Literature DB >> 28558231

X-ray Scattering Studies of Protein Structural Dynamics.

Steve P Meisburger1, William C Thomas1, Maxwell B Watkins1, Nozomi Ando1.   

Abstract

X-ray scattering is uniquely suited to the study of disordered systems and thus has the potential to provide insight into dynamic processes where diffraction methods fail. In particular, while X-ray crystallography has been a staple of structural biology for more than half a century and will continue to remain so, a major limitation of this technique has been the lack of dynamic information. Solution X-ray scattering has become an invaluable tool in structural and mechanistic studies of biological macromolecules where large conformational changes are involved. Such systems include allosteric enzymes that play key roles in directing metabolic fluxes of biochemical pathways, as well as large, assembly-line type enzymes that synthesize secondary metabolites with pharmaceutical applications. Furthermore, crystallography has the potential to provide information on protein dynamics via the diffuse scattering patterns that are overlaid with Bragg diffraction. Historically, these patterns have been very difficult to interpret, but recent advances in X-ray detection have led to a renewed interest in diffuse scattering analysis as a way to probe correlated motions. Here, we will review X-ray scattering theory and highlight recent advances in scattering-based investigations of protein solutions and crystals, with a particular focus on complex enzymes.

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Year:  2017        PMID: 28558231      PMCID: PMC5562295          DOI: 10.1021/acs.chemrev.6b00790

Source DB:  PubMed          Journal:  Chem Rev        ISSN: 0009-2665            Impact factor:   60.622


  270 in total

Review 1.  Ribonucleotide reductase: A new target for antiparasite therapies.

Authors:  G M Ingram; J H Kinnaird
Journal:  Parasitol Today       Date:  1999-08

2.  Compactness of the denatured state of a fast-folding protein measured by submillisecond small-angle x-ray scattering.

Authors:  L Pollack; M W Tate; N C Darnton; J B Knight; S M Gruner; W A Eaton; R H Austin
Journal:  Proc Natl Acad Sci U S A       Date:  1999-08-31       Impact factor: 11.205

3.  Insights into the mechanisms of catalysis and heterotropic regulation of Escherichia coli aspartate transcarbamoylase based upon a structure of the enzyme complexed with the bisubstrate analogue N-phosphonacetyl-L-aspartate at 2.1 A.

Authors:  L Jin; B Stec; W N Lipscomb; E R Kantrowitz
Journal:  Proteins       Date:  1999-12-01

4.  Gleaning non-trivial structural, functional and evolutionary information about proteins by iterative database searches.

Authors:  L Aravind; E V Koonin
Journal:  J Mol Biol       Date:  1999-04-16       Impact factor: 5.469

5.  Dissecting and exploiting intermodular communication in polyketide synthases.

Authors:  R S Gokhale; S Y Tsuji; D E Cane; C Khosla
Journal:  Science       Date:  1999-04-16       Impact factor: 47.728

6.  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

7.  Towards structural determination of the water-splitting enzyme. Purification, crystallization, and preliminary crystallographic studies of photosystem II from a thermophilic cyanobacterium.

Authors:  H Kuhl; J Kruip; A Seidler; A Krieger-Liszkay; M Bunker; D Bald; A J Scheidig; M Rögner
Journal:  J Biol Chem       Date:  2000-07-07       Impact factor: 5.157

8.  Crystal structure of phenylalanine-regulated 3-deoxy-D-arabino-heptulosonate-7-phosphate synthase from Escherichia coli.

Authors:  I A Shumilin; R H Kretsinger; R H Bauerle
Journal:  Structure       Date:  1999-07-15       Impact factor: 5.006

9.  Surface exposure of the methionine side chains of calmodulin in solution. A nitroxide spin label and two-dimensional NMR study.

Authors:  T Yuan; H Ouyang; H J Vogel
Journal:  J Biol Chem       Date:  1999-03-26       Impact factor: 5.157

10.  Structural basis of autoregulation of phenylalanine hydroxylase.

Authors:  B Kobe; I G Jennings; C M House; B J Michell; K E Goodwill; B D Santarsiero; R C Stevens; R G Cotton; B E Kemp
Journal:  Nat Struct Biol       Date:  1999-05
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  21 in total

1.  Imaging electron-density fluctuations by multidimensional X-ray photon-coincidence diffraction.

Authors:  Lyuzhou Ye; Jérémy R Rouxel; Daeheum Cho; Shaul Mukamel
Journal:  Proc Natl Acad Sci U S A       Date:  2018-12-24       Impact factor: 11.205

2.  X-rays in the Cryo-Electron Microscopy Era: Structural Biology's Dynamic Future.

Authors:  Susannah C Shoemaker; Nozomi Ando
Journal:  Biochemistry       Date:  2018-01-11       Impact factor: 3.162

3.  Visualizing Disordered Single-Stranded RNA: Connecting Sequence, Structure, and Electrostatics.

Authors:  Alex Plumridge; Kurt Andresen; Lois Pollack
Journal:  J Am Chem Soc       Date:  2019-12-19       Impact factor: 15.419

4.  Refining conformational ensembles of flexible proteins against small-angle x-ray scattering data.

Authors:  Francesco Pesce; Kresten Lindorff-Larsen
Journal:  Biophys J       Date:  2021-10-08       Impact factor: 4.033

5.  Diffuse X-ray scattering from correlated motions in a protein crystal.

Authors:  Steve P Meisburger; David A Case; Nozomi Ando
Journal:  Nat Commun       Date:  2020-03-09       Impact factor: 14.919

6.  Molecular Dynamics Simulations of Macromolecular Crystals.

Authors:  David S Cerutti; David A Case
Journal:  Wiley Interdiscip Rev Comput Mol Sci       Date:  2018-11-16

Review 7.  Correlated Motions in Structural Biology.

Authors:  Da Xu; Steve P Meisburger; Nozomi Ando
Journal:  Biochemistry       Date:  2021-07-22       Impact factor: 3.321

8.  Structures of Class Id Ribonucleotide Reductase Catalytic Subunits Reveal a Minimal Architecture for Deoxynucleotide Biosynthesis.

Authors:  Hannah R Rose; Ailiena O Maggiolo; Molly J McBride; Gavin M Palowitch; Maria-Eirini Pandelia; Katherine M Davis; Neela H Yennawar; Amie K Boal
Journal:  Biochemistry       Date:  2019-03-22       Impact factor: 3.162

9.  Reproducibility of protein x-ray diffuse scattering and potential utility for modeling atomic displacement parameters.

Authors:  Zhen Su; Medhanjali Dasgupta; Frédéric Poitevin; Irimpan I Mathews; Henry van den Bedem; Michael E Wall; Chun Hong Yoon; Mark A Wilson
Journal:  Struct Dyn       Date:  2021-07-08       Impact factor: 2.920

10.  Interactions that know no boundaries.

Authors:  Michael E Wall
Journal:  IUCrJ       Date:  2018-02-26       Impact factor: 4.769

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