Literature DB >> 15299635

Molecular rigid-body displacements in a tetragonal lysozyme crystal confirmed by X-ray diffuse scattering.

J Pérez1, P Faure, J P Benoit.   

Abstract

X-ray diffuse scattering from protein crystals is, at the moment, the only available experimental process to be directly sensitive to long-range correlations between protein-atom displacements. It is shown here that calculations based on independent rigid-body displacements of individual molecules yield a description in good agreement with the experimental diffuse-scattering pattern displayed by tetragonal crystals of hen egg-white lysozyme (HEWL) In particular, it appears that molecular rigid-body translations and rigid- body rotations appear roughly in the same proportion as the average atomic mean-square positional fluctuations. The crystallographic temperature-factor analysis by TLS (translation/libration/screw) refinement, performed by Sternberg, Grace & Phillips [Sternberg, Grace, & Phillips (1979). J. Mol. Biol. 130, 231-253], is then confirmed and completed by a quantitative estimation of the molecular rigid-body translation contributions. The major contribution of molecular rigid- body displacements to the average atomic mean-square positional fluctuations, contradicts a previous analysis of the tetragonal HEWL diffuse-scattering data by Clarage, Clarage, Phillips, Sweet & Caspar [Clarage, Clarage, Phillips, Sweet & Caspar (1992). Proteins Struct. Funct. Genet. 12, 145-157] which concluded that short-range correlations dominate. The origin of these opposite conclusions mostly lies in the different hypotheses made to model diffuse scattering, underlying the limits of the 'homogeneous disorder' model.

Entities:  

Year:  1996        PMID: 15299635     DOI: 10.1107/S0907444996002594

Source DB:  PubMed          Journal:  Acta Crystallogr D Biol Crystallogr        ISSN: 0907-4449


  14 in total

1.  Evolution of the internal dynamics of two globular proteins from dry powder to solution.

Authors:  J Pérez; J M Zanotti; D Durand
Journal:  Biophys J       Date:  1999-07       Impact factor: 4.033

Review 2.  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

3.  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

4.  Correlated Motions from Crystallography beyond Diffraction.

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

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.  TLS from fundamentals to practice.

Authors:  Alexandre Urzhumtsev; Pavel V Afonine; Paul D Adams
Journal:  Crystallogr Rev       Date:  2013-07-01       Impact factor: 2.467

Review 7.  Mining electron density for functionally relevant protein polysterism in crystal structures.

Authors:  James S Fraser; Colin J Jackson
Journal:  Cell Mol Life Sci       Date:  2010-12-29       Impact factor: 9.261

8.  Macromolecular diffractive imaging using imperfect crystals.

Authors:  Kartik Ayyer; Oleksandr M Yefanov; Dominik Oberthür; Shatabdi Roy-Chowdhury; Lorenzo Galli; Valerio Mariani; Shibom Basu; Jesse Coe; Chelsie E Conrad; Raimund Fromme; Alexander Schaffer; Katerina Dörner; Daniel James; Christopher Kupitz; Markus Metz; Garrett Nelson; Paulraj Lourdu Xavier; Kenneth R Beyerlein; Marius Schmidt; Iosifina Sarrou; John C H Spence; Uwe Weierstall; Thomas A White; Jay-How Yang; Yun Zhao; Mengning Liang; Andrew Aquila; Mark S Hunter; Joseph S Robinson; Jason E Koglin; Sébastien Boutet; Petra Fromme; Anton Barty; Henry N Chapman
Journal:  Nature       Date:  2016-02-11       Impact factor: 49.962

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.  Predicting X-ray diffuse scattering from translation-libration-screw structural ensembles.

Authors:  Andrew H Van Benschoten; Pavel V Afonine; Thomas C Terwilliger; Michael E Wall; Colin J Jackson; Nicholas K Sauter; Paul D Adams; Alexandre Urzhumtsev; James S Fraser
Journal:  Acta Crystallogr D Biol Crystallogr       Date:  2015-07-28
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