Literature DB >> 20120026

Small-angle scattering for structural biology--expanding the frontier while avoiding the pitfalls.

David A Jacques1, Jill Trewhella.   

Abstract

The last decade has seen a dramatic increase in the use of small-angle scattering for the study of biological macromolecules in solution. The drive for more complete structural characterization of proteins and their interactions, coupled with the increasing availability of instrumentation and easy-to-use software for data analysis and interpretation, is expanding the utility of the technique beyond the domain of the biophysicist and into the realm of the protein scientist. However, the absence of publication standards and the ease with which 3D models can be calculated against the inherently 1D scattering data means that an understanding of sample quality, data quality, and modeling assumptions is essential to have confidence in the results. This review is intended to provide a road map through the small-angle scattering experiment, while also providing a set of guidelines for the critical evaluation of scattering data. Examples of current best practice are given that also demonstrate the power of the technique to advance our understanding of protein structure and function.

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Year:  2010        PMID: 20120026      PMCID: PMC2867006          DOI: 10.1002/pro.351

Source DB:  PubMed          Journal:  Protein Sci        ISSN: 0961-8368            Impact factor:   6.725


  49 in total

1.  The complete atomic structure of the large ribosomal subunit at 2.4 A resolution.

Authors:  N Ban; P Nissen; J Hansen; P B Moore; T A Steitz
Journal:  Science       Date:  2000-08-11       Impact factor: 47.728

2.  Structure and mechanism of action of Sda, an inhibitor of the histidine kinases that regulate initiation of sporulation in Bacillus subtilis.

Authors:  Susan L Rowland; William F Burkholder; Katherine A Cunningham; Mark W Maciejewski; Alan D Grossman; Glenn F King
Journal:  Mol Cell       Date:  2004-03-12       Impact factor: 17.970

3.  The SWISS-MODEL workspace: a web-based environment for protein structure homology modelling.

Authors:  Konstantin Arnold; Lorenza Bordoli; Jürgen Kopp; Torsten Schwede
Journal:  Bioinformatics       Date:  2005-11-13       Impact factor: 6.937

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.  Calculation of standard atomic volumes for RNA and comparison with proteins: RNA is packed more tightly.

Authors:  N R Voss; M Gerstein
Journal:  J Mol Biol       Date:  2005-01-05       Impact factor: 5.469

6.  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

7.  The SAXS solution structure of RF1 differs from its crystal structure and is similar to its ribosome bound cryo-EM structure.

Authors:  Bente Vestergaard; Suparna Sanyal; Manfred Roessle; Liliana Mora; Richard H Buckingham; Jette S Kastrup; Michael Gajhede; Dmitri I Svergun; Måns Ehrenberg
Journal:  Mol Cell       Date:  2005-12-22       Impact factor: 17.970

8.  Conformation of polypyrimidine tract binding protein in solution.

Authors:  Maxim V Petoukhov; Tom P Monie; Frédéric H-T Allain; Stephen Matthews; Stephen Curry; Dmitri I Svergun
Journal:  Structure       Date:  2006-06       Impact factor: 5.006

9.  Radiation damage to a protein solution, detected by synchrotron X-ray small-angle scattering: dose-related considerations and suppression by cryoprotectants.

Authors:  Shigeo Kuwamoto; Shuji Akiyama; Tetsuro Fujisawa
Journal:  J Synchrotron Radiat       Date:  2004-10-22       Impact factor: 2.616

10.  Effects of urea and trimethylamine-N-oxide (TMAO) on the interactions of lysozyme in solution.

Authors:  Marc Niebuhr; Michel H J Koch
Journal:  Biophys J       Date:  2005-06-24       Impact factor: 4.033

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  135 in total

1.  Solution structure analysis of cytoplasmic domain of podocyte protein Neph1 using small/wide angle x-ray scattering (SWAXS).

Authors:  Leena Mallik; Ehtesham Arif; Pankaj Sharma; Yogendra S Rathore; Hetty N Wong; Lawrence B Holzman; Deepak Nihalani
Journal:  J Biol Chem       Date:  2012-01-17       Impact factor: 5.157

2.  High-throughput biological small-angle X-ray scattering with a robotically loaded capillary cell.

Authors:  S S Nielsen; M Møller; R E Gillilan
Journal:  J Appl Crystallogr       Date:  2012-02-09       Impact factor: 3.304

3.  Accurate flexible fitting of high-resolution protein structures to small-angle x-ray scattering data using a coarse-grained model with implicit hydration shell.

Authors:  Wenjun Zheng; Mustafa Tekpinar
Journal:  Biophys J       Date:  2011-12-20       Impact factor: 4.033

4.  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

5.  Modeling the hydration layer around proteins: applications to small- and wide-angle x-ray scattering.

Authors:  Jouko Juhani Virtanen; Lee Makowski; Tobin R Sosnick; Karl F Freed
Journal:  Biophys J       Date:  2011-10-19       Impact factor: 4.033

6.  Cpl-7, a lysozyme encoded by a pneumococcal bacteriophage with a novel cell wall-binding motif.

Authors:  Noemí Bustamante; Nuria E Campillo; Ernesto García; Cristina Gallego; Benet Pera; Gregory P Diakun; José Luis Sáiz; Pedro García; J Fernando Díaz; Margarita Menéndez
Journal:  J Biol Chem       Date:  2010-08-18       Impact factor: 5.157

7.  Progress in protein crystallography.

Authors:  Zbigniew Dauter; Alexander Wlodawer
Journal:  Protein Pept Lett       Date:  2016       Impact factor: 1.890

8.  Visual insight into how low pH alone can induce actin-severing ability in gelsolin under calcium-free conditions.

Authors:  Renu Garg; Nagesh Peddada; Amin Sagar; Deepak Nihalani
Journal:  J Biol Chem       Date:  2011-04-15       Impact factor: 5.157

9.  Water loading driven size, shape, and composition of cetyltrimethylammonium/hexanol/pentane reverse micelles.

Authors:  Brian Fuglestad; Kushol Gupta; A Joshua Wand; Kim A Sharp
Journal:  J Colloid Interface Sci       Date:  2019-01-06       Impact factor: 8.128

10.  Minimal effects of macromolecular crowding on an intrinsically disordered protein: a small-angle neutron scattering study.

Authors:  David P Goldenberg; Brian Argyle
Journal:  Biophys J       Date:  2014-02-18       Impact factor: 4.033

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