Literature DB >> 9600889

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

G M Clore1, A M Gronenborn.   

Abstract

Recent advances in multidimensional NMR methodology have permitted solution structures of proteins in excess of 250 residues to be solved. In this paper, we discuss several methods of structure refinement that promise to increase the accuracy of macromolecular structures determined by NMR. These methods include the use of a conformational database potential and direct refinement against three-bond coupling constants, secondary 13C shifts, 1H shifts, T1/T2 ratios, and residual dipolar couplings. The latter two measurements provide long range restraints that are not accessible by other solution NMR parameters.

Entities:  

Mesh:

Substances:

Year:  1998        PMID: 9600889      PMCID: PMC34492          DOI: 10.1073/pnas.95.11.5891

Source DB:  PubMed          Journal:  Proc Natl Acad Sci U S A        ISSN: 0027-8424            Impact factor:   11.205


  48 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.  Model building and refinement practice.

Authors:  G J Kleywegt; T A Jones
Journal:  Methods Enzymol       Date:  1997       Impact factor: 1.600

3.  The solution structure of an HMG-I(Y)-DNA complex defines a new architectural minor groove binding motif.

Authors:  J R Huth; C A Bewley; M S Nissen; J N Evans; R Reeves; A M Gronenborn; G M Clore
Journal:  Nat Struct Biol       Date:  1997-08

4.  Application of molecular dynamics with interproton distance restraints to three-dimensional protein structure determination. A model study of crambin.

Authors:  G M Clore; A T Brünger; M Karplus; A M Gronenborn
Journal:  J Mol Biol       Date:  1986-10-05       Impact factor: 5.469

Review 5.  Determination of three-dimensional structures of proteins and nucleic acids in solution by nuclear magnetic resonance spectroscopy.

Authors:  G M Clore; A M Gronenborn
Journal:  Crit Rev Biochem Mol Biol       Date:  1989       Impact factor: 8.250

6.  Comparison of the solution and X-ray structures of barley serine proteinase inhibitor 2.

Authors:  G M Clore; A M Gronenborn; M N James; M Kjaer; C A McPhalen; F M Poulsen
Journal:  Protein Eng       Date:  1987 Aug-Sep

7.  Assessing the quality of solution nuclear magnetic resonance structures by complete cross-validation.

Authors:  A T Brünger; G M Clore; A M Gronenborn; R Saffrich; M Nilges
Journal:  Science       Date:  1993-07-16       Impact factor: 47.728

8.  The impact of direct refinement against three-bond HN-C alpha H coupling constants on protein structure determination by NMR.

Authors:  D S Garrett; J Kuszewski; T J Hancock; P J Lodi; G W Vuister; A M Gronenborn; G M Clore
Journal:  J Magn Reson B       Date:  1994-05

9.  Refined solution structure of the oligomerization domain of the tumour suppressor p53.

Authors:  G M Clore; J Ernst; R Clubb; J G Omichinski; W M Kennedy; K Sakaguchi; E Appella; A M Gronenborn
Journal:  Nat Struct Biol       Date:  1995-04

Review 10.  Chemical shifts and three-dimensional protein structures.

Authors:  E Oldfield
Journal:  J Biomol NMR       Date:  1995-04       Impact factor: 2.835

View more
  68 in total

1.  Sign determination of dipolar couplings in field-oriented bicelles by variable angle sample spinning (VASS).

Authors:  F Tian; J A Losonczi; M W Fischer; J H Prestegard
Journal:  J Biomol NMR       Date:  1999-10       Impact factor: 2.835

2.  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

3.  Accurate and rapid docking of protein-protein complexes on the basis of intermolecular nuclear overhauser enhancement data and dipolar couplings by rigid body minimization.

Authors:  G M Clore
Journal:  Proc Natl Acad Sci U S A       Date:  2000-08-01       Impact factor: 11.205

4.  A novel interactive tool for rigid-body modeling of multi-domain macromolecules using residual dipolar couplings.

Authors:  P Dosset; J C Hus; D Marion; M Blackledge
Journal:  J Biomol NMR       Date:  2001-07       Impact factor: 2.835

5.  Solution structure of the MEF2A-DNA complex: structural basis for the modulation of DNA bending and specificity by MADS-box transcription factors.

Authors:  K Huang; J M Louis; L Donaldson; F L Lim; A D Sharrocks; G M Clore
Journal:  EMBO J       Date:  2000-06-01       Impact factor: 11.598

6.  A refined solution structure of hen lysozyme determined using residual dipolar coupling data.

Authors:  H Schwalbe; S B Grimshaw; A Spencer; M Buck; J Boyd; C M Dobson; C Redfield; L J Smith
Journal:  Protein Sci       Date:  2001-04       Impact factor: 6.725

7.  Residual dipolar coupling constants and structure determination of large DNA duplexes.

Authors:  Olivier Mauffret; Georges Tevanian; Serge Fermandjian
Journal:  J Biomol NMR       Date:  2002-12       Impact factor: 2.835

8.  A use of Ramachandran potentials in protein solution structure determinations.

Authors:  Ivano Bertini; Gabriele Cavallaro; Claudio Luchinat; Irene Poli
Journal:  J Biomol NMR       Date:  2003-08       Impact factor: 2.835

9.  Effects of volatile anesthetic on channel structure of gramicidin A.

Authors:  Pei Tang; Pravat K Mandal; Martha Zegarra
Journal:  Biophys J       Date:  2002-09       Impact factor: 4.033

10.  Topology and dynamics of the 10 kDa C-terminal domain of DnaK in solution.

Authors:  E B Bertelsen; H Zhou; D F Lowry; G C Flynn; F W Dahlquist
Journal:  Protein Sci       Date:  1999-02       Impact factor: 6.725

View more

北京卡尤迪生物科技股份有限公司 © 2022-2023.