Literature DB >> 29188538

Analytical ultracentrifugation in structural biology.

Satoru Unzai1.   

Abstract

Researchers in the field of structural biology, especially X-ray crystallography and protein nuclear magnetic resonance, are interested in knowing as much as possible about the state of their target protein in solution. Not only is this knowledge relevant to studies of biological function, it also facilitates determination of a protein structure using homogeneous monodisperse protein samples. A researcher faced with a new protein to study will have many questions even after that protein has been purified. Analytical ultracentrifugation (AUC) can provide all of this information readily from a small sample in a non-destructive way, without the need for labeling, enabling structure determination experiments without any wasting time and material on uncharacterized samples. In this article, I use examples to illustrate how AUC can contribute to protein structural analysis. Integrating information from a variety of biophysical experimental methods, such as X-ray crystallography, small angle X-ray scattering, electrospray ionization-mass spectrometry, AUC allows a more complete understanding of the structure and function of biomacromolecules.

Keywords:  AUC; Crystallography; Interaction; Protein

Year:  2017        PMID: 29188538      PMCID: PMC5899701          DOI: 10.1007/s12551-017-0340-0

Source DB:  PubMed          Journal:  Biophys Rev        ISSN: 1867-2450


  26 in total

1.  Studying multiprotein complexes by multisignal sedimentation velocity analytical ultracentrifugation.

Authors:  Andrea Balbo; Kenneth H Minor; Carlos A Velikovsky; Roy A Mariuzza; Cynthia B Peterson; Peter Schuck
Journal:  Proc Natl Acad Sci U S A       Date:  2004-12-21       Impact factor: 11.205

2.  Extracting equilibrium constants from kinetically limited reacting systems.

Authors:  John J Correia; Walter F Stafford
Journal:  Methods Enzymol       Date:  2009       Impact factor: 1.600

3.  Enhanced resolution of sedimentation coefficient distribution profiles by extrapolation to infinite time.

Authors:  Joachim Behlke; Otto Ristau
Journal:  Eur Biophys J       Date:  2009-03-06       Impact factor: 1.733

4.  Regulatory features of the trp operon and the crystal structure of the trp RNA-binding attenuation protein from Bacillus stearothermophilus.

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Journal:  J Mol Biol       Date:  1999-06-18       Impact factor: 5.469

5.  Factors involved in specific transcription by mammalian RNA polymerase II: purification and characterization of general transcription factor TFIIE.

Authors:  Y Ohkuma; H Sumimoto; M Horikoshi; R G Roeder
Journal:  Proc Natl Acad Sci U S A       Date:  1990-12       Impact factor: 11.205

6.  Rounding up: Engineering 12-membered rings from the cyclic 11-mer TRAP.

Authors:  Jonathan G Heddle; Takeshi Yokoyama; Ichiro Yamashita; Sam-Yong Park; Jeremy R H Tame
Journal:  Structure       Date:  2006-05       Impact factor: 5.006

7.  Tandem mass spectrometry defines the stoichiometry and quaternary structural arrangement of tryptophan molecules in the multiprotein complex TRAP.

Authors:  Margaret G McCammon; Helena Hernández; Frank Sobott; Carol V Robinson
Journal:  J Am Chem Soc       Date:  2004-05-19       Impact factor: 15.419

Review 8.  Regulation of transcription attenuation and translation initiation by allosteric control of an RNA-binding protein: the Bacillus subtilis TRAP protein.

Authors:  Paul Babitzke
Journal:  Curr Opin Microbiol       Date:  2004-04       Impact factor: 7.934

9.  TRAP, the trp RNA-binding attenuation protein of Bacillus subtilis, is a multisubunit complex that appears to recognize G/UAG repeats in the trpEDCFBA and trpG transcripts.

Authors:  P Babitzke; J T Stults; S J Shire; C Yanofsky
Journal:  J Biol Chem       Date:  1994-06-17       Impact factor: 5.157

10.  A two-dimensional spectrum analysis for sedimentation velocity experiments of mixtures with heterogeneity in molecular weight and shape.

Authors:  Emre Brookes; Weiming Cao; Borries Demeler
Journal:  Eur Biophys J       Date:  2009-02-27       Impact factor: 1.733

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  6 in total

Review 1.  Analytical ultracentrifuge: an ideal tool for characterization of non-coding RNAs.

Authors:  Maulik D Badmalia; M Quadir Siddiqui; Tyler Mrozowich; Darren L Gemmill; Trushar R Patel
Journal:  Eur Biophys J       Date:  2020-10-16       Impact factor: 1.733

2.  Efficient data acquisition with three-channel centerpieces in sedimentation velocity.

Authors:  Kristian Juul-Madsen; Huaying Zhao; Thomas Vorup-Jensen; Peter Schuck
Journal:  Anal Biochem       Date:  2019-09-04       Impact factor: 3.365

3.  Resuspending samples in analytical ultracentrifugation.

Authors:  Leonardo M Schuck; Huaying Zhao
Journal:  Anal Biochem       Date:  2020-05-11       Impact factor: 3.365

4.  Neutron scattering maps the higher-order assembly of NADPH-dependent assimilatory sulfite reductase.

Authors:  Daniel T Murray; Nidhi Walia; Kevin L Weiss; Christopher B Stanley; Peter S Randolph; Gergely Nagy; M Elizabeth Stroupe
Journal:  Biophys J       Date:  2022-04-20       Impact factor: 3.699

5.  A database of calculated solution parameters for the AlphaFold predicted protein structures.

Authors:  Emre Brookes; Mattia Rocco
Journal:  Sci Rep       Date:  2022-05-05       Impact factor: 4.996

6.  Nanoscale Structure Determination of Murray Valley Encephalitis and Powassan Virus Non-Coding RNAs.

Authors:  Tyler Mrozowich; Amy Henrickson; Borries Demeler; Trushar R Patel
Journal:  Viruses       Date:  2020-02-08       Impact factor: 5.048

  6 in total

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