Literature DB >> 23151743

Sample preparation, data collection, and preliminary data analysis in biomolecular solution X-ray scattering.

Alexander Grishaev1.   

Abstract

In addition to the classic methods of structural biology--X-ray crystallography and NMR--solution X-ray scattering (SAXS) is playing an increasingly important role in structural investigation of biological macromolecules. However, the simultaneous ease of SAXS data collection and sophistication of its data analysis tools can present challenges to the investigator. Any sample, whether pure or contaminated, whether monodisperse or polydisperse, will yield scattering data, and it is up to the user to ensure the absence of artifacts and to choose a proper structural modeling strategy. This unit discusses experimental aspects of X-ray solution scattering, including sample preparation and data collection, as well as the steps in data processing and preliminary analysis required to ensure the absence of artifacts. The goal is to summarize everything than can go wrong with SAXS data measurement so the user can have confidence in the data before undertaking structural modeling.
© 2012 by John Wiley & Sons, Inc.

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Year:  2012        PMID: 23151743      PMCID: PMC3523188          DOI: 10.1002/0471140864.ps1714s70

Source DB:  PubMed          Journal:  Curr Protoc Protein Sci        ISSN: 1934-3655


  22 in total

1.  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

2.  Restoring low resolution structure of biological macromolecules from solution scattering using simulated annealing.

Authors:  D I Svergun
Journal:  Biophys J       Date:  1999-06       Impact factor: 4.033

Review 3.  Small-angle scattering: a view on the properties, structures and structural changes of biological macromolecules in solution.

Authors:  Michel H Koch; Patrice Vachette; Dmitri I Svergun
Journal:  Q Rev Biophys       Date:  2003-05       Impact factor: 5.318

4.  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

5.  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

6.  A physical picture of atomic motions within the Dickerson DNA dodecamer in solution derived from joint ensemble refinement against NMR and large-angle X-ray scattering data.

Authors:  Charles D Schwieters; G Marius Clore
Journal:  Biochemistry       Date:  2007-02-06       Impact factor: 3.162

7.  Structural characterization of flexible proteins using small-angle X-ray scattering.

Authors:  Pau Bernadó; Efstratios Mylonas; Maxim V Petoukhov; Martin Blackledge; Dmitri I Svergun
Journal:  J Am Chem Soc       Date:  2007-04-06       Impact factor: 15.419

Review 8.  Analysis of X-ray and neutron scattering from biomacromolecular solutions.

Authors:  Maxim V Petoukhov; Dmitri I Svergun
Journal:  Curr Opin Struct Biol       Date:  2007-08-21       Impact factor: 6.809

9.  Low-resolution structures of proteins in solution retrieved from X-ray scattering with a genetic algorithm.

Authors:  P Chacón; F Morán; J F Díaz; E Pantos; J M Andreu
Journal:  Biophys J       Date:  1998-06       Impact factor: 4.033

10.  Combined use of residual dipolar couplings and solution X-ray scattering to rapidly probe rigid-body conformational transitions in a non-phosphorylatable active-site mutant of the 128 kDa enzyme I dimer.

Authors:  Yuki Takayama; Charles D Schwieters; Alexander Grishaev; Rodolfo Ghirlando; G Marius Clore
Journal:  J Am Chem Soc       Date:  2010-12-16       Impact factor: 15.419

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  7 in total

1.  The Interplay between Molten Globules and Heme Disassociation Defines Human Hemoglobin Disassembly.

Authors:  Premila P Samuel; Mark A White; William C Ou; David A Case; George N Phillips; John S Olson
Journal:  Biophys J       Date:  2020-02-04       Impact factor: 4.033

2.  Biochemical and structural characterization of two variants of uncertain significance in the PMS2 gene.

Authors:  Brandon M D'Arcy; Jessa Blount; Aishwarya Prakash
Journal:  Hum Mutat       Date:  2019-01-30       Impact factor: 4.878

3.  Preparing monodisperse macromolecular samples for successful biological small-angle X-ray and neutron-scattering experiments.

Authors:  Cy M Jeffries; Melissa A Graewert; Clément E Blanchet; David B Langley; Andrew E Whitten; Dmitri I Svergun
Journal:  Nat Protoc       Date:  2016-10-06       Impact factor: 13.491

Review 4.  Hybrid Approaches to Structural Characterization of Conformational Ensembles of Complex Macromolecular Systems Combining NMR Residual Dipolar Couplings and Solution X-ray Scattering.

Authors:  Vincenzo Venditti; Timothy K Egner; G Marius Clore
Journal:  Chem Rev       Date:  2016-01-07       Impact factor: 60.622

5.  Self-association of a highly charged arginine-rich cell-penetrating peptide.

Authors:  Giulio Tesei; Mario Vazdar; Malene Ringkjøbing Jensen; Carolina Cragnell; Phil E Mason; Jan Heyda; Marie Skepö; Pavel Jungwirth; Mikael Lund
Journal:  Proc Natl Acad Sci U S A       Date:  2017-10-11       Impact factor: 11.205

6.  Consensus Bayesian assessment of protein molecular mass from solution X-ray scattering data.

Authors:  Nelly R Hajizadeh; Daniel Franke; Cy M Jeffries; Dmitri I Svergun
Journal:  Sci Rep       Date:  2018-05-08       Impact factor: 4.379

7.  Effects of Monovalent Salt on Protein-Protein Interactions of Dilute and Concentrated Monoclonal Antibody Formulations.

Authors:  Amy Y Xu; Nicholas J Clark; Joseph Pollastrini; Maribel Espinoza; Hyo-Jin Kim; Sekhar Kanapuram; Bruce Kerwin; Michael J Treuheit; Susan Krueger; Arnold McAuley; Joseph E Curtis
Journal:  Antibodies (Basel)       Date:  2022-03-31
  7 in total

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