Literature DB >> 16636827

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

Maxim V Petoukhov1, Dmitri I Svergun.   

Abstract

Novel techniques for simultaneous analysis of X-ray and neutron scattering patterns from macromolecular complexes in solution are presented. They include ab initio shape and internal structure determination of multicomponent particles and more detailed rigid body modeling of complexes using high resolution structures of subunits. The methods fit simultaneously X-ray and neutron scattering curves including contrast variation data sets from selectively deuterated complexes. Biochemically sound interconnected models without steric clashes between the components displaying a pre-defined symmetry are generated. For rigid body modeling, distance restraints between specified residues/nucleotides or their ranges are taken into account. The efficiency of the methods is demonstrated in model examples, and potential sources of ambiguity are discussed.

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Year:  2006        PMID: 16636827     DOI: 10.1007/s00249-006-0063-9

Source DB:  PubMed          Journal:  Eur Biophys J        ISSN: 0175-7571            Impact factor:   1.733


  37 in total

1.  The Protein Data Bank.

Authors:  H M Berman; J Westbrook; Z Feng; G Gilliland; T N Bhat; H Weissig; I N Shindyalov; P E Bourne
Journal:  Nucleic Acids Res       Date:  2000-01-01       Impact factor: 16.971

2.  A structural model of the catalytic subunit-regulatory subunit dimeric complex of the cAMP-dependent protein kinase.

Authors:  Chang-Shung Tung; Donal A Walsh; Jill Trewhella
Journal:  J Biol Chem       Date:  2002-01-17       Impact factor: 5.157

Review 3.  From words to literature in structural proteomics.

Authors:  Andrej Sali; Robert Glaeser; Thomas Earnest; Wolfgang Baumeister
Journal:  Nature       Date:  2003-03-13       Impact factor: 49.962

4.  Structure-based assembly of protein complexes in yeast.

Authors:  Patrick Aloy; Bettina Böttcher; Hugo Ceulemans; Christina Leutwein; Christian Mellwig; Susanne Fischer; Anne-Claude Gavin; Peer Bork; Giulio Superti-Furga; Luis Serrano; Robert B Russell
Journal:  Science       Date:  2004-03-26       Impact factor: 47.728

5.  SAS solution structures of the apo and Mg2+/BeF3(-)-bound receiver domain of DctD from Sinorhizobium meliloti.

Authors:  B Tracy Nixon; Hemant P Yennawar; Michaeleen Doucleff; Jeffrey G Pelton; David E Wemmer; Susan Krueger; Elena Kondrashkina
Journal:  Biochemistry       Date:  2005-10-25       Impact factor: 3.162

6.  Refinement of multidomain protein structures by combination of solution small-angle X-ray scattering and NMR data.

Authors:  Alexander Grishaev; Justin Wu; Jill Trewhella; Ad Bax
Journal:  J Am Chem Soc       Date:  2005-11-30       Impact factor: 15.419

7.  Comparative structural analysis of low-molecular mass fragments of Rapana venosa hemocyanin obtained using two different procedures.

Authors:  Annalaura Sabatucci; Patrice Vachette; Mariano Beltramini; Benedetto Salvato; Enrico Dainese
Journal:  J Struct Biol       Date:  2005-02       Impact factor: 2.867

Review 8.  Signalling mechanisms underlying subversion of the immune response by the filarial nematode secreted product ES-62.

Authors:  Helen S Goodridge; Gillian Stepek; William Harnett; Margaret M Harnett
Journal:  Immunology       Date:  2005-07       Impact factor: 7.397

9.  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

Review 10.  Small angle neutron scattering.

Authors:  G Zaccaï; B Jacrot
Journal:  Annu Rev Biophys Bioeng       Date:  1983
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  21 in total

1.  Low-resolution solution structures of Munc18:Syntaxin protein complexes indicate an open binding mode driven by the Syntaxin N-peptide.

Authors:  Michelle P Christie; Andrew E Whitten; Gordon J King; Shu-Hong Hu; Russell J Jarrott; Kai-En Chen; Anthony P Duff; Philip Callow; Brett M Collins; David E James; Jennifer L Martin
Journal:  Proc Natl Acad Sci U S A       Date:  2012-06-05       Impact factor: 11.205

2.  Activation of nanoscale allosteric protein domain motion revealed by neutron spin echo spectroscopy.

Authors:  Bela Farago; Jianquan Li; Gabriel Cornilescu; David J E Callaway; Zimei Bu
Journal:  Biophys J       Date:  2010-11-17       Impact factor: 4.033

Review 3.  Small angle neutron and X-ray scattering in structural biology: recent examples from the literature.

Authors:  Cameron Neylon
Journal:  Eur Biophys J       Date:  2008-01-23       Impact factor: 1.733

Review 4.  Experimental approaches for solution X-ray scattering and fiber diffraction.

Authors:  H Tsuruta; T C Irving
Journal:  Curr Opin Struct Biol       Date:  2008-09-29       Impact factor: 6.809

5.  Evidence for an elongated dimeric structure of heparin-binding hemagglutinin from Mycobacterium tuberculosis.

Authors:  Carla Esposito; Maxim V Pethoukov; Dmitri I Svergun; Alessia Ruggiero; Carlo Pedone; Emilia Pedone; Rita Berisio
Journal:  J Bacteriol       Date:  2008-04-25       Impact factor: 3.490

6.  Combining NMR and small angle X-ray and neutron scattering in the structural analysis of a ternary protein-RNA complex.

Authors:  Janosch Hennig; Iren Wang; Miriam Sonntag; Frank Gabel; Michael Sattler
Journal:  J Biomol NMR       Date:  2013-03-03       Impact factor: 2.835

7.  RAID3--An interleukin-6 receptor-binding aptamer with post-selective modification-resistant affinity.

Authors:  Florian Mittelberger; Cindy Meyer; Georg H Waetzig; Martin Zacharias; Erica Valentini; Dmitri I Svergun; Katharina Berg; Inken Lorenzen; Joachim Grötzinger; Stefan Rose-John; Ulrich Hahn
Journal:  RNA Biol       Date:  2015       Impact factor: 4.652

8.  Solution structure of poly(ethylene) glycol-conjugated hemoglobin revealed by small-angle X-ray scattering: implications for a new oxygen therapeutic.

Authors:  Dmitri I Svergun; Fredrik Ekström; Kim D Vandegriff; Ashok Malavalli; Dale A Baker; Calle Nilsson; Robert M Winslow
Journal:  Biophys J       Date:  2007-09-07       Impact factor: 4.033

9.  Selective deuteration of tryptophan and methionine residues in maltose binding protein: a model system for neutron scattering.

Authors:  Valerie Laux; Phil Callow; Dmitri I Svergun; Peter A Timmins; V Trevor Forsyth; Michael Haertlein
Journal:  Eur Biophys J       Date:  2008-02-15       Impact factor: 1.733

10.  Structural basis for calcium sensing by GCaMP2.

Authors:  Qi Wang; Bo Shui; Michael I Kotlikoff; Holger Sondermann
Journal:  Structure       Date:  2008-12-10       Impact factor: 5.006

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