Diffuse X-ray scattering to model protein motions.

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.

[1]  Jeremy C. Smith,et al.  X-ray diffuse scattering and rigid-body motion in crystalline lysozyme probed by molecular dynamics simulation. , 1998, Journal of molecular biology.

[2]  G. Phillips,et al.  Diffuse x-ray scattering from tropomyosin crystals. , 1992, Biophysical journal.

[3]  Axel T Brunger,et al.  Exploring the structural dynamics of the E.coli chaperonin GroEL using translation-libration-screw crystallographic refinement of intermediate states. , 2004, Journal of molecular biology.

[4]  B. Borie.  X-Ray Diffraction in Crystals, Imperfect Crystals, and Amorphous Bodies. , 1965 .

[5]  Nicholas K. Sauter,et al.  Robust indexing for automatic data collection , 2004, Journal of applied crystallography.

[6]  P. Moore,et al.  On the relationship between diffraction patterns and motions in macromolecular crystals. , 2009, Structure.

[7]  Randy J. Read,et al.  Acta Crystallographica Section D Biological , 2003 .

[8]  Loes M. J. Kroon-Batenburg,et al.  EVAL15: a diffraction data integration method based on ab initio predicted profiles , 2010 .

[9]  M. Wall,et al.  High-resolution macromolecular structure determination using CCD detectors and synchrotron radiation. , 1995, Structure.

[10]  Jeremy C Smith,et al.  Correlated dynamics determining x-ray diffuse scattering from a crystalline protein revealed by molecular dynamics simulation. , 2005, Physical review letters.

[11]  S M Gruner,et al.  Three-dimensional diffuse x-ray scattering from crystals of Staphylococcal nuclease. , 1997, Proceedings of the National Academy of Sciences of the United States of America.

[12]  A. W. Pryor,et al.  Thermal vibrations in crystallography , 1975 .

[13]  Franci Merzel,et al.  Lattice dynamics of a protein crystal. , 2007, Physical review letters.

[14]  Mark A. Wilson,et al.  Visualizing networks of mobility in proteins , 2013, Nature Methods.

[15]  J. Amorós,et al.  Molecular crystals : their transforms and diffuse scattering , 1968 .

[16]  J. Clarage,et al.  Liquid-like movements in crystalline insulin , 1988, Nature.

[17]  Reginald W. James,et al.  The Optical principles of the diffraction of X-rays , 1948 .

[18]  T. Welberry,et al.  Diffuse X-ray Scattering and Models of Disorder , 2004 .

[19]  J B Clarage,et al.  Analysis of diffuse scattering from yeast initiator tRNA crystals. , 1994, Acta crystallographica. Section D, Biological crystallography.

[20]  Nicholas K. Sauter,et al.  The Computational Crystallography Toolbox: crystallographic algorithms in a reusable software framework , 2002 .

[21]  Michael E Wall.  Methods and software for diffuse X-ray scattering from protein crystals. , 2009, Methods in molecular biology.

[22]  Vijay S. Pande,et al.  Everything you wanted to know about Markov State Models but were afraid to ask. , 2010, Methods.

[23]  André Guinier,et al.  X-ray Crystallography. (Book Reviews: X-Ray Diffraction in Crystals, Imperfect Crystals, and Amorphous Bodies) , 1963 .

[24]  D. Moss,et al.  The Variety of X-ray Diffuse Scattering from Macromolecular Crystals and its Respective Components , 1991 .

[25]  J. P. Grossman,et al.  Biomolecular simulation: a computational microscope for molecular biology. , 2012, Annual review of biophysics.

[26]  Nobuhiro Gō,et al.  Collective motions in proteins investigated by X-ray diffuse scattering , 1993 .

[27]  M E Wall,et al.  Motions of calmodulin characterized using both Bragg and diffuse X-ray scattering. , 1997, Structure.

[28]  Paul D Adams,et al.  Modelling dynamics in protein crystal structures by ensemble refinement , 2012, eLife.

[29]  J. Doucet,et al.  Molecular dynamics studied by analysis of the X-ray diffuse scattering from lysozyme crystals , 1987, Nature.

[30]  R M Sweet,et al.  Correlations of atomic movements in lysozyme crystals , 1992, Proteins.

[31]  Jeremy C. Smith,et al.  Protein dynamics from X‐ray crystallography: Anisotropic, global motion in diffuse scattering patterns , 2006, Proteins.

[32]  W. Wooster.  Diffuse X-Ray Reflections from Crystals , 1962 .

[33]  G. Phillips,et al.  Motions of tropomyosin. Crystal as metaphor. , 1980, Biophysical journal.

[34]  H. V. D. Bedem,et al.  Automated identification of functional dynamic contact networks from X-ray crystallography , 2013 .

[35]  Sol M. Gruner.  X-ray imaging detectors , 2012 .

[36]  B M Pettitt,et al.  A sampling problem in molecular dynamics simulations of macromolecules. , 1995, Proceedings of the National Academy of Sciences of the United States of America.

[37]  Matthias Schroder,et al.  Theory Of X Ray Diffraction In Crystals , 2016 .

[38]  Henry van den Bedem,et al.  Automated identification of functional dynamic networks from X-ray crystallography , 2013, Nature Methods.

[39]  Jeremy C. Smith,et al.  Correlated intramolecular motions and diffuse x–ray scattering in lysozyme , 1994, Nature Structural Biology.

[40]  Jeremy C. Smith,et al.  Fluctuations and correlations in crystalline protein dynamics: a simulation analysis of staphylococcal nuclease. , 2005, Biophysical journal.

[41]  Michael W Deem,et al.  Parallel tempering: theory, applications, and new perspectives. , 2005, Physical chemistry chemical physics : PCCP.

[42]  W. Zachariasen,et al.  Theory of X-Ray Diffraction in Crystals , 1968 .

[43]  B. Warren,et al.  X-Ray Diffraction , 2014 .

[44]  George N Phillips,et al.  Evaluating elastic network models of crystalline biological molecules with temperature factors, correlated motions, and diffuse x-ray scattering. , 2010, Biophysical journal.