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Cryo-EM

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https://www.readbyqxmd.com/read/28646653/cryo-em-beyond-the-microscope
#1
REVIEW
Lesley A Earl, Veronica Falconieri, Jacqueline Ls Milne, Sriram Subramaniam
The pace at which cryo-EM is being adopted as a mainstream tool in structural biology has continued unabated over the past year. Initial successes in obtaining near-atomic resolution structures with cryo-EM were enabled to a large extent by advances in microscope and detector technology. Here, we review some of the complementary technical improvements that are helping sustain the cryo-EM revolution. We highlight advances in image processing that permit high resolution structure determination even in the presence of structural and conformational heterogeneity...
June 21, 2017: Current Opinion in Structural Biology
https://www.readbyqxmd.com/read/28640808/transmembrane-helical-interactions-in-the-cftr-channel-pore
#2
Jhuma Das, Andrei A Aleksandrov, Liying Cui, Lihua He, John R Riordan, Nikolay V Dokholyan
Mutations in the Cystic Fibrosis Transmembrane Conductance Regulator (CFTR) gene affect CFTR protein biogenesis or its function as a chloride channel, resulting in dysregulation of epithelial fluid transport in the lung, pancreas and other organs in cystic fibrosis (CF). Development of pharmaceutical strategies to treat CF requires understanding of the mechanisms underlying channel function. However, incomplete 3D structural information on the unique ABC ion channel, CFTR, hinders elucidation of its functional mechanism and correction of cystic fibrosis causing mutants...
June 22, 2017: PLoS Computational Biology
https://www.readbyqxmd.com/read/28639939/model-for-a-novel-membrane-envelope-in-a-filamentous-hyperthermophilic-virus
#3
Edward H Egelman, Peter M Kasson, Frank DiMaio, Xiong Yu, Soizick Lucas-Staat, Mart Krupovic, Stefan Schouten, David Prangishvili
Biological membranes create compartments, and are usually formed by lipid bilayers. However, in hyperthermophilic archaea that live optimally at temperatures above 80°C the membranes are monolayers which resemble fused bilayers. Many double-stranded DNA viruses which parasitize such hosts, including the filamentous virus AFV1 of Acidianus hospitalis, are enveloped with a lipid-containing membrane. Using cryo-EM, we show that the membrane in AFV1 is a ~2 nm-thick monolayer, approximately half the expected membrane thickness, formed by host membrane-derived lipids which adopt a U-shaped 'horseshoe' conformation...
June 22, 2017: ELife
https://www.readbyqxmd.com/read/28638320/membrane-fusion-involved-in-neurotransmission-glimpse-from-electron-microscope-and-molecular-simulation
#4
REVIEW
Zhiwei Yang, Lu Gou, Shuyu Chen, Na Li, Shengli Zhang, Lei Zhang
Membrane fusion is one of the most fundamental physiological processes in eukaryotes for triggering the fusion of lipid and content, as well as the neurotransmission. However, the architecture features of neurotransmitter release machinery and interdependent mechanism of synaptic membrane fusion have not been extensively studied. This review article expounds the neuronal membrane fusion processes, discusses the fundamental steps in all fusion reactions (membrane aggregation, membrane association, lipid rearrangement and lipid and content mixing) and the probable mechanism coupling to the delivery of neurotransmitters...
2017: Frontiers in Molecular Neuroscience
https://www.readbyqxmd.com/read/28636915/probing-the-structural-dynamics-of-the-nmda-receptor-activation-by-coarse-grained-modeling
#5
Wenjun Zheng, Han Wen, Gary J Iacobucci, Gabriela K Popescu
N-Methyl-D-aspartate (NMDA) receptors are glutamate-gated excitatory channels that play essential roles in brain functions. High-resolution structures have been solved for an allosterically inhibited and agonist-bound form of a functional NMDA receptor; however, other key functional states (particularly the active open-channel state) were only resolved at moderate resolutions by cryo-electron microscopy (cryo-EM). To decrypt the mechanism of the NMDA receptor activation, structural modeling is essential to provide presently missing information about structural dynamics...
