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5 Janelia Publications

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    Gonen Lab
    06/24/17 | MicroED structure of Au146(p-MBA)57 at subatomic resolution reveals a twinned FCC cluster.
    Vergara S, Lukes DA, Martynowycz MW, Santiago U, Plascencia-Villa G, Weiss SC, de la Cruz MJ, Black DM, Alvarez MM, Lopez-Lozano X, Barnes CO, Lin G, Weissker H, Whetten RL, Gonen T, Calero G
    Journal of Physical Chemistry Letters. 2017 Oct 31;8(5523-30):arXiv:1706.07902 [physics.atm-clus]. doi: 10.1021/acs.jpclett.7b02621

    Solving the atomic structure of metallic clusters is fundamental to understanding their optical, electronic, and chemical properties. We report the structure of Au146(p-MBA)57 at subatomic resolution (0.85 {\AA}) using electron diffraction (MicroED) and atomic resolution by X-ray diffraction. The 146 gold atoms may be decomposed into two constituent sets consisting of 119 core and 27 peripheral atoms. The core atoms are organized in a twinned FCC structure whereas the surface gold atoms follow a C2 rotational symmetry about an axis bisecting the twinning plane. The protective layer of 57 p-MBAs fully encloses the cluster and comprises bridging, monomeric, and dimeric staple motifs. Au146(p-MBA)57 is the largest cluster observed exhibiting a bulk-like FCC structure as well as the smallest gold particle exhibiting a stacking fault.

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    Gonen Lab
    06/22/17 | Low-complexity domains adhere by reversible amyloid-like interactions between kinked β-sheets.
    Hughes MP, Sawaya MR, Goldschmidt L, Rodriguez JA, Cascio D, Gonen T, Eisenberg DS
    bioRxiv. 2017 Jun 22:. doi: 10.1101/153817

    Control of metabolism by compartmentation is a widespread feature of higher cells. Recent studies have focused on dynamic intracellular bodies such as stress granules, P-bodies, nucleoli, and metabolic puncta. These bodies appear as separate phases, some containing reversible, amyloid-like fibrils formed by interactions of low-complexity protein domains. Here we report five atomic structures of segments of low-complexity domains from granule-forming proteins, one determined to 1.1 Å resolution by micro-electron diffraction. Four of these interacting protein segments show common characteristics, all in contrast to pathogenic amyloid: kinked peptide backbones, small surface areas of interaction, and predominate attractions between aromatic side-chains. By computationally threading the human proteome on three of our kinked structures, we identified hundreds of low-complexity segments potentially capable of forming such reversible interactions. These segments are found in proteins as diverse as RNA binders, nuclear pore proteins, keratins, and cornified envelope proteins, consistent with the capacity of cells to form a wide variety of dynamic intracellular bodies.

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    Gonen Lab
    06/22/17 | Taking the measure of MicroED.
    Rodriguez JA, Eisenberg DS, Gonen T
    Current Opinion in Structural Biology. 2017 Jun 22;46:79-86. doi: 10.1016/j.sbi.2017.06.004

    It is now possible to routinely determine atomic resolution structures by electron cryo-microscopy (cryoEM), facilitated in part by the method known as micro electron-diffraction (MicroED). Since its initial demonstration in 2013, MicroED has helped determine a variety of protein structures ranging in molecular weight from a few hundred Daltons to several hundred thousand Daltons. Some of these structures were novel while others were previously known. The resolutions of structures obtained thus far by MicroED range from 3.2Å to 1.0Å, with most better than 2.5Å. Crystals of various sizes and shapes, with different space group symmetries, and with a range of solvent content have all been studied by MicroED. The wide range of crystals explored to date presents the community with a landscape of opportunity for structure determination from nano crystals. Here we summarize the lessons we have learned during the first few years of MicroED, and from our attempts at the first ab initio structure determined by the method. We re-evaluate theoretical considerations in choosing the appropriate crystals for MicroED and for extracting the most meaning out of measured data. With more laboratories worldwide adopting the technique, we speculate what the first decade might hold for MicroED.

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    Gonen Lab
    06/21/17 | A method to minimize condenser lens-induced hysteresis effects in a JEOL JEM-3200FSC microscope to enable stable cryoEM low-dose operations.
    de la Cruz MJ, Martynowycz M, Hattne J, Shi D, Gonen T
    bioRxiv. 2017 Jun 21:. doi: 10.1101/153395

    Low dose imaging procedures are key for a successful cryoEM experiment (whether by electron cryotomography, single particle analysis, electron crystallography, or MicroED). We present a method to minimize magnetic hysteresis of the condenser lens system in the JEOL JEM-3200FSC transmission electron microscope (TEM) in order to maintain a stable optical axis for the beam path of low-dose imaging. The simple procedure involves independent voltage ramping of the CL1 and CL2 lenses immediately before switching to the focusing and exposure beam settings for data collection.

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    Gonen Lab
    06/20/17 | MicroED structures from micrometer thick protein crystals.
    Martynowycz M, Glynn C, Miao J, de la Cruz MJ, Hattne J, Shi D, Cascio D, Rodriguez J, Gonen T
    bioRxiv. 2017 Jun 20:. doi: 10.1101/152504

    Theoretical calculations suggest that crystals exceeding 100 nm thickness are excluded by dynamical scattering from successful structure determination using microcrystal electron diffraction (MicroED). These calculations are at odds with experimental results where MicroED structures have been determined from significantly thicker crystals. Here we systematically evaluate the influence of thickness on the accuracy of MicroED intensities and the ability to determine structures from protein crystals one micrometer thick. To do so, we compare ab initio structures of a human prion protein segment determined from thin crystals to those determined from crystals up to one micrometer thick. We also compare molecular replacement solutions from crystals of varying thickness for a larger globular protein, proteinase K. Our results indicate that structures can be reliably determined from crystals at least an order of magnitude thicker than previously suggested by simulation, opening the possibility for an even broader range of MicroED experiments.

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