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Molecular Transport in Membranes
Published in Allen J. Bard, Michael V. Mirkin, Scanning Electrochemical Microscopy, 2022
The permeability of NPCs with and without WGA was analyzed by the effective medium theory (Equation 8.3) to determine the dimensions of peripheral and central routes. The theory indicates that the passive permeability of 5.9 × 10−2 cm/s without WGA is consistent with Equation 8.3 with N = 40 NPCs/µm2, r = 24 nm, and l = 35 nm. These r and l values agree with those measured through the cryo-electron tomography of the nucleus isolated from a Xenopus oocyte [59]. Moreover, the NPC density is consistent with a typical density of ∼46 NPCs/µm2 for a Xenopus oocyte nucleus as determined by AFM [60]. The high density corresponds to the close packing of NPCs with an external diameter of ∼140 nm, thereby observing FcTMA+ transport through ∼22 NPCs under the ∼0.84-µm-diameter Pt tip with an area of 0.55 µm2. Overall, a good agreement between experimental and theoretical permeability indicates that FcTMA+ freely diffuses through the entire nanopore without significant interactions with transport barriers. By contrast, peripheral routes were blocked by WGA to yield a lower permeability of 3.1 × 10−2 cm/s, which corresponds to the 17-nm-radius central route in Equation 8.3 with otherwise same parameters. A difference of ∼7 nm between pore radii with and without WGA is similar to the diameter of WGA (∼5 nm) [55] and corresponds to the static thickness of the peripheral route, which must expand transiently and locally to transport large importin–cargo complexes.
Axonemal Dyneins in Cilia and Flagella
Published in Keiko Hirose, Handbook of Dynein, 2019
In this section we will overview tools for structural analysis of dynein in the axoneme. While the motor domain structure of cytoplasmic dynein was solved by X-ray crystallography [10, 33, 34, 58, 59], atomic structures of axonemal dyneins have not yet been analyzed at an atomic resolution. While we can consider the motor domain of axonemal dyneins as similar to that of cytoplasmic dynein based on sequence homology, conformation of the N-terminal tails is completely unknown. Diversity of sequences of axonemal dynein isoforms and associated proteins (see the Chapter 11) suggests wide variation of 3D conformations. Currently our knowledge about axonemal dyneins is limited to intermediate (2–3 nm) resolution by cryo-electron microscopy. Already at this resolution, we learned a lot about molecular arrangement in the axoneme, by combining with analysis of deletion mutants, genetic tagging and biochemistry. As shown in the following paragraphs, detailed structures of microtubule doublets were analyzed by single particle cryo-EM analysis, in which many particles (in this case computationally segmented microtubule doublets) in electron micrographs are analyzed to determine the view angles and back-projected to reconstruct a 3D structure. Single particle analysis, which requires particles in identical conformation but randomly oriented, is not suitable for the entire axoneme, since axonemes have flexibility and cannot be identical to each other. Cryo-electron tomography (cryo-ET) plays an indispensable role for axoneme analysis.
Optimizing Reporter Gene Expression for Molecular Magnetic Resonance Imaging
Published in Shoogo Ueno, Bioimaging, 2020
Qin Sun, Frank S. Prato, Donna E. Goldhawk
In MTB, these three genes are not likely to be sufficient for vesicle formation. Raschdorf et al. reported that MTB mutants expressing seven Mam proteins, including MamI, MamL, and MamB, will form vesicular structures identified by cryo-electron tomography.51 However, in mammalian cells, fewer genes may be necessary. Since eukaryotic cells are equipped with intracellular vesicles, then presumably only those magnetosome proteins that attract iron biomineralization function(s) to an existing vesicle would be necessary (Figure 9.2).
HIV-1 immature virion and other networks formation with simple patchy disks
Published in Molecular Physics, 2022
Anthony B. Gutiérrez, Brian Ignacio Machorro-Martínez, Jaqueline Quintana, Julio C. Armas-Pérez, Paola Mendoza, Juan Marcos Esparza Lucero, Gustavo A. Chapela
Structure of viral capsids has been a matter of intense study over the last years. HIV-1 virus has received much of these efforts, resulting in a large body of information about immature and mature networks to form capsids [2–5]. Alfadhli et al. [6] published a two-dimensional reconstruction of HIV-1 Myr-MA proteins assembled on membranes, obtained by light scattering experiments. This network forms the immature virion of the HIV-1 virus. Zhao et al. [7] published the first mature HIV-1 capsid structure by cryo-electron microscopy and all-atom molecular dynamics. Recent cryo-electron tomography results [8] determined the structure of immature and mature HIV-1.