June 20, 2017: Biophysical Journal
https://www.readbyqxmd.com/read/28636906/flexible-fitting-of-atomic-models-into-cryo-em-density-maps-guided-by-helix-correspondences
#6
Hang Dou, Derek W Burrows, Matthew L Baker, Tao Ju
Although electron cryo-microscopy (cryo-EM) has recently achieved resolutions of better than 3 Å, at which point molecular modeling can be done directly from the density map, analysis and annotation of a cryo-EM density map still primarily rely on fitting atomic or homology models to the density map. In this article, we present, to our knowledge, a new method for flexible fitting of known or modeled protein structures into cryo-EM density maps. Unlike existing methods that are guided by local density gradients, our method is guided by correspondences between the α-helices in the density map and model, and does not require an initial rigid-body fitting step...
June 20, 2017: Biophysical Journal
https://www.readbyqxmd.com/read/28628789/challenges-and-opportunities-in-the-high-resolution-cryo-em-visualization-of-microtubules-and-their-binding-partners
#7
REVIEW
Eva Nogales, Elizabeth H Kellogg
As non-crystallizable polymers, microtubules have been the target of cryo-electron microscopy (cryo-EM) studies since the technique was first established. Over the years, image processing strategies have been developed that take care of the unique, pseudo-helical symmetry of the microtubule. With recent progress in data quality and data processing, cryo-EM reconstructions are now reaching resolutions that allow the generation of atomic models of microtubules and the factors that bind them. These include cellular partners that contribute to microtubule cellular functions, or small ligands that interfere with those functions in the treatment of cancer...
June 16, 2017: Current Opinion in Structural Biology
https://www.readbyqxmd.com/read/28628788/cryo-em-structures-of-human-%C3%AE-secretase
#8
REVIEW
Guanghui Yang, Rui Zhou, Yigong Shi
γ-secretase, a membrane-embedded aspartate protease, catalyzes peptide bond hydrolysis of a large variety of type I integral membrane proteins exemplified by amyloid precursor protein (APP). Cleavage of APP leads to formation of β-amyloid plaque, which is a hallmark of Alzheimer's disease (AD). Over 200 AD-associated mutations are mapped to presenilin 1 (PS1), the catalytic component of γ-secretase. In the past three years, several cryo-electron microscopy (cryo-EM) structures of human γ-secretase have been determined at near atomic resolutions...
June 16, 2017: Current Opinion in Structural Biology
https://www.readbyqxmd.com/read/28628127/rosettaes-a-sampling-strategy-enabling-automated-interpretation-of-difficult-cryo-em-maps
#9
Brandon Frenz, Alexandra C Walls, Edward H Egelman, David Veesler, Frank DiMaio
Accurate atomic modeling of macromolecular structures into cryo-electron microscopy (cryo-EM) maps is a major challenge, as the moderate resolution makes accurate placement of atoms difficult. We present Rosetta enumerative sampling (RosettaES), an automated tool that uses a fragment-based sampling strategy for de novo model completion of macromolecular structures from cryo-EM density maps at 3-5-Å resolution. On a benchmark set of nine proteins, RosettaES was able to identify near-native conformations in 85% of segments...
June 19, 2017: Nature Methods
https://www.readbyqxmd.com/read/28625887/time-resolved-cryo-electron-microscopy-recent-progress
#10
Joachim Frank
Time-resolved cryo-electron microscopy (cryo-EM) combines the known advantages of single-particle cryo-EM in visualizing molecular structure with the ability to dissect the time progress of a reaction between molecules in vitro. Here some of the recent progress of this methodology and its first biological applications are outlined.
June 16, 2017: Journal of Structural Biology
https://www.readbyqxmd.com/read/28624735/advances-in-high-resolution-cryo-em-of-oligomeric-enzymes
#11
REVIEW
Janet Vonck, Deryck J Mills
Recent advances in cryo-electron microscopy instrumentation and software have made it possible to obtain atomic resolution structures of macromolecular complexes with a small amount of material at low concentration and without the need for crystallisation. Oligomeric enzymes are particularly well suited for this technique because of their symmetry and often large size or rigid structure and can be used to explore the limits of the technique. Conformational changes can reach their full extent in solution, not hampered by crystal contacts, and multiple conformations in a sample can be separated computationally...
