Literature DB >> 23695239

Resolution of structural heterogeneity in dynamic crystallography.

Zhong Ren1, Peter W Y Chan, Keith Moffat, Emil F Pai, William E Royer, Vukica Šrajer, Xiaojing Yang.   

Abstract

Dynamic behavior of proteins is critical to their function. X-ray crystallography, a powerful yet mostly static technique, faces inherent challenges in acquiring dynamic information despite decades of effort. Dynamic `structural changes' are often indirectly inferred from `structural differences' by comparing related static structures. In contrast, the direct observation of dynamic structural changes requires the initiation of a biochemical reaction or process in a crystal. Both the direct and the indirect approaches share a common challenge in analysis: how to interpret the structural heterogeneity intrinsic to all dynamic processes. This paper presents a real-space approach to this challenge, in which a suite of analytical methods and tools to identify and refine the mixed structural species present in multiple crystallographic data sets have been developed. These methods have been applied to representative scenarios in dynamic crystallography, and reveal structural information that is otherwise difficult to interpret or inaccessible using conventional methods.

Keywords:  dynamic crystallography; structural heterogeneity

Mesh:

Substances:

Year:  2013        PMID: 23695239      PMCID: PMC3663119          DOI: 10.1107/S0907444913003454

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


  18 in total

Review 1.  Time-resolved biochemical crystallography: a mechanistic perspective.

Authors:  K Moffat
Journal:  Chem Rev       Date:  2001-06       Impact factor: 60.622

2.  Bayesian difference refinement.

Authors:  T C Terwilliger; J Berendzen
Journal:  Acta Crystallogr D Biol Crystallogr       Date:  1996-09-01

3.  Analysis of experimental time-resolved crystallographic data by singular value decomposition.

Authors:  Sudarshan Rajagopal; Marius Schmidt; Spencer Anderson; Hyotcherl Ihee; Keith Moffat
Journal:  Acta Crystallogr D Biol Crystallogr       Date:  2004-04-21

4.  Cooperative macromolecular device revealed by meta-analysis of static and time-resolved structures.

Authors:  Zhong Ren; Vukica Srajer; James E Knapp; William E Royer
Journal:  Proc Natl Acad Sci U S A       Date:  2011-12-14       Impact factor: 11.205

5.  Automated electron-density sampling reveals widespread conformational polymorphism in proteins.

Authors:  P Therese Lang; Ho-Leung Ng; James S Fraser; Jacob E Corn; Nathaniel Echols; Mark Sales; James M Holton; Tom Alber
Journal:  Protein Sci       Date:  2010-07       Impact factor: 6.725

6.  Dynamics of the trimeric AcrB transporter protein inferred from a B-factor analysis of the crystal structure.

Authors:  W C Lu; C Z Wang; E W Yu; K M Ho
Journal:  Proteins       Date:  2006-01-01

7.  Allosteric action in real time: time-resolved crystallographic studies of a cooperative dimeric hemoglobin.

Authors:  James E Knapp; Reinhard Pahl; Vukica Srajer; William E Royer
Journal:  Proc Natl Acad Sci U S A       Date:  2006-05-09       Impact factor: 11.205

8.  Inclusion of thermal motion in crystallographic structures by restrained molecular dynamics.

Authors:  P Gros; W F van Gunsteren; W G Hol
Journal:  Science       Date:  1990-09-07       Impact factor: 47.728

9.  Watching DNA polymerase η make a phosphodiester bond.

Authors:  Teruya Nakamura; Ye Zhao; Yuriko Yamagata; Yue-jin Hua; Wei Yang
Journal:  Nature       Date:  2012-07-11       Impact factor: 49.962

10.  Interpretation of ensembles created by multiple iterative rebuilding of macromolecular models.

Authors:  Thomas C Terwilliger; Ralf W Grosse-Kunstleve; Pavel V Afonine; Paul D Adams; Nigel W Moriarty; Peter Zwart; Randy J Read; Dusan Turk; Li Wei Hung
Journal:  Acta Crystallogr D Biol Crystallogr       Date:  2007-04-21
View more
  15 in total

1.  In situ serial Laue diffraction on a microfluidic crystallization device.

Authors:  Sarah L Perry; Sudipto Guha; Ashtamurthy S Pawate; Robert Henning; Irina Kosheleva; Vukica Srajer; Paul J A Kenis; Zhong Ren
Journal:  J Appl Crystallogr       Date:  2014-11-18       Impact factor: 3.304

2.  Molecular dynamics simulation of triclinic lysozyme in a crystal lattice.

Authors:  Pawel A Janowski; Chunmei Liu; Jason Deckman; David A Case
Journal:  Protein Sci       Date:  2015-06-11       Impact factor: 6.725

3.  Towards time-resolved serial crystallography in a microfluidic device.

Authors:  Ashtamurthy S Pawate; Vukica Šrajer; Jeremy Schieferstein; Sudipto Guha; Robert Henning; Irina Kosheleva; Marius Schmidt; Zhong Ren; Paul J A Kenis; Sarah L Perry
Journal:  Acta Crystallogr F Struct Biol Commun       Date:  2015-06-27       Impact factor: 1.056

4.  Photoactivation mechanism of a carotenoid-based photoreceptor.

Authors:  Sepalika Bandara; Zhong Ren; Lu Lu; Xiaoli Zeng; Heewhan Shin; Kai-Hong Zhao; Xiaojing Yang
Journal:  Proc Natl Acad Sci U S A       Date:  2017-05-30       Impact factor: 11.205

5.  Graphene-based microfluidics for serial crystallography.

Authors:  Shuo Sui; Yuxi Wang; Kristopher W Kolewe; Vukica Srajer; Robert Henning; Jessica D Schiffman; Christos Dimitrakopoulos; Sarah L Perry
Journal:  Lab Chip       Date:  2016-08-02       Impact factor: 6.799

6.  Singular value decomposition as a tool for background corrections in time-resolved XFEL scattering data.

Authors:  Kristoffer Haldrup
Journal:  Philos Trans R Soc Lond B Biol Sci       Date:  2014-07-17       Impact factor: 6.237

7.  Real-space analysis of radiation-induced specific changes with independent component analysis.

Authors:  Dominika Borek; Raquel Bromberg; Johan Hattne; Zbyszek Otwinowski
Journal:  J Synchrotron Radiat       Date:  2018-02-22       Impact factor: 2.616

8.  Microfocus diffraction from different regions of a protein crystal: structural variations and unit-cell polymorphism.

Authors:  Michael C Thompson; Duilio Cascio; Todd O Yeates
Journal:  Acta Crystallogr D Struct Biol       Date:  2018-04-24       Impact factor: 7.652

9.  Structural basis of molecular logic OR in a dual-sensor histidine kinase.

Authors:  Heewhan Shin; Zhong Ren; Xiaoli Zeng; Sepalika Bandara; Xiaojing Yang
Journal:  Proc Natl Acad Sci U S A       Date:  2019-09-16       Impact factor: 11.205

10.  Dynamic Crystallography Reveals Early Signalling Events in Ultraviolet Photoreceptor UVR8.

Authors:  Xiaoli Zeng; Zhong Ren; Qi Wu; Jun Fan; Pan-Pan Peng; Kun Tang; Ruiqin Zhang; Kai-Hong Zhao; Xiaojing Yang
Journal:  Nat Plants       Date:  2015       Impact factor: 15.793

View more

北京卡尤迪生物科技股份有限公司 © 2022-2023.