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  • in-cell NMRnuclear magnetic resonancecellular structural biologycellular environmentprotein interactions  (2)
  • Bayesian particle polishingbeam-induced motion correctioncryo-EMsingle-particle analysiselectron cryo-microscopy  (1)
  • International Union of Crystallography (IUCr)  (3)
  • American Institute of Physics
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  • International Union of Crystallography (IUCr)  (3)
  • American Institute of Physics
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  • 1
    Publication Date: 2018-11-09
    Description: A new method to estimate the trajectories of particle motion and the amount of cumulative beam damage in electron cryo-microscopy (cryo-EM) single-particle analysis is presented. The motion within the sample is modelled through the use of Gaussian process regression. This allows a prior likelihood that favours spatially and temporally smooth motion to be associated with each hypothetical set of particle trajectories without imposing hard constraints. This formulation enables the a posteriori likelihood of a set of particle trajectories to be expressed as a product of that prior likelihood and an observation likelihood given by the data, and this a posteriori likelihood to then be maximized. Since the smoothness prior requires three parameters that describe the statistics of the observed motion, an efficient stochastic method to estimate these parameters is also proposed. Finally, a practical algorithm is proposed that estimates the average amount of cumulative radiation damage as a function of radiation dose and spatial frequency, and then fits relative B factors to that damage in a robust way. The method is evaluated on three publicly available data sets, and its usefulness is illustrated by comparison with state-of-the-art methods and previously published results. The new method has been implemented as Bayesian polishing in RELION-3, where it replaces the existing particle-polishing method, as it outperforms the latter in all tests conducted.
    Keywords: Bayesian particle polishingbeam-induced motion correctioncryo-EMsingle-particle analysiselectron cryo-microscopy
    Electronic ISSN: 2052-2525
    Topics: Geosciences , Physics
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  • 2
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    International Union of Crystallography (IUCr)
    In: IUCrJ
    Publication Date: 2017-02-15
    Description: Classical structural biology approaches allow structural characterization of biological macromolecules in vitro, far from their physiological context. Nowadays, thanks to the wealth of structural data available and to technological and methodological advances, the interest of the research community is gradually shifting from pure structural determination towards the study of functional aspects of biomolecules. Therefore, a cellular structural approach is ideally needed to characterize biological molecules, such as proteins, in their native cellular environment and the functional processes that they are involved in. In-cell NMR is a new application of high-resolution nuclear magnetic resonance spectroscopy that allows structural and dynamical features of proteins and other macromolecules to be analyzed directly in living cells. Owing to its challenging nature, this methodology has shown slow, but steady, development over the past 15 years. To date, several in-cell NMR approaches have been successfully applied to both bacterial and eukaryotic cells, including several human cell lines, and important structural and functional aspects have been elucidated. In this topical review, the major advances of in-cell NMR are summarized, with a special focus on recent developments in eukaryotic and mammalian cells.
    Keywords: in-cell NMRnuclear magnetic resonancecellular structural biologycellular environmentprotein interactions
    Electronic ISSN: 2052-2525
    Topics: Geosciences , Physics
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  • 3
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    International Union of Crystallography (IUCr)
    In: IUCrJ
    Publication Date: 2017-02-24
    Keywords: in-cell NMRnuclear magnetic resonancecellular structural biologycellular environmentprotein interactions
    Electronic ISSN: 2052-2525
    Topics: Geosciences , Physics
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