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- W1978958536 abstract "Ensemble models of proteins have been developed using X-ray crystallography, and important advances have been made using translation-libration-screw motions of locally rigid domains, detection of alternative side chain conformations and contact networks, and X-ray restrained molecular dynamics (MD) simulations. Experimental validation is hindered, however, because Bragg peak data are unable to distinguish among different models that yield the same mean electron density. By contrast diffuse X-ray scattering reports on correlated motions and can be used to distinguish models that yield the same Bragg data. In particular it has long been recognized that diffuse scattering could be used to validate MD simulations if adequate sampling of the conformational ensemble were achieved. We have performed a 1.1 microsecond MD simulation of crystalline Staphylococcal nuclease (SNase) and have evaluated the resulting ensemble using existing diffuse X-ray scattering data (Wall, Ealick, and Gruner, 1997). The global R-factor between the simulated and calculated diffuse intensity is 0.066, and the Pearson correlation coefficient is 0.86. Discrepancies are highlighted when comparing just the anisotropic component of the diffuse signal; this comparison reveals a strong resolution dependence of the agreement with the anisotropic component, which is best at about 5 Angstroms, and is worst at about 3.5 Angstroms. The diffuse R-factor is improved compared to an earlier 10 ns simulation of crystalline SNase (Meinhold and Smith, 2007), reflecting the 100-fold greater sampling of the conformational ensemble. Our results support the validity and feasibility of using diffuse X-ray scattering to model molecular motions.M.E. Wall, S.E. Ealick and S.M. Gruner. 1997. Three-dimensional diffuse X-ray scattering from crystals of Staphylococcal nuclease. Proc. Natl. Acad. Sci. USA 94:6180-6184.Reference:L. Meinhold and J.C. Smith. 2005. Fluctuations and correlations in crystalline protein dynamics: A simulation analysis of Staphylococcal nuclease. Biophys. J. 88: 2554-2563." @default.
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- W1978958536 date "2014-01-01" @default.
- W1978958536 modified "2023-09-26" @default.
- W1978958536 title "Diffuse X-Ray Scattering for Ensemble Modeling of Crystalline Proteins" @default.
- W1978958536 doi "https://doi.org/10.1016/j.bpj.2013.11.2171" @default.
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