June 15, 2017: Current Opinion in Structural Biology
https://www.readbyqxmd.com/read/28624568/towards-a-mechanistic-understanding-of-core-promoter-recognition-from-cryo-em-studies-of-human-tfiid
#12
REVIEW
Eva Nogales, Avinash B Patel, Robert K Louder
TFIID is a critical component of the eukaryotic transcription pre-initiation complex (PIC) required for the recruitment of RNA Pol II to the start site of protein-coding genes. Within the PIC, TFIID's role is to recognize and bind core promoter sequences and recruit the rest of the PIC components. Due to its size and its conformational complexity, TFIID poses a serious challenge for structural characterization. The small amounts of purified TFIID that can be obtained by present methods of purification from endogenous sources has limited structural studies to cryo-EM visualization, which requires very small amounts of sample...
June 15, 2017: Current Opinion in Structural Biology
https://www.readbyqxmd.com/read/28622523/intracellular-ca-2-sensing-its-role-in-calcium-homeostasis-and-signaling
#13
REVIEW
Rafaela Bagur, György Hajnóczky
Ca(2+) is a ubiquitous intracellular messenger that controls diverse cellular functions but can become toxic and cause cell death. Selective control of specific targets depends on spatiotemporal patterning of the calcium signal and decoding it by multiple, tunable, and often strategically positioned Ca(2+)-sensing elements. Ca(2+) is detected by specialized motifs on proteins that have been biochemically characterized decades ago. However, the field of Ca(2+) sensing has been reenergized by recent progress in fluorescent technology, genetics, and cryo-EM...
June 15, 2017: Molecular Cell
https://www.readbyqxmd.com/read/28619716/ratchet-like-polypeptide-translocation-mechanism-of-the-aaa-disaggregase-hsp104
#14
Stephanie N Gates, Adam L Yokom, JiaBei Lin, Meredith E Jackrel, Alexandrea N Rizo, Nathan M Kendsersky, Courtney E Buell, Elizabeth A Sweeny, Korrie L Mack, Edward Chuang, Mariana P Torrente, Min Su, James Shorter, Daniel R Southworth
Hsp100 polypeptide translocases are conserved AAA+ machines that maintain proteostasis by unfolding aberrant and toxic proteins for refolding or proteolytic degradation. The Hsp104 disaggregase from S. cerevisiae solubilizes stress-induced amorphous aggregates and amyloid. The structural basis for substrate recognition and translocation is unknown. Using a model substrate (casein), we report cryo-EM structures at near-atomic resolution of Hsp104 in different translocation states. Substrate interactions are mediated by conserved, pore-loop tyrosines that contact an 80 Å-long unfolded polypeptide along the axial channel...
June 15, 2017: Science
https://www.readbyqxmd.com/read/28618351/structure-of-ip3r-channel-high-resolution-insights-from-cryo-em
#15
REVIEW
Mariah R Baker, Guizhen Fan, Irina I Serysheva
Inositol 1,4,5-trisphosphate receptors (IP3Rs) are ubiquitously expressed intracellular Ca(2+) channels and the major mediators of cellular Ca(2+) signals generated by the release of Ca(2+) ions from intracellular stores in response to a variety of extracellular stimuli. Despite established physiological significance and proven involvements of IP3R channels in many human diseases, detailed structural basis for signal detection by these ion channels and their gating remain obscure. Recently, single particle electron cryomicroscopy (cryo-EM) has yielded a long-awaited near-atomic resolution structure of the entire full-length type 1 IP3R...
June 12, 2017: Current Opinion in Structural Biology
https://www.readbyqxmd.com/read/28609682/cryo-em-of-bacterial-pili-and-archaeal-flagellar-filaments
#16
REVIEW
Edward H Egelman
Recent advances in cryo-electron microscopy (cryo-EM) have opened up the possibility that a large class of biological structures, helical polymers, may now be readily reconstructed at near-atomic resolution. This will have a huge impact, since most of these structures are unlikely to be crystallized. This review focuses on new cryo-EM studies involving three classes of bacterial pili (chaperone-usher, mating, and Type IV) as well as on archaeal flagellar filaments. While it has long been known that one domain within archaeal flagellar filaments is homologous to a domain within bacterial Type IV pilins, the new studies shed light on how homologous and even highly conserved subunits can pack together in different ways with only small changes in sequence...
