Journal of Molecular Biology
Regular ArticleElectron Cryomicroscopy of Bacillus stearothermophilus 50 S Ribosomal Subunits Crystallized on Phospholipid Monolayers
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FASTDEF: Fast defocus and astigmatism estimation for high-throughput transmission electron microscopy
2013, Journal of Structural BiologyCitation Excerpt :Typically, the CTF is described analytically using a parametric form that takes into account defocus, astigmatism and spherical aberrations. These contrast transfer functions are estimated from the power spectrum density (PSD) that, in turn, is usually obtained by periodogram averaging (Avila-Sakar et al., 1994; Fernández et al., 1997) or parametric methods such as AR or ARMA (Velázquez-Muriel et al., 2003). In the past, different methods have been proposed to model and estimate the CTF using the PSD (Ludtke et al., 1999; Huang et al., 2003; Mindell and Grigorieff, 2003; Sander et al., 2003; Velázquez-Muriel et al., 2003; Mallick et al., 2005; Sorzano et al., 2007; Vulović et al., 2012).
Electron cryomicroscopy of membrane proteins: Specimen preparation for two-dimensional crystals and single particles
2011, MicronCitation Excerpt :The most common method is reconstitution into a lipid bilayer of the purified and detergent-solubilized protein by dialysis (Stahlberg et al., 2001; Kühlbrandt, 2003; Schmidt-Krey, 2007). Incubation of detergent-protein solutions with detergent-adsorbing polystyrene ‘BioBeads’ and the monolayer technique, where 2D crystals are grown at an air–water interface (Auer et al., 1998, 1999) or with the help of interactions with lipid monolayers (Fromherz, 1971; Uzgiris and Kornberg, 1983; Kubalek et al., 1991; Avila-Sakar et al., 1994; Chiu et al., 1997; Vénien-Bryan et al., 1998; Brisson et al., 1999; Lebeau et al., 2001; Isoda et al., 2004; Richter and Brisson, 2005; Mancheño et al., 2006; Dryden et al., 2009; Fezoua-Boubegtiten et al., 2010), are frequently used when only small quantities of protein are available. BioBeads and monolayers generally have the advantage of short times until crystal formation, usually varying from hours to 1–2 days, while reconstitution by dialysis can take considerably longer.
Membrane trafficking in protozoa: Snare proteins, H<sup>+</sup>-ATPase, actin, and other key players in ciliates
2010, International Review of Cell and Molecular BiologyCitation Excerpt :Figures 3.4–3.7 present some examples of this approach (H. Plattner, B. Schönemann, and C. Schilde, unpublished observation). In detail, we observed unusually extensive vesicle aggregates and stacks of rough ER, intermingled with aggregates of ribosomes (as described in fungi [Garrison and Boyd, 1974], chicken embryos [Birks and Weldon, 1971], or in crystals after isolation from bacteria [Avila-Sakar et al., 1994]), together with a substantial number of autophagosomes (Figs. 3.4 and 3.6). These features, including increased autophagy (Kuma et al., 2004), are clearly indications of inhibited metabolic activity, as one might expect from vesicle trafficking impairment.
Fast, robust, and accurate determination of transmission electron microscopy contrast transfer function
2007, Journal of Structural BiologyCitation Excerpt :The experimental PSD must be first estimated from the micrograph image in real space. Periodogram averaging (Avila-Sakar et al., 1994; Frank, 2006; Zhu et al., 1997) is a very popular algorithm to do this due to its simplicity and computational speed. The main drawback of this estimator is that it is very noisy having a standard deviation of the same size as the quantity to be estimated (Broersen, 2000).