Literature DB >> 24507780

Diffuse X-ray scattering to model protein motions.

Michael E Wall1, Paul D Adams2, James S Fraser3, Nicholas K Sauter4.   

Abstract

Problems in biology increasingly need models of protein flexibility to understand and control protein function. At the same time, as they improve, crystallographic methods are marching closer to the limits of what can be learned from Bragg data in isolation. It is thus inevitable that mainstream protein crystallography will turn to diffuse scattering to model protein motions and improve crystallographic models. The time is ripe to make it happen.
Copyright © 2014 Elsevier Ltd. All rights reserved.

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Year:  2014        PMID: 24507780      PMCID: PMC4070675          DOI: 10.1016/j.str.2014.01.002

Source DB:  PubMed          Journal:  Structure        ISSN: 0969-2126            Impact factor:   5.006


  29 in total

1.  Correlated dynamics determining x-ray diffuse scattering from a crystalline protein revealed by molecular dynamics simulation.

Authors:  Lars Meinhold; Jeremy C Smith
Journal:  Phys Rev Lett       Date:  2005-11-17       Impact factor: 9.161

2.  Protein dynamics from X-ray crystallography: anisotropic, global motion in diffuse scattering patterns.

Authors:  Lars Meinhold; Jeremy C Smith
Journal:  Proteins       Date:  2007-03-01

3.  Lattice dynamics of a protein crystal.

Authors:  Lars Meinhold; Franci Merzel; Jeremy C Smith
Journal:  Phys Rev Lett       Date:  2007-09-25       Impact factor: 9.161

Review 4.  Biomolecular simulation: a computational microscope for molecular biology.

Authors:  Ron O Dror; Robert M Dirks; J P Grossman; Huafeng Xu; David E Shaw
Journal:  Annu Rev Biophys       Date:  2012       Impact factor: 12.981

Review 5.  Parallel tempering: theory, applications, and new perspectives.

Authors:  David J Earl; Michael W Deem
Journal:  Phys Chem Chem Phys       Date:  2005-12-07       Impact factor: 3.676

6.  X-ray diffuse scattering and rigid-body motion in crystalline lysozyme probed by molecular dynamics simulation.

Authors:  S Héry; D Genest; J C Smith
Journal:  J Mol Biol       Date:  1998-05-29       Impact factor: 5.469

Review 7.  Everything you wanted to know about Markov State Models but were afraid to ask.

Authors:  Vijay S Pande; Kyle Beauchamp; Gregory R Bowman
Journal:  Methods       Date:  2010-06-04       Impact factor: 3.608

8.  Motions of tropomyosin. Crystal as metaphor.

Authors:  G N Phillips; J P Fillers; C Cohen
Journal:  Biophys J       Date:  1980-10       Impact factor: 4.033

9.  Motions of calmodulin characterized using both Bragg and diffuse X-ray scattering.

Authors:  M E Wall; J B Clarage; G N Phillips
Journal:  Structure       Date:  1997-12-15       Impact factor: 5.006

10.  Analysis of diffuse scattering from yeast initiator tRNA crystals.

Authors:  A R Kolatkar; J B Clarage; G N Phillips
Journal:  Acta Crystallogr D Biol Crystallogr       Date:  1994-03-01
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  19 in total

1.  Acoustic vibrations contribute to the diffuse scatter produced by ribosome crystals.

Authors:  Yury S Polikanov; Peter B Moore
Journal:  Acta Crystallogr D Biol Crystallogr       Date:  2015-09-26

2.  Conformational dynamics of a crystalline protein from microsecond-scale molecular dynamics simulations and diffuse X-ray scattering.

Authors:  Michael E Wall; Andrew H Van Benschoten; Nicholas K Sauter; Paul D Adams; James S Fraser; Thomas C Terwilliger
Journal:  Proc Natl Acad Sci U S A       Date:  2014-12-01       Impact factor: 11.205

Review 3.  X-ray Scattering Studies of Protein Structural Dynamics.

Authors:  Steve P Meisburger; William C Thomas; Maxwell B Watkins; Nozomi Ando
Journal:  Chem Rev       Date:  2017-05-30       Impact factor: 60.622

4.  Multiscale Methods in Drug Design Bridge Chemical and Biological Complexity in the Search for Cures.

Authors:  Rommie E Amaro; Adrian J Mulholland
Journal:  Nat Rev Chem       Date:  2018-04-11       Impact factor: 34.035

Review 5.  E pluribus unum, no more: from one crystal, many conformations.

Authors:  Rahel A Woldeyes; David A Sivak; James S Fraser
Journal:  Curr Opin Struct Biol       Date:  2014-08-09       Impact factor: 6.809

Review 6.  Integrative, dynamic structural biology at atomic resolution--it's about time.

Authors:  Henry van den Bedem; James S Fraser
Journal:  Nat Methods       Date:  2015-04       Impact factor: 28.547

7.  Measuring and modeling diffuse scattering in protein X-ray crystallography.

Authors:  Andrew H Van Benschoten; Lin Liu; Ana Gonzalez; Aaron S Brewster; Nicholas K Sauter; James S Fraser; Michael E Wall
Journal:  Proc Natl Acad Sci U S A       Date:  2016-03-28       Impact factor: 11.205

8.  Correlated Motions from Crystallography beyond Diffraction.

Authors:  Steve P Meisburger; Nozomi Ando
Journal:  Acc Chem Res       Date:  2017-03-21       Impact factor: 22.384

Review 9.  Synchrotron radiation macromolecular crystallography: science and spin-offs.

Authors:  John R Helliwell; Edward P Mitchell
Journal:  IUCrJ       Date:  2015-02-03       Impact factor: 4.769

10.  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

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