Literature DB >> 12124297

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

Maija-Liisa Mattinen1, Kimmo Pääkkönen, Teemu Ikonen, Jeremy Craven, Torbjörn Drakenberg, Ritva Serimaa, Jonathan Waltho, Arto Annila.   

Abstract

A new principle in constructing molecular complexes from the known high-resolution domain structures joining data from NMR and small-angle x-ray scattering (SAXS) measurements is described. Structure of calmodulin in complex with trifluoperazine was built from N- and C-terminal domains oriented based on residual dipolar couplings measured by NMR in a dilute liquid crystal, and the overall shape of the complex was derived from SAXS data. The residual dipolar coupling data serves to reduce angular degrees of freedom, and the small-angle scattering data serves to confine the translational degrees of freedom. The complex built by this method was found to be consistent with the known crystal structure. The study demonstrates how approximate tertiary structures of modular proteins or quaternary structures composed of subunits can be assembled from high-resolution structures of domains or subunits using mutually complementary NMR and SAXS data.

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Year:  2002        PMID: 12124297      PMCID: PMC1302219          DOI: 10.1016/S0006-3495(02)75241-7

Source DB:  PubMed          Journal:  Biophys J        ISSN: 0006-3495            Impact factor:   4.033


  43 in total

1.  Variation of molecular alignment as a means of resolving orientational ambiguities in protein structures from dipolar couplings.

Authors:  H M Al-Hashimi; H Valafar; M Terrell; E R Zartler; M K Eidsness; J H Prestegard
Journal:  J Magn Reson       Date:  2000-04       Impact factor: 2.229

2.  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

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.  Model-free approach to the dynamic interpretation of residual dipolar couplings in globular proteins.

Authors:  J Meiler; J J Prompers; W Peti; C Griesinger; R Brüschweiler
Journal:  J Am Chem Soc       Date:  2001-06-27       Impact factor: 15.419

5.  Determination of domain structure of proteins from X-ray solution scattering.

Authors:  D I Svergun; M V Petoukhov; M H Koch
Journal:  Biophys J       Date:  2001-06       Impact factor: 4.033

6.  MOLMOL: a program for display and analysis of macromolecular structures.

Authors:  R Koradi; M Billeter; K Wüthrich
Journal:  J Mol Graph       Date:  1996-02

7.  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

8.  NMR approaches for monitoring domain orientations in calcium-binding proteins in solution using partial replacement of Ca2+ by Tb3+.

Authors:  R R Biekofsky; F W Muskett; J M Schmidt; S R Martin; J P Browne; P M Bayley; J Feeney
Journal:  FEBS Lett       Date:  1999-11-05       Impact factor: 4.124

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

Authors:  N R Skrynnikov; L E Kay
Journal:  J Biomol NMR       Date:  2000-11       Impact factor: 2.835

10.  Ca2+-bound calmodulin forms a compact globular structure on binding four trifluoperazine molecules in solution.

Authors:  N Matsushima; N Hayashi; Y Jinbo; Y Izumi
Journal:  Biochem J       Date:  2000-04-01       Impact factor: 3.857

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  19 in total

1.  Alignment of chain-like molecules.

Authors:  Martti Louhivuori; Kai Fredriksson; Kimmo Pääkkönen; Perttu Permi; Arto Annila
Journal:  J Biomol NMR       Date:  2004-08       Impact factor: 2.835

2.  A simple procedure to evaluate the efficiency of bio-macromolecular rigid-body refinement by small-angle scattering.

Authors:  Frank Gabel
Journal:  Eur Biophys J       Date:  2011-09-24       Impact factor: 1.733

3.  Global rigid body modeling of macromolecular complexes against small-angle scattering data.

Authors:  Maxim V Petoukhov; Dmitri I Svergun
Journal:  Biophys J       Date:  2005-05-27       Impact factor: 4.033

4.  Joint use of small-angle X-ray and neutron scattering to study biological macromolecules in solution.

Authors:  Maxim V Petoukhov; Dmitri I Svergun
Journal:  Eur Biophys J       Date:  2006-04-25       Impact factor: 1.733

5.  A target function for quaternary structural refinement from small angle scattering and NMR orientational restraints.

Authors:  Frank Gabel; Bernd Simon; Michael Sattler
Journal:  Eur Biophys J       Date:  2006-01-14       Impact factor: 1.733

6.  The structure of free L11 and functional dynamics of L11 in free, L11-rRNA(58 nt) binary and L11-rRNA(58 nt)-thiostrepton ternary complexes.

Authors:  Donghan Lee; Joseph D Walsh; Ping Yu; Michelle A Markus; Theodora Choli-Papadopoulou; Charles D Schwieters; Susan Krueger; David E Draper; Yun-Xing Wang
Journal:  J Mol Biol       Date:  2007-01-10       Impact factor: 5.469

7.  Structural assembly of multidomain proteins and protein complexes guided by the overall rotational diffusion tensor.

Authors:  Yaroslav Ryabov; David Fushman
Journal:  J Am Chem Soc       Date:  2007-06-06       Impact factor: 15.419

8.  A simple genetic algorithm for the optimization of multidomain protein homology models driven by NMR residual dipolar coupling and small angle X-ray scattering data.

Authors:  Fabien Mareuil; Christina Sizun; Javier Perez; Marc Schoenauer; Jean-Yves Lallemand; François Bontems
Journal:  Eur Biophys J       Date:  2007-05-24       Impact factor: 1.733

9.  Refined solution structure of the 82-kDa enzyme malate synthase G from joint NMR and synchrotron SAXS restraints.

Authors:  Alexander Grishaev; Vitali Tugarinov; Lewis E Kay; Jill Trewhella; Ad Bax
Journal:  J Biomol NMR       Date:  2007-11-16       Impact factor: 2.835

Review 10.  Nuclear magnetic resonance analysis of protein-DNA interactions.

Authors:  S Campagne; V Gervais; A Milon
Journal:  J R Soc Interface       Date:  2011-03-09       Impact factor: 4.118

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