June 10, 2017: Current Opinion in Structural Biology
https://www.readbyqxmd.com/read/28604725/subunit-and-chlorophyll-organization-of-the-plant-photosystem-ii-supercomplex
#17
Laura S van Bezouwen, Stefano Caffarri, Ravindra S Kale, Roman Kouřil, Andy-Mark W H Thunnissen, Gert T Oostergetel, Egbert J Boekema
Photosystem II (PSII) is a light-driven protein, involved in the primary reactions of photosynthesis. In plant photosynthetic membranes PSII forms large multisubunit supercomplexes, containing a dimeric core and up to four light-harvesting complexes (LHCs), which act as antenna proteins. Here we solved a three-dimensional (3D) structure of the C2S2M2 supercomplex from Arabidopsis thaliana using cryo-transmission electron microscopy (cryo-EM) and single-particle analysis at an overall resolution of 5.3 Å...
June 12, 2017: Nature Plants
https://www.readbyqxmd.com/read/28602352/cryo-em-reveals-how-human-cytoplasmic-dynein-is-auto-inhibited-and-activated
#18
Kai Zhang, Helen E Foster, Arnaud Rondelet, Samuel E Lacey, Nadia Bahi-Buisson, Alexander W Bird, Andrew P Carter
Cytoplasmic dynein-1 binds dynactin and cargo adaptor proteins to form a transport machine capable of long-distance processive movement along microtubules. However, it is unclear why dynein-1 moves poorly on its own or how it is activated by dynactin. Here, we present a cryoelectron microscopy structure of the complete 1.4-megadalton human dynein-1 complex in an inhibited state known as the phi-particle. We reveal the 3D structure of the cargo binding dynein tail and show how self-dimerization of the motor domains locks them in a conformation with low microtubule affinity...
June 15, 2017: Cell
https://www.readbyqxmd.com/read/28602350/structure-of-the-human-lipid-exporter-abca1
#19
Hongwu Qian, Xin Zhao, Pingping Cao, Jianlin Lei, Nieng Yan, Xin Gong
ABCA1, an ATP-binding cassette (ABC) subfamily A exporter, mediates the cellular efflux of phospholipids and cholesterol to the extracellular acceptor apolipoprotein A-I (apoA-I) for generation of nascent high-density lipoprotein (HDL). Mutations of human ABCA1 are associated with Tangier disease and familial HDL deficiency. Here, we report the cryo-EM structure of human ABCA1 with nominal resolutions of 4.1 Å for the overall structure and 3.9 Å for the massive extracellular domain. The nucleotide-binding domains (NBDs) display a nucleotide-free state, while the two transmembrane domains (TMDs) contact each other through a narrow interface in the intracellular leaflet of the membrane...
June 15, 2017: Cell
https://www.readbyqxmd.com/read/28591576/regulation-of-rvb1-rvb2-by-a-domain-within-the-ino80-chromatin-remodeling-complex-implicates-the-yeast-rvbs-as-protein-assembly-chaperones
#20
Coral Y Zhou, Caitlin I Stoddard, Jonathan B Johnston, Michael J Trnka, Ignacia Echeverria, Eugene Palovcak, Andrej Sali, Alma L Burlingame, Yifan Cheng, Geeta J Narlikar
The hexameric AAA+ ATPases Rvb1 and Rvb2 (Rvbs) are essential for diverse processes ranging from metabolic signaling to chromatin remodeling, but their functions are unknown. While originally thought to act as helicases, recent proposals suggest that Rvbs act as protein assembly chaperones. However, experimental evidence for chaperone-like behavior is lacking. Here, we identify a potent protein activator of the Rvbs, a domain in the Ino80 ATPase subunit of the INO80 chromatin-remodeling complex, termed Ino80INS...
June 6, 2017: Cell Reports
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