Literature DB >> 15666559

Improved simulation of NOESY spectra by RELAX-JT2 including effects of J-coupling, transverse relaxation and chemical shift anisotrophy.

Andreas Ried1, Wolfram Gronwald, Jochen M Trenner, Konrad Brunner, Klaus-Peter Neidig, Hans Robert Kalbitzer.   

Abstract

RELAX-JT2 is an extension of RELAX, a program for the simulation of 1H 2D NOESY spectra and (15)N or (13)C edited 3D NOESY-HSQC spectra of biological macromolecules. In addition to the already existing NOE-simulation it allows the proper simulation of line shapes by the integrated calculation of T(2) times and multiplet structures caused by J-couplings. Additionally the effects of relaxation mediated by chemical shift anisotropy are taken into account. The new routines have been implemented in the program AUREMOL, which aims at the automated NMR structure determination of proteins in solution. For a manual or automatic assignment of experimental spectra that is based on the comparison with the corresponding simulated spectra, the additional line shape information now available is a valuable aid. The new features have been successfully tested with the histidine-containing phosphocarrier protein HPr from Staphylococcus carnosus.

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Year:  2004        PMID： 15666559     DOI： 10.1023/b:jnmr.0000048945.88968.af

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


  19 in total

1.  Relaxation matrix refinement of the solution structure of squash trypsin inhibitor.

Authors:  M Nilges; J Habazettl; A T Brünger; T A Holak
Journal:  J Mol Biol       Date:  1991-06-05       Impact factor: 5.469

2.  Three-dimensional structure of the histidine-containing phosphocarrier protein (HPr) from Enterococcus faecalis in solution.

Authors:  T Maurer; R Döker; A Görler; W Hengstenberg; H R Kalbitzer
Journal:  Eur J Biochem       Date:  2001-02

3.  Direct NOE refinement of biomolecular structures using 2D NMR data.

Authors:  A M Bonvin; R Boelens; R Kaptein
Journal:  J Biomol NMR       Date:  1991-09       Impact factor: 2.835

4.  An improved NOESY simulation program for partially relaxed spectra: BIRDER.

Authors:  L Zhu; B R Reid
Journal:  J Magn Reson B       Date:  1995-03

5.  A NOESY-HSQC simulation program, SPIRIT.

Authors:  L Zhu; H J Dyson; P E Wright
Journal:  J Biomol NMR       Date:  1998-01       Impact factor: 2.835

6.  Three-dimensional solution structure of a DNA duplex containing the BclI restriction sequence: two-dimensional NMR studies, distance geometry calculations, and refinement by back-calculation of the NOESY spectrum.

Authors:  K M Banks; D R Hare; B R Reid
Journal:  Biochemistry       Date:  1989-08-22       Impact factor: 3.162

7.  Active-centre torsion-angle strain revealed in 1.6 A-resolution structure of histidine-containing phosphocarrier protein.

Authors:  Z Jia; M Vandonselaar; J W Quail; L T Delbaere
Journal:  Nature       Date:  1993-01-07       Impact factor: 49.962

8.  Exploring the limits of precision and accuracy of protein structures determined by nuclear magnetic resonance spectroscopy.

Authors:  G M Clore; M A Robien; A M Gronenborn
Journal:  J Mol Biol       Date:  1993-05-05       Impact factor: 5.469

9.  RFAC, a program for automated NMR R-factor estimation.

Authors:  W Gronwald; R Kirchhöfer; A Görler; W Kremer; B Ganslmeier; K P Neidig; H R Kalbitzer
Journal:  J Biomol NMR       Date:  2000-06       Impact factor: 2.835

10.  Structural determinants of protein dynamics: analysis of 15N NMR relaxation measurements for main-chain and side-chain nuclei of hen egg white lysozyme.

Authors:  M Buck; J Boyd; C Redfield; D A MacKenzie; D J Jeenes; D B Archer; C M Dobson
Journal:  Biochemistry       Date:  1995-03-28       Impact factor: 3.162
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  5 in total

1.  Automated solvent artifact removal and base plane correction of multidimensional NMR protein spectra by AUREMOL-SSA.

Authors:  Wilhelm M Malloni; Silvia De Sanctis; Ana M Tomé; Elmar W Lang; Claudia E Munte; Klaus Peter Neidig; Hans Robert Kalbitzer
Journal:  J Biomol NMR       Date:  2010-04-23       Impact factor: 2.835

2.  AUREMOL-RFAC-3D, combination of R-factors and their use for automated quality assessment of protein solution structures.

Authors:  Wolfram Gronwald; Konrad Brunner; Renate Kirchhöfer; Jochen Trenner; Klaus-Peter Neidig; Hans Robert Kalbitzer
Journal:  J Biomol NMR       Date:  2006-11-29       Impact factor: 2.835

3.  Chemical shift optimization in multidimensional NMR spectra by AUREMOL-SHIFTOPT.

Authors:  Kumaran Baskaran; Renate Kirchhöfer; Fritz Huber; Jochen Trenner; Konrad Brunner; Wolfram Gronwald; Klaus-Peter Neidig; Hans Robert Kalbitzer
Journal:  J Biomol NMR       Date:  2009-02-21       Impact factor: 2.835

4.  Infrequent cavity-forming fluctuations in HPr from Staphylococcus carnosus revealed by pressure- and temperature-dependent tyrosine ring flips.

Authors:  Mineyuki Hattori; Hua Li; Hiroaki Yamada; Kazuyuki Akasaka; Wolfgang Hengstenberg; Wolfram Gronwald; Hans Robert Kalbitzer
Journal:  Protein Sci       Date:  2004-12       Impact factor: 6.725

5.  Evolutionary Pareto-optimization of stably folding peptides.

Authors:  Wolfram Gronwald; Tim Hohm; Daniel Hoffmann
Journal:  BMC Bioinformatics       Date:  2008-02-19       Impact factor: 3.169
  5 in total

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