

Authors:  Jens Meiler; David Baker
Journal:  Proc Natl Acad Sci U S A       Date:  2003-12-10       Impact factor: 11.205

5.  Exact solutions for internuclear vectors and backbone dihedral angles from NH residual dipolar couplings in two media, and their application in a systematic search algorithm for determining protein backbone structure.

Authors:  Lincong Wang; Bruce Randall Donald
Journal:  J Biomol NMR       Date:  2004-07       Impact factor: 2.835

6.  The HADDOCK web server for data-driven biomolecular docking.

Authors:  Sjoerd J de Vries; Marc van Dijk; Alexandre M J J Bonvin
Journal:  Nat Protoc       Date:  2010-04-15       Impact factor: 13.491

7.  Measurement of eight scalar and dipolar couplings for methine-methylene pairs in proteins and nucleic acids.

Authors:  Emeric Miclet; Jérôme Boisbouvier; Ad Bax
Journal:  J Biomol NMR       Date:  2005-03       Impact factor: 2.835

8.  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

9.  Structure of the C-Terminal Helical Repeat Domain of Eukaryotic Elongation Factor 2 Kinase.

Authors:  Nathan Will; Andrea Piserchio; Isaac Snyder; Scarlet B Ferguson; David H Giles; Kevin N Dalby; Ranajeet Ghose
Journal:  Biochemistry       Date:  2016-09-14       Impact factor: 3.162